From d7977ae9d01feae09d2b3648d8e497a7c112a097 Mon Sep 17 00:00:00 2001
From: gmillot <gael.millot@pasteur.fr>
Date: Mon, 21 Mar 2022 14:36:31 +0100
Subject: [PATCH] v11.3 release: fun_gg_scatter() now correctly plot log2 and
 log10 scales, as in fun_gg_boxplot()

---
 README.md                 |     5 +
 cute_little_R_functions.R | 26434 ++++++++++++++++++------------------
 fun_gg_boxplot.docx       |   Bin 115723 -> 115756 bytes
 fun_gg_scatter.docx       |   Bin 121412 -> 121137 bytes
 4 files changed, 13216 insertions(+), 13223 deletions(-)

diff --git a/README.md b/README.md
index f8e35bb..fbb1fd1 100755
--- a/README.md
+++ b/README.md
@@ -170,6 +170,11 @@ Gitlab developers
 
 ## WHAT'S NEW IN
 
+### v11.3.0
+
+1) fun_gg_scatter() now correctly plot log2 and log10 scales, as in fun_gg_boxplot()
+
+
 ### v11.2.0
 
 1) fun_open() improved for parallelization
diff --git a/cute_little_R_functions.R b/cute_little_R_functions.R
index e270834..0503ba6 100755
--- a/cute_little_R_functions.R
+++ b/cute_little_R_functions.R
@@ -98,343 +98,343 @@
 # -> transferred into the cute package
 # Do not modify this function in cute_little_R_function anymore. See the cute repo
 fun_check <- function(
-data, 
-class = NULL, 
-typeof = NULL, 
-mode = NULL, 
-length = NULL, 
-prop = FALSE, 
-double.as.integer.allowed = FALSE, 
-options = NULL, 
-all.options.in.data = FALSE, 
-na.contain = FALSE, 
-neg.values = TRUE, 
-print = FALSE, 
-data.name = NULL, 
-fun.name = NULL
+    data, 
+    class = NULL, 
+    typeof = NULL, 
+    mode = NULL, 
+    length = NULL, 
+    prop = FALSE, 
+    double.as.integer.allowed = FALSE, 
+    options = NULL, 
+    all.options.in.data = FALSE, 
+    na.contain = FALSE, 
+    neg.values = TRUE, 
+    print = FALSE, 
+    data.name = NULL, 
+    fun.name = NULL
 ){
-# AIM
-# Check the class, type, mode and length of the data argument
-# Mainly used to check the arguments of other functions
-# Check also other kind of data parameters, is it a proportion? Is it type double but numbers without decimal part?
-# If options == NULL, then at least class or type or mode or length argument must be non-null
-# If options is non-null, then class, type and mode must be NULL, and length can be NULL or specified
-# WARNINGS
-# The function tests what is written in its arguments, even if what is written is incoherent. For instance, fun_check(data = factor(1), class = "factor", mode = "character") will return a problem, whatever the object tested in the data argument, because no object can be class "factor" and mode "character" (factors are class "factor" and mode "numeric"). Of note, length of object of class "environment" is always 0
-# If the tested object is NULL, then the function will always return a checking problem
-# Since R >= 4.0.0, class(matrix()) returns "matrix" "array", and not "matrix" alone as before. However, use argument class = "matrix" to check for matrix object (of class "matrix" "array" in R >= 4.0.0) and use argument class = "array" to check for array object (of class "array" in R >= 4.0.0)
-# ARGUMENTS
-# data: object to test
-# class: character string. Either one of the class() result (But see the warning section above) or "vector" or "ggplot2" (i.e., objects of class c("gg", "ggplot")) or NULL
-# typeof: character string. Either one of the typeof() result or NULL
-# mode: character string. Either one of the mode() result (for non-vector object) or NULL
-# length: numeric value indicating the length of the object. Not considered if NULL
-# prop: logical. Are the numeric values between 0 and 1 (proportion)? If TRUE, can be used alone, without considering class, etc.
-# double.as.integer.allowed: logical. If TRUE, no error is reported in the cheking message if argument is set to typeof == "integer" or class == "integer", while the reality is typeof == "double" or class == "numeric" but the numbers strictly have zero as modulo (remainder of a division). This means that i <- 1, which is typeof(i) -> "double" is considered as integer with double.as.integer.allowed = TRUE. WARNING: data%%1 == 0L but not isTRUE(all.equal(data%%1, 0)) is used here because the argument checks for integers stored as double (does not check for decimal numbers that are approximate integers)
-# options: a vector of character strings or integers indicating all the possible option values for the data argument, or NULL. Numbers of type "double" are accepted if they have a 0 modulo
-# all.options.in.data: logical. If TRUE, all of the options must be present at least once in the data argument, and nothing else. If FALSE, some or all of the options must be present in the data argument, and nothing else. Ignored if options is NULL
-# na.contain: logical. Can the data argument contain NA?
-# neg.values: logical. Are negative numeric values authorized? Warning: the default setting is TRUE, meaning that, in that case, no check is performed for the presence of negative values. The neg.values argument is activated only when set to FALSE. In addition, (1) neg.values = FALSE can only be used when class, typeof or mode arguments are not NULL, otherwise return an error message, (2) the presence of negative values is not checked with neg.values = FALSE if the tested object is a factor and the following checking message is returned "OBJECT MUST BE MADE OF NON NEGATIVE VALUES BUT IS A FACTOR"
-# print: logical. Print the message if $problem is TRUE? Warning: set by default to FALSE, which facilitates the control of the checking message output when using fun_check() inside functions. See the example section
-# data.name: character string indicating the name of the object to test. If NULL, use what is assigned to the data argument for the returned message
-# fun.name: character string indicating the name of the function checked (i.e., when fun_check() is used to check the arguments of this function). If non-null, the value of fun.name will be added into the message returned by fun_check()
-# RETURN
-# A list containing:
-# $problem: logical. Is there any problem detected?
-# $text: message indicating the details of the problem, or the absence of problem
-# $object.name: value of the data.name argument (i.e., name of the checked object if provided, NULL otherwise)
-# REQUIRED PACKAGES
-# None
-# REQUIRED FUNCTIONS FROM THE cute PACKAGE
-# None
-# EXAMPLE
-# test <- matrix(1:3) ; fun_check(data = test, print = TRUE, class = "vector", mode = "numeric")
-# see http
-# DEBUGGING
-# data = mean ; class = NULL ; typeof = NULL ; mode = NULL ; length = NULL ; prop = FALSE ; double.as.integer.allowed = FALSE ; options = "a" ; all.options.in.data = FALSE ; na.contain = FALSE ; neg.values = TRUE ; print = TRUE ; data.name = NULL ; fun.name = NULL
-# function name
-# no used in this function for the error message, to avoid env colliding
-# end function name
-# required function checking
-# end required function checking
-# reserved words
-# end reserved words
-# fun.name checked first because required next
-if( ! is.null(fun.name)){ # I have to use this way to deal with every kind of class for fun.name
-if(all(base::class(fun.name) == "character")){ # all() without na.rm -> ok because class(NA) is "logical"
-if(base::length(fun.name) != 1){
-tempo.cat <- paste0("ERROR IN fun_check(): THE fun.name ARGUMENT MUST BE A CHARACTER VECTOR OF LENGTH 1: ", paste(fun.name, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(any(is.na(fun.name))){ # normally no NA with is.na()
-tempo.cat <- paste0("ERROR IN fun_check(): NO ARGUMENT EXCEPT data AND options CAN HAVE NA VALUES\nPROBLEMATIC ARGUMENT IS fun.name")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}else{
-tempo.cat <- paste0("ERROR IN fun_check(): THE fun.name ARGUMENT MUST BE A CHARACTER VECTOR OF LENGTH 1") # paste(fun.name, collapse = " ") removed here because does not work with objects like function
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end fun.name checked first because required next
-# arg with no default values
-mandat.args <- c(
-"data"
-)
-tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
-if(any(tempo)){ # normally no NA for missing() output
-tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end arg with no default values
-# argument primary checking
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) # activate this line and use the function to check arguments status
-# end argument primary checking
-# second round of checking and data preparation
-# management of special classes
-basic.class <- c(
-"NULL", # because class(NULL) is "NULL". The NULL aspect will be dealt later
-"logical", 
-"integer", 
-"numeric", 
-# "complex", 
-"character"
-# "matrix", 
-# "array", 
-# "data.frame", 
-# "list", 
-# "factor", 
-# "table", 
-# "expression", 
-# "name", 
-# "symbol", 
-# "function", 
-# "uneval", 
-# "environment", 
-# "ggplot2", 
-# "ggplot_built", 
-# "call"
-)
-tempo.arg.base <-c( # no names(formals(fun = sys.function(sys.parent(n = 2)))) used with fun_check() to be sure to deal with the correct environment
-"class", 
-"typeof", 
-"mode", 
-"length", 
-"prop", 
-"double.as.integer.allowed", 
-"options", 
-"all.options.in.data", 
-"na.contain", 
-"neg.values", 
-"print", 
-"data.name", 
-"fun.name"
-)
-tempo.class <-list( # no get() used to be sure to deal with the correct environment
-base::class(class), 
-base::class(typeof), 
-base::class(mode), 
-base::class(length), 
-base::class(prop), 
-base::class(double.as.integer.allowed), 
-base::class(options), 
-base::class(all.options.in.data), 
-base::class(na.contain), 
-base::class(neg.values), 
-base::class(print), 
-base::class(data.name), 
-base::class(fun.name)
-)
-tempo <- ! sapply(lapply(tempo.class, FUN = "%in%", basic.class), FUN = all)
-if(any(tempo)){
-tempo.cat1 <- tempo.arg.base[tempo]
-tempo.cat2 <- sapply(tempo.class[tempo], FUN = paste0, collapse = " ")
-tempo.sep <- sapply(mapply(" ", max(nchar(tempo.cat1)) - nchar(tempo.cat1) + 3, FUN = rep, SIMPLIFY = FALSE), FUN = paste0, collapse = "")
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": ANY ARGUMENT EXCEPT data MUST HAVE A BASIC CLASS\nPROBLEMATIC ARGUMENT", ifelse(base::length(tempo.cat1) > 1, "S", ""), " AND ASSOCIATED CLASS", ifelse(base::length(tempo.cat1) > 1, "ES ARE", " IS"), ":\n", paste0(tempo.cat1, tempo.sep, tempo.cat2, collapse = "\n")) # normally no NA with is.na()
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of special classes
-# management of NA arguments
-if(any(is.na(data.name)) | any(is.na(class)) | any(is.na(typeof)) | any(is.na(mode)) | any(is.na(length)) | any(is.na(prop)) | any(is.na(double.as.integer.allowed)) | any(is.na(all.options.in.data)) | any(is.na(na.contain)) | any(is.na(neg.values)) | any(is.na(print)) | any(is.na(fun.name))){ # normally no NA with is.na()
-tempo <- c("data.name", "class", "typeof", "mode", "length", "prop", "double.as.integer.allowed", "all.options.in.data", "na.contain", "neg.values", "print", "fun.name")[c(any(is.na(data.name)), any(is.na(class)), any(is.na(typeof)), any(is.na(mode)), any(is.na(length)), any(is.na(prop)), any(is.na(double.as.integer.allowed)), any(is.na(all.options.in.data)), any(is.na(na.contain)), any(is.na(neg.values)), any(is.na(print)), any(is.na(fun.name)))]
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": NO ARGUMENT EXCEPT data AND options CAN HAVE NA VALUES\nPROBLEMATIC ARGUMENT", ifelse(length(tempo) > 1, "S ARE", " IS"), ":\n", paste(tempo, collapse = "\n")) # normally no NA with is.na()
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NA arguments
-# management of NULL arguments
-tempo.arg <-c(
-"prop", 
-"double.as.integer.allowed", 
-"all.options.in.data", 
-"na.contain",
-"neg.values",
-"print"
-)
-tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
-if(any(tempo.log) == TRUE){ # normally no NA with is.null()
-tempo.cat <- paste0("ERROR IN fun.check():\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS", "THIS ARGUMENT"), " CANNOT BE NULL:\n", paste0(tempo.arg[tempo.log], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NULL arguments
-# dealing with logical
-# tested below
-# end dealing with logical
-# code that protects set.seed() in the global environment
-# end code that protects set.seed() in the global environment
-# warning initiation
-# end warning initiation
-# other checkings
-if( ! is.null(data.name)){
-if( ! (base::length(data.name) == 1L & all(base::class(data.name) == "character"))){ # all() without na.rm -> ok because class(NA) is "logical"
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": data.name ARGUMENT MUST BE A SINGLE CHARACTER ELEMENT AND NOT ", paste(data.name, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if(is.null(options) & is.null(class) & is.null(typeof) & is.null(mode) &  prop == FALSE & is.null(length)){
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": AT LEAST ONE OF THE options, class, typeof, mode, prop, OR length ARGUMENT MUST BE SPECIFIED (I.E, TRUE FOR prop)")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! is.null(options) & ( ! is.null(class) | ! is.null(typeof) | ! is.null(mode) | prop == TRUE)){
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": THE class, typeof, mode ARGUMENTS MUST BE NULL, AND prop FALSE, IF THE options ARGUMENT IS SPECIFIED\nTHE options ARGUMENT MUST BE NULL IF THE class AND/OR typeof AND/OR mode AND/OR prop ARGUMENT IS SPECIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! (all(base::class(neg.values) == "logical") & base::length(neg.values) == 1L)){ # all() without na.rm -> ok because class(NA) is "logical" 
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": THE neg.values ARGUMENT MUST BE TRUE OR FALSE ONLY")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(neg.values == FALSE & is.null(class) & is.null(typeof) & is.null(mode)){
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": THE neg.values ARGUMENT CANNOT BE SWITCHED TO FALSE IF class, typeof AND mode ARGUMENTS ARE NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! is.null(class)){ # may add "formula" and "Date" as in https://renenyffenegger.ch/notes/development/languages/R/functions/class
-if( ! all(class %in% c("vector", "logical", "integer", "numeric", "complex", "character", "matrix", "array", "data.frame", "list", "factor", "table", "expression", "name", "symbol", "function", "uneval", "environment", "ggplot2", "ggplot_built", "call") & base::length(class) == 1L)){ # length == 1L here because of class(matrix()) since R4.0.0  # all() without na.rm -> ok because class cannot be NA (tested above)
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": class ARGUMENT MUST BE ONE OF THESE VALUE:\n\"vector\", \"logical\", \"integer\", \"numeric\", \"complex\", \"character\", \"matrix\", \"array\", \"data.frame\", \"list\", \"factor\", \"table\", \"expression\", \"name\", \"symbol\", \"function\", \"environment\", \"ggplot2\", \"ggplot_built\", \"call\"")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(neg.values == FALSE & ! any(class %in% c("vector", "numeric", "integer", "matrix", "array", "data.frame", "table"))){ # no need of na.rm = TRUE for any() because %in% does not output NA
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": class ARGUMENT CANNOT BE OTHER THAN \"vector\", \"numeric\", \"integer\", \"matrix\", \"array\", \"data.frame\", \"table\" IF neg.values ARGUMENT IS SWITCHED TO FALSE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if( ! is.null(typeof)){ # all the types are here: https://renenyffenegger.ch/notes/development/languages/R/functions/typeof
-if( ! (all(typeof %in% c("logical", "integer", "double", "complex", "character", "list", "expression", "symbol", "closure", "special", "builtin", "environment", "S4", "language")) & base::length(typeof) == 1L)){ # "language" is the type of object of class "call" # all() without na.rm -> ok because typeof cannot be NA (tested above)
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": typeof ARGUMENT MUST BE ONE OF THESE VALUE:\n\"logical\", \"integer\", \"double\", \"complex\", \"character\", \"list\", \"expression\", \"name\", \"symbol\", \"closure\", \"special\", \"builtin\", \"environment\", \"S4\", \"language\"")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(neg.values == FALSE & ! typeof %in% c("double", "integer")){
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": typeof ARGUMENT CANNOT BE OTHER THAN \"double\" OR \"integer\" IF neg.values ARGUMENT IS SWITCHED TO FALSE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if( ! is.null(mode)){ # all the types are here: https://renenyffenegger.ch/notes/development/languages/R/functions/typeof
-if( ! (all(mode %in% c("logical", "numeric", "complex", "character", "list", "expression", "name", "symbol", "function", "environment", "S4", "call")) & base::length(mode) == 1L)){ # all() without na.rm -> ok because mode cannot be NA (tested above)
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": mode ARGUMENT MUST BE ONE OF THESE VALUE:\n\"logical\", \"numeric\", \"complex\", \"character\", \"list\", \"expression\", \"name\", \"symbol\", \"function\", \"environment\", \"S4\", \"call\"")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(neg.values == FALSE & mode != "numeric"){
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": mode ARGUMENT CANNOT BE OTHER THAN \"numeric\" IF neg.values ARGUMENT IS SWITCHED TO FALSE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if( ! is.null(length)){
-if( ! (is.numeric(length) & base::length(length) == 1L & all( ! grepl(length, pattern = "\\.")))){
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": length ARGUMENT MUST BE A SINGLE INTEGER VALUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if( ! (is.logical(prop) & base::length(prop) == 1L)){ # is.na() already checked for prop
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": prop ARGUMENT MUST BE TRUE OR FALSE ONLY")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(prop == TRUE){
-if( ! is.null(class)){
-if( ! any(class %in% c("vector", "numeric", "matrix", "array", "data.frame", "table"))){ # no need of na.rm = TRUE for any() because %in% does not output NA
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": class ARGUMENT CANNOT BE OTHER THAN NULL, \"vector\", \"numeric\", \"matrix\", \"array\", \"data.frame\", \"table\" IF prop ARGUMENT IS TRUE") # not integer because prop
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if( ! is.null(mode)){
-if(mode != "numeric"){
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": mode ARGUMENT CANNOT BE OTHER THAN NULL OR \"numeric\" IF prop ARGUMENT IS TRUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if( ! is.null(typeof)){
-if(typeof != "double"){
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": typeof ARGUMENT CANNOT BE OTHER THAN NULL OR \"double\" IF prop ARGUMENT IS TRUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-}
-if( ! (all(base::class(double.as.integer.allowed) == "logical") & base::length(double.as.integer.allowed) == 1L)){ # all() without na.rm -> ok because class() never returns NA
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": THE double.as.integer.allowed ARGUMENT MUST BE TRUE OR FALSE ONLY: ", paste(double.as.integer.allowed, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! (is.logical(all.options.in.data) & base::length(all.options.in.data) == 1L)){
-tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": all.options.in.data ARGUMENT MUST BE A SINGLE LOGICAL VALUE (TRUE OR FALSE ONLY): ", paste(all.options.in.data, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! (all(base::class(na.contain) == "logical") & base::length(na.contain) == 1L)){ # all() without na.rm -> ok because class() never returns NA
-tempo.cat <- paste0("ERROR IN fun_check(): THE na.contain ARGUMENT MUST BE TRUE OR FALSE ONLY: ", paste(na.contain, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! (all(base::class(print) == "logical") & base::length(print) == 1L)){ # all() without na.rm -> ok because class() never returns NA
-tempo.cat <- paste0("ERROR IN fun_check(): THE print ARGUMENT MUST BE TRUE OR FALSE ONLY: ", paste(print, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# data.name and fun.name tested at the beginning
-# end other checkings
-# end second round of checking and data preparation
-# package checking
-# end package checking
-# main code
-if(is.null(data.name)){
-data.name <- deparse(substitute(data))
-}
-problem <- FALSE
-text <- paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT")
-if(( ! is.null(options)) & (all(base::typeof(data) == "character") | all(base::typeof(data) == "integer") | all(base::typeof(data) == "double"))){ # all() without na.rm -> ok because typeof() never returns NA
-if(all(base::typeof(data) == "double")){
-if( ! all(data %% 1 == 0L, na.rm = TRUE)){
-problem <- TRUE
-text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": THE ", data.name, " OBJECT MUST BE SOME OF THESE OPTIONS: ", paste(options, collapse = " "), "\nBUT IS NOT EVEN TYPE CHARACTER OR INTEGER")
-}
-}else{
-text <- ""
-if( ! all(data %in% options)){ # no need of na.rm = TRUE for all() because %in% does not output NA
-problem <- TRUE
-text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": THE ", data.name, " OBJECT MUST BE SOME OF THESE OPTIONS: ", paste(options, collapse = " "), "\nTHE PROBLEMATIC ELEMENTS OF ", data.name, " ARE: ", paste(unique(data[ ! (data %in% options)]), collapse = " "))
-}
-if(all.options.in.data == TRUE){
-if( ! all(options %in% data)){ # no need of na.rm = TRUE for all() because %in% does not output NA
-problem <- TRUE
-text <- paste0(ifelse(text == "", "", paste0(text, "\n")), ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": THE ", data.name, " OBJECT MUST BE MADE OF ALL THESE OPTIONS: ", paste(options, collapse = " "), "\nTHE MISSING ELEMENTS OF THE options ARGUMENT ARE: ",  paste(unique(options[ ! (options %in% data)]), collapse = " "))
-}
-}
-if( ! is.null(length)){
-if(base::length(data) != length){
-problem <- TRUE
-text <- paste0(ifelse(text == "", "", paste0(text, "\n")), ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": THE LENGTH OF ", data.name, " MUST BE ", length, " AND NOT ", base::length(data))
-}
-}
-if(text == ""){
-text <- paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT")
-}
-}
-}else if( ! is.null(options)){
-problem <- TRUE
-text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": THE ", data.name, " OBJECT MUST BE SOME OF THESE OPTIONS: ", paste(options, collapse = " "), "\nBUT IS NOT EVEN TYPE CHARACTER OR INTEGER")
-}
-arg.names <- c("class", "typeof", "mode", "length")
-if( ! is.null(class)){
-if(class == "matrix"){ # because of class(matric()) since R4.0.0
-class <- c("matrix", "array")
-}else if(class == "factor" & all(base::class(data) %in% c("factor", "ordered"))){ # to deal with ordered factors # all() without na.rm -> ok because class(NA) is "logical"
-class <- c("factor", "ordered")
-}
-}
-if(is.null(options)){
-for(i2 in 1:base::length(arg.names)){
-if( ! is.null(get(arg.names[i2], env = sys.nframe(), inherit = FALSE))){
-# script to execute
-tempo.script <- '
+    # AIM
+    # Check the class, type, mode and length of the data argument
+    # Mainly used to check the arguments of other functions
+    # Check also other kind of data parameters, is it a proportion? Is it type double but numbers without decimal part?
+    # If options == NULL, then at least class or type or mode or length argument must be non-null
+    # If options is non-null, then class, type and mode must be NULL, and length can be NULL or specified
+    # WARNINGS
+    # The function tests what is written in its arguments, even if what is written is incoherent. For instance, fun_check(data = factor(1), class = "factor", mode = "character") will return a problem, whatever the object tested in the data argument, because no object can be class "factor" and mode "character" (factors are class "factor" and mode "numeric"). Of note, length of object of class "environment" is always 0
+    # If the tested object is NULL, then the function will always return a checking problem
+    # Since R >= 4.0.0, class(matrix()) returns "matrix" "array", and not "matrix" alone as before. However, use argument class = "matrix" to check for matrix object (of class "matrix" "array" in R >= 4.0.0) and use argument class = "array" to check for array object (of class "array" in R >= 4.0.0)
+    # ARGUMENTS
+    # data: object to test
+    # class: character string. Either one of the class() result (But see the warning section above) or "vector" or "ggplot2" (i.e., objects of class c("gg", "ggplot")) or NULL
+    # typeof: character string. Either one of the typeof() result or NULL
+    # mode: character string. Either one of the mode() result (for non-vector object) or NULL
+    # length: numeric value indicating the length of the object. Not considered if NULL
+    # prop: logical. Are the numeric values between 0 and 1 (proportion)? If TRUE, can be used alone, without considering class, etc.
+    # double.as.integer.allowed: logical. If TRUE, no error is reported in the cheking message if argument is set to typeof == "integer" or class == "integer", while the reality is typeof == "double" or class == "numeric" but the numbers strictly have zero as modulo (remainder of a division). This means that i <- 1, which is typeof(i) -> "double" is considered as integer with double.as.integer.allowed = TRUE. WARNING: data%%1 == 0L but not isTRUE(all.equal(data%%1, 0)) is used here because the argument checks for integers stored as double (does not check for decimal numbers that are approximate integers)
+    # options: a vector of character strings or integers indicating all the possible option values for the data argument, or NULL. Numbers of type "double" are accepted if they have a 0 modulo
+    # all.options.in.data: logical. If TRUE, all of the options must be present at least once in the data argument, and nothing else. If FALSE, some or all of the options must be present in the data argument, and nothing else. Ignored if options is NULL
+    # na.contain: logical. Can the data argument contain NA?
+    # neg.values: logical. Are negative numeric values authorized? Warning: the default setting is TRUE, meaning that, in that case, no check is performed for the presence of negative values. The neg.values argument is activated only when set to FALSE. In addition, (1) neg.values = FALSE can only be used when class, typeof or mode arguments are not NULL, otherwise return an error message, (2) the presence of negative values is not checked with neg.values = FALSE if the tested object is a factor and the following checking message is returned "OBJECT MUST BE MADE OF NON NEGATIVE VALUES BUT IS A FACTOR"
+    # print: logical. Print the message if $problem is TRUE? Warning: set by default to FALSE, which facilitates the control of the checking message output when using fun_check() inside functions. See the example section
+    # data.name: character string indicating the name of the object to test. If NULL, use what is assigned to the data argument for the returned message
+    # fun.name: character string indicating the name of the function checked (i.e., when fun_check() is used to check the arguments of this function). If non-null, the value of fun.name will be added into the message returned by fun_check()
+    # RETURN
+    # A list containing:
+    # $problem: logical. Is there any problem detected?
+    # $text: message indicating the details of the problem, or the absence of problem
+    # $object.name: value of the data.name argument (i.e., name of the checked object if provided, NULL otherwise)
+    # REQUIRED PACKAGES
+    # None
+    # REQUIRED FUNCTIONS FROM THE cute PACKAGE
+    # None
+    # EXAMPLE
+    # test <- matrix(1:3) ; fun_check(data = test, print = TRUE, class = "vector", mode = "numeric")
+    # see http
+    # DEBUGGING
+    # data = mean ; class = NULL ; typeof = NULL ; mode = NULL ; length = NULL ; prop = FALSE ; double.as.integer.allowed = FALSE ; options = "a" ; all.options.in.data = FALSE ; na.contain = FALSE ; neg.values = TRUE ; print = TRUE ; data.name = NULL ; fun.name = NULL
+    # function name
+    # no used in this function for the error message, to avoid env colliding
+    # end function name
+    # required function checking
+    # end required function checking
+    # reserved words
+    # end reserved words
+    # fun.name checked first because required next
+    if( ! is.null(fun.name)){ # I have to use this way to deal with every kind of class for fun.name
+        if(all(base::class(fun.name) == "character")){ # all() without na.rm -> ok because class(NA) is "logical"
+            if(base::length(fun.name) != 1){
+                tempo.cat <- paste0("ERROR IN fun_check(): THE fun.name ARGUMENT MUST BE A CHARACTER VECTOR OF LENGTH 1: ", paste(fun.name, collapse = " "))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }else if(any(is.na(fun.name))){ # normally no NA with is.na()
+                tempo.cat <- paste0("ERROR IN fun_check(): NO ARGUMENT EXCEPT data AND options CAN HAVE NA VALUES\nPROBLEMATIC ARGUMENT IS fun.name")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+        }else{
+            tempo.cat <- paste0("ERROR IN fun_check(): THE fun.name ARGUMENT MUST BE A CHARACTER VECTOR OF LENGTH 1") # paste(fun.name, collapse = " ") removed here because does not work with objects like function
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # end fun.name checked first because required next
+    # arg with no default values
+    mandat.args <- c(
+        "data"
+    )
+    tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
+    if(any(tempo)){ # normally no NA for missing() output
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end arg with no default values
+    # argument primary checking
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) # activate this line and use the function to check arguments status
+    # end argument primary checking
+    # second round of checking and data preparation
+    # management of special classes
+    basic.class <- c(
+        "NULL", # because class(NULL) is "NULL". The NULL aspect will be dealt later
+        "logical", 
+        "integer", 
+        "numeric", 
+        # "complex", 
+        "character"
+        # "matrix", 
+        # "array", 
+        # "data.frame", 
+        # "list", 
+        # "factor", 
+        # "table", 
+        # "expression", 
+        # "name", 
+        # "symbol", 
+        # "function", 
+        # "uneval", 
+        # "environment", 
+        # "ggplot2", 
+        # "ggplot_built", 
+        # "call"
+    )
+    tempo.arg.base <-c( # no names(formals(fun = sys.function(sys.parent(n = 2)))) used with fun_check() to be sure to deal with the correct environment
+        "class", 
+        "typeof", 
+        "mode", 
+        "length", 
+        "prop", 
+        "double.as.integer.allowed", 
+        "options", 
+        "all.options.in.data", 
+        "na.contain", 
+        "neg.values", 
+        "print", 
+        "data.name", 
+        "fun.name"
+    )
+    tempo.class <-list( # no get() used to be sure to deal with the correct environment
+        base::class(class), 
+        base::class(typeof), 
+        base::class(mode), 
+        base::class(length), 
+        base::class(prop), 
+        base::class(double.as.integer.allowed), 
+        base::class(options), 
+        base::class(all.options.in.data), 
+        base::class(na.contain), 
+        base::class(neg.values), 
+        base::class(print), 
+        base::class(data.name), 
+        base::class(fun.name)
+    )
+    tempo <- ! sapply(lapply(tempo.class, FUN = "%in%", basic.class), FUN = all)
+    if(any(tempo)){
+        tempo.cat1 <- tempo.arg.base[tempo]
+        tempo.cat2 <- sapply(tempo.class[tempo], FUN = paste0, collapse = " ")
+        tempo.sep <- sapply(mapply(" ", max(nchar(tempo.cat1)) - nchar(tempo.cat1) + 3, FUN = rep, SIMPLIFY = FALSE), FUN = paste0, collapse = "")
+        tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": ANY ARGUMENT EXCEPT data MUST HAVE A BASIC CLASS\nPROBLEMATIC ARGUMENT", ifelse(base::length(tempo.cat1) > 1, "S", ""), " AND ASSOCIATED CLASS", ifelse(base::length(tempo.cat1) > 1, "ES ARE", " IS"), ":\n", paste0(tempo.cat1, tempo.sep, tempo.cat2, collapse = "\n")) # normally no NA with is.na()
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of special classes
+    # management of NA arguments
+    if(any(is.na(data.name)) | any(is.na(class)) | any(is.na(typeof)) | any(is.na(mode)) | any(is.na(length)) | any(is.na(prop)) | any(is.na(double.as.integer.allowed)) | any(is.na(all.options.in.data)) | any(is.na(na.contain)) | any(is.na(neg.values)) | any(is.na(print)) | any(is.na(fun.name))){ # normally no NA with is.na()
+        tempo <- c("data.name", "class", "typeof", "mode", "length", "prop", "double.as.integer.allowed", "all.options.in.data", "na.contain", "neg.values", "print", "fun.name")[c(any(is.na(data.name)), any(is.na(class)), any(is.na(typeof)), any(is.na(mode)), any(is.na(length)), any(is.na(prop)), any(is.na(double.as.integer.allowed)), any(is.na(all.options.in.data)), any(is.na(na.contain)), any(is.na(neg.values)), any(is.na(print)), any(is.na(fun.name)))]
+        tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": NO ARGUMENT EXCEPT data AND options CAN HAVE NA VALUES\nPROBLEMATIC ARGUMENT", ifelse(length(tempo) > 1, "S ARE", " IS"), ":\n", paste(tempo, collapse = "\n")) # normally no NA with is.na()
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NA arguments
+    # management of NULL arguments
+    tempo.arg <-c(
+        "prop", 
+        "double.as.integer.allowed", 
+        "all.options.in.data", 
+        "na.contain",
+        "neg.values",
+        "print"
+    )
+    tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
+    if(any(tempo.log) == TRUE){ # normally no NA with is.null()
+        tempo.cat <- paste0("ERROR IN fun.check():\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS", "THIS ARGUMENT"), " CANNOT BE NULL:\n", paste0(tempo.arg[tempo.log], collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NULL arguments
+    # dealing with logical
+    # tested below
+    # end dealing with logical
+    # code that protects set.seed() in the global environment
+    # end code that protects set.seed() in the global environment
+    # warning initiation
+    # end warning initiation
+    # other checkings
+    if( ! is.null(data.name)){
+        if( ! (base::length(data.name) == 1L & all(base::class(data.name) == "character"))){ # all() without na.rm -> ok because class(NA) is "logical"
+            tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": data.name ARGUMENT MUST BE A SINGLE CHARACTER ELEMENT AND NOT ", paste(data.name, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if(is.null(options) & is.null(class) & is.null(typeof) & is.null(mode) &  prop == FALSE & is.null(length)){
+        tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": AT LEAST ONE OF THE options, class, typeof, mode, prop, OR length ARGUMENT MUST BE SPECIFIED (I.E, TRUE FOR prop)")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! is.null(options) & ( ! is.null(class) | ! is.null(typeof) | ! is.null(mode) | prop == TRUE)){
+        tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": THE class, typeof, mode ARGUMENTS MUST BE NULL, AND prop FALSE, IF THE options ARGUMENT IS SPECIFIED\nTHE options ARGUMENT MUST BE NULL IF THE class AND/OR typeof AND/OR mode AND/OR prop ARGUMENT IS SPECIFIED")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! (all(base::class(neg.values) == "logical") & base::length(neg.values) == 1L)){ # all() without na.rm -> ok because class(NA) is "logical" 
+        tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": THE neg.values ARGUMENT MUST BE TRUE OR FALSE ONLY")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(neg.values == FALSE & is.null(class) & is.null(typeof) & is.null(mode)){
+        tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": THE neg.values ARGUMENT CANNOT BE SWITCHED TO FALSE IF class, typeof AND mode ARGUMENTS ARE NULL")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! is.null(class)){ # may add "formula" and "Date" as in https://renenyffenegger.ch/notes/development/languages/R/functions/class
+        if( ! all(class %in% c("vector", "logical", "integer", "numeric", "complex", "character", "matrix", "array", "data.frame", "list", "factor", "table", "expression", "name", "symbol", "function", "uneval", "environment", "ggplot2", "ggplot_built", "call") & base::length(class) == 1L)){ # length == 1L here because of class(matrix()) since R4.0.0  # all() without na.rm -> ok because class cannot be NA (tested above)
+            tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": class ARGUMENT MUST BE ONE OF THESE VALUE:\n\"vector\", \"logical\", \"integer\", \"numeric\", \"complex\", \"character\", \"matrix\", \"array\", \"data.frame\", \"list\", \"factor\", \"table\", \"expression\", \"name\", \"symbol\", \"function\", \"environment\", \"ggplot2\", \"ggplot_built\", \"call\"")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(neg.values == FALSE & ! any(class %in% c("vector", "numeric", "integer", "matrix", "array", "data.frame", "table"))){ # no need of na.rm = TRUE for any() because %in% does not output NA
+            tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": class ARGUMENT CANNOT BE OTHER THAN \"vector\", \"numeric\", \"integer\", \"matrix\", \"array\", \"data.frame\", \"table\" IF neg.values ARGUMENT IS SWITCHED TO FALSE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if( ! is.null(typeof)){ # all the types are here: https://renenyffenegger.ch/notes/development/languages/R/functions/typeof
+        if( ! (all(typeof %in% c("logical", "integer", "double", "complex", "character", "list", "expression", "symbol", "closure", "special", "builtin", "environment", "S4", "language")) & base::length(typeof) == 1L)){ # "language" is the type of object of class "call" # all() without na.rm -> ok because typeof cannot be NA (tested above)
+            tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": typeof ARGUMENT MUST BE ONE OF THESE VALUE:\n\"logical\", \"integer\", \"double\", \"complex\", \"character\", \"list\", \"expression\", \"name\", \"symbol\", \"closure\", \"special\", \"builtin\", \"environment\", \"S4\", \"language\"")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(neg.values == FALSE & ! typeof %in% c("double", "integer")){
+            tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": typeof ARGUMENT CANNOT BE OTHER THAN \"double\" OR \"integer\" IF neg.values ARGUMENT IS SWITCHED TO FALSE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if( ! is.null(mode)){ # all the types are here: https://renenyffenegger.ch/notes/development/languages/R/functions/typeof
+        if( ! (all(mode %in% c("logical", "numeric", "complex", "character", "list", "expression", "name", "symbol", "function", "environment", "S4", "call")) & base::length(mode) == 1L)){ # all() without na.rm -> ok because mode cannot be NA (tested above)
+            tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": mode ARGUMENT MUST BE ONE OF THESE VALUE:\n\"logical\", \"numeric\", \"complex\", \"character\", \"list\", \"expression\", \"name\", \"symbol\", \"function\", \"environment\", \"S4\", \"call\"")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(neg.values == FALSE & mode != "numeric"){
+            tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": mode ARGUMENT CANNOT BE OTHER THAN \"numeric\" IF neg.values ARGUMENT IS SWITCHED TO FALSE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if( ! is.null(length)){
+        if( ! (is.numeric(length) & base::length(length) == 1L & all( ! grepl(length, pattern = "\\.")))){
+            tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": length ARGUMENT MUST BE A SINGLE INTEGER VALUE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if( ! (is.logical(prop) & base::length(prop) == 1L)){ # is.na() already checked for prop
+        tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": prop ARGUMENT MUST BE TRUE OR FALSE ONLY")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else if(prop == TRUE){
+        if( ! is.null(class)){
+            if( ! any(class %in% c("vector", "numeric", "matrix", "array", "data.frame", "table"))){ # no need of na.rm = TRUE for any() because %in% does not output NA
+                tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": class ARGUMENT CANNOT BE OTHER THAN NULL, \"vector\", \"numeric\", \"matrix\", \"array\", \"data.frame\", \"table\" IF prop ARGUMENT IS TRUE") # not integer because prop
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+        }
+        if( ! is.null(mode)){
+            if(mode != "numeric"){
+                tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": mode ARGUMENT CANNOT BE OTHER THAN NULL OR \"numeric\" IF prop ARGUMENT IS TRUE")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+        }
+        if( ! is.null(typeof)){
+            if(typeof != "double"){
+                tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": typeof ARGUMENT CANNOT BE OTHER THAN NULL OR \"double\" IF prop ARGUMENT IS TRUE")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+        }
+    }
+    if( ! (all(base::class(double.as.integer.allowed) == "logical") & base::length(double.as.integer.allowed) == 1L)){ # all() without na.rm -> ok because class() never returns NA
+        tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": THE double.as.integer.allowed ARGUMENT MUST BE TRUE OR FALSE ONLY: ", paste(double.as.integer.allowed, collapse = " "))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! (is.logical(all.options.in.data) & base::length(all.options.in.data) == 1L)){
+        tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" INSIDE ", fun.name)), ": all.options.in.data ARGUMENT MUST BE A SINGLE LOGICAL VALUE (TRUE OR FALSE ONLY): ", paste(all.options.in.data, collapse = " "))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! (all(base::class(na.contain) == "logical") & base::length(na.contain) == 1L)){ # all() without na.rm -> ok because class() never returns NA
+        tempo.cat <- paste0("ERROR IN fun_check(): THE na.contain ARGUMENT MUST BE TRUE OR FALSE ONLY: ", paste(na.contain, collapse = " "))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! (all(base::class(print) == "logical") & base::length(print) == 1L)){ # all() without na.rm -> ok because class() never returns NA
+        tempo.cat <- paste0("ERROR IN fun_check(): THE print ARGUMENT MUST BE TRUE OR FALSE ONLY: ", paste(print, collapse = " "))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # data.name and fun.name tested at the beginning
+    # end other checkings
+    # end second round of checking and data preparation
+    # package checking
+    # end package checking
+    # main code
+    if(is.null(data.name)){
+        data.name <- deparse(substitute(data))
+    }
+    problem <- FALSE
+    text <- paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT")
+    if(( ! is.null(options)) & (all(base::typeof(data) == "character") | all(base::typeof(data) == "integer") | all(base::typeof(data) == "double"))){ # all() without na.rm -> ok because typeof() never returns NA
+        if(all(base::typeof(data) == "double")){
+            if( ! all(data %% 1 == 0L, na.rm = TRUE)){
+                problem <- TRUE
+                text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": THE ", data.name, " OBJECT MUST BE SOME OF THESE OPTIONS: ", paste(options, collapse = " "), "\nBUT IS NOT EVEN TYPE CHARACTER OR INTEGER")
+            }
+        }else{
+            text <- ""
+            if( ! all(data %in% options)){ # no need of na.rm = TRUE for all() because %in% does not output NA
+                problem <- TRUE
+                text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": THE ", data.name, " OBJECT MUST BE SOME OF THESE OPTIONS: ", paste(options, collapse = " "), "\nTHE PROBLEMATIC ELEMENTS OF ", data.name, " ARE: ", paste(unique(data[ ! (data %in% options)]), collapse = " "))
+            }
+            if(all.options.in.data == TRUE){
+                if( ! all(options %in% data)){ # no need of na.rm = TRUE for all() because %in% does not output NA
+                    problem <- TRUE
+                    text <- paste0(ifelse(text == "", "", paste0(text, "\n")), ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": THE ", data.name, " OBJECT MUST BE MADE OF ALL THESE OPTIONS: ", paste(options, collapse = " "), "\nTHE MISSING ELEMENTS OF THE options ARGUMENT ARE: ",  paste(unique(options[ ! (options %in% data)]), collapse = " "))
+                }
+            }
+            if( ! is.null(length)){
+                if(base::length(data) != length){
+                    problem <- TRUE
+                    text <- paste0(ifelse(text == "", "", paste0(text, "\n")), ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": THE LENGTH OF ", data.name, " MUST BE ", length, " AND NOT ", base::length(data))
+                }
+            }
+            if(text == ""){
+                text <- paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT")
+            }
+        }
+    }else if( ! is.null(options)){
+        problem <- TRUE
+        text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": THE ", data.name, " OBJECT MUST BE SOME OF THESE OPTIONS: ", paste(options, collapse = " "), "\nBUT IS NOT EVEN TYPE CHARACTER OR INTEGER")
+    }
+    arg.names <- c("class", "typeof", "mode", "length")
+    if( ! is.null(class)){
+        if(class == "matrix"){ # because of class(matric()) since R4.0.0
+            class <- c("matrix", "array")
+        }else if(class == "factor" & all(base::class(data) %in% c("factor", "ordered"))){ # to deal with ordered factors # all() without na.rm -> ok because class(NA) is "logical"
+            class <- c("factor", "ordered")
+        }
+    }
+    if(is.null(options)){
+        for(i2 in 1:base::length(arg.names)){
+            if( ! is.null(get(arg.names[i2], env = sys.nframe(), inherit = FALSE))){
+                # script to execute
+                tempo.script <- '
 problem <- TRUE ;
 if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
 text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": THE ", data.name, " OBJECT MUST BE ") ;
@@ -443,75 +443,75 @@ text <- paste0(text, " AND ") ;
 }
 text <- paste0(text, toupper(arg.names[i2]), " ", if(all(get(arg.names[i2], env = sys.nframe(), inherit = FALSE) %in% c("matrix", "array"))){"matrix"}else if(all(get(arg.names[i2], env = sys.nframe(), inherit = FALSE) %in% c("factor", "ordered"))){"factor"}else{get(arg.names[i2], env = sys.nframe(), inherit = FALSE)})
 ' # no need of na.rm = TRUE for all() because %in% does not output NA
-# end script to execute
-if(base::typeof(data) == "double" & double.as.integer.allowed == TRUE & ((arg.names[i2] == "class" & all(get(arg.names[i2], env = sys.nframe(), inherit = FALSE) == "integer")) | (arg.names[i2] == "typeof" & all(get(arg.names[i2], env = sys.nframe(), inherit = FALSE) == "integer")))){ # no need of na.rm = TRUE for all() because == does not output NA if no NA in left of ==, which is the case for arg.names # typeof(data) == "double" means no factor allowed
-if( ! all(data %% 1 == 0L, na.rm = TRUE)){ # to check integers (use %%, meaning the remaining of a division): see the precedent line. isTRUE(all.equal(data%%1, rep(0, length(data)))) not used because we strictly need zero as a result. Warning: na.rm = TRUE required here for all()
-eval(parse(text = tempo.script)) # execute tempo.script
-}
-}else if( ! any(all(get(arg.names[i2], env = sys.nframe(), inherit = FALSE) %in% c("vector", "ggplot2"))) & ! all(eval(parse(text = paste0(arg.names[i2], "(data)"))) %in% get(arg.names[i2], env = sys.nframe(), inherit = FALSE))){ # test the four c("class", "typeof", "mode", "length") arguments with their corresponding function. No need of na.rm = TRUE for all() because %in% does not output NA # no need of na.rm = TRUE for all() because %in% does not output NA # no need of na.rm = TRUE for any() because get get(arg.names) does not contain NA
-eval(parse(text = tempo.script)) # execute tempo.script
-}else if(arg.names[i2] == "class" & all(get(arg.names[i2], env = sys.nframe(), inherit = FALSE) == "vector") & ! (all(base::class(data) %in% "numeric") | all(base::class(data) %in% "integer") | all(base::class(data) %in% "character") | all(base::class(data) %in% "logical"))){ # test class == "vector". No need of na.rm = TRUE for all() because %in% does not output NA # no need of na.rm = TRUE for all() because == does not output NA if no NA in left of ==, which is the case for arg.names
-eval(parse(text = tempo.script)) # execute tempo.script
-}else if(arg.names[i2] == "class" & all(get(arg.names[i2], env = sys.nframe(), inherit = FALSE) == "ggplot2") & ! all(base::class(data) %in% c("gg", "ggplot"))){ # test ggplot object # no need of na.rm = TRUE for all() because == does not output NA if no NA in left of ==, which is the case for arg.names # no need of na.rm = TRUE for all() because %in% does not output NA
-eval(parse(text = tempo.script)) # execute tempo.script
-}
-}
-}
-}
+            # end script to execute
+            if(base::typeof(data) == "double" & double.as.integer.allowed == TRUE & ((arg.names[i2] == "class" & all(get(arg.names[i2], env = sys.nframe(), inherit = FALSE) == "integer")) | (arg.names[i2] == "typeof" & all(get(arg.names[i2], env = sys.nframe(), inherit = FALSE) == "integer")))){ # no need of na.rm = TRUE for all() because == does not output NA if no NA in left of ==, which is the case for arg.names # typeof(data) == "double" means no factor allowed
+                if( ! all(data %% 1 == 0L, na.rm = TRUE)){ # to check integers (use %%, meaning the remaining of a division): see the precedent line. isTRUE(all.equal(data%%1, rep(0, length(data)))) not used because we strictly need zero as a result. Warning: na.rm = TRUE required here for all()
+                    eval(parse(text = tempo.script)) # execute tempo.script
+                }
+            }else if( ! any(all(get(arg.names[i2], env = sys.nframe(), inherit = FALSE) %in% c("vector", "ggplot2"))) & ! all(eval(parse(text = paste0(arg.names[i2], "(data)"))) %in% get(arg.names[i2], env = sys.nframe(), inherit = FALSE))){ # test the four c("class", "typeof", "mode", "length") arguments with their corresponding function. No need of na.rm = TRUE for all() because %in% does not output NA # no need of na.rm = TRUE for all() because %in% does not output NA # no need of na.rm = TRUE for any() because get get(arg.names) does not contain NA
+                eval(parse(text = tempo.script)) # execute tempo.script
+            }else if(arg.names[i2] == "class" & all(get(arg.names[i2], env = sys.nframe(), inherit = FALSE) == "vector") & ! (all(base::class(data) %in% "numeric") | all(base::class(data) %in% "integer") | all(base::class(data) %in% "character") | all(base::class(data) %in% "logical"))){ # test class == "vector". No need of na.rm = TRUE for all() because %in% does not output NA # no need of na.rm = TRUE for all() because == does not output NA if no NA in left of ==, which is the case for arg.names
+                eval(parse(text = tempo.script)) # execute tempo.script
+            }else if(arg.names[i2] == "class" & all(get(arg.names[i2], env = sys.nframe(), inherit = FALSE) == "ggplot2") & ! all(base::class(data) %in% c("gg", "ggplot"))){ # test ggplot object # no need of na.rm = TRUE for all() because == does not output NA if no NA in left of ==, which is the case for arg.names # no need of na.rm = TRUE for all() because %in% does not output NA
+                eval(parse(text = tempo.script)) # execute tempo.script
+            }
+            }
+        }
+    }
 if(prop == TRUE & all(base::typeof(data) == "double")){ # all() without na.rm -> ok because typeof(NA) is "logical"
-if(is.null(data) | any(data < 0 | data > 1, na.rm = TRUE)){ # works if data is NULL # Warning: na.rm = TRUE required here for any() # typeof(data) == "double" means no factor allowed
-problem <- TRUE
-if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
-text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
-}else{
-text <- paste0(text, " AND ")
-}
-text <- paste0(text, "THE ", data.name, " OBJECT MUST BE DECIMAL VALUES BETWEEN 0 AND 1")
-}
+    if(is.null(data) | any(data < 0 | data > 1, na.rm = TRUE)){ # works if data is NULL # Warning: na.rm = TRUE required here for any() # typeof(data) == "double" means no factor allowed
+        problem <- TRUE
+        if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
+            text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
+        }else{
+            text <- paste0(text, " AND ")
+        }
+        text <- paste0(text, "THE ", data.name, " OBJECT MUST BE DECIMAL VALUES BETWEEN 0 AND 1")
+    }
 }else if(prop == TRUE){
-problem <- TRUE
-if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
-text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
-}else{
-text <- paste0(text, " AND ")
-}
-text <- paste0(text, "THE ", data.name, " OBJECT MUST BE DECIMAL VALUES BETWEEN 0 AND 1")
+    problem <- TRUE
+    if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
+        text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
+    }else{
+        text <- paste0(text, " AND ")
+    }
+    text <- paste0(text, "THE ", data.name, " OBJECT MUST BE DECIMAL VALUES BETWEEN 0 AND 1")
 }
 if(all(base::class(data) %in% "expression")){ # no need of na.rm = TRUE for all() because %in% does not output NA
-data <- as.character(data) # to evaluate the presence of NA
+    data <- as.character(data) # to evaluate the presence of NA
 }
 if(na.contain == FALSE & (base::mode(data) %in% c("logical", "numeric", "complex", "character", "list"))){ # before it was ! (class(data) %in% c("function", "environment"))
-if(any(is.na(data)) == TRUE){ # not on the same line because when data is class envir or function , do not like that # normally no NA with is.na()
-problem <- TRUE
-if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
-text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
-}else{
-text <- paste0(text, " AND ")
-}
-text <- paste0(text, "THE ", data.name, " OBJECT CONTAINS NA WHILE NOT AUTHORIZED")
-}
+    if(any(is.na(data)) == TRUE){ # not on the same line because when data is class envir or function , do not like that # normally no NA with is.na()
+        problem <- TRUE
+        if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
+            text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
+        }else{
+            text <- paste0(text, " AND ")
+        }
+        text <- paste0(text, "THE ", data.name, " OBJECT CONTAINS NA WHILE NOT AUTHORIZED")
+    }
 }
 if(neg.values == FALSE & all(base::mode(data) %in% "numeric") & ! any(base::class(data) %in% "factor")){ # no need of na.rm = TRUE for all() because %in% does not output NA
-if(any(data < 0, na.rm = TRUE)){ # Warning: na.rm = TRUE required here for any()
-problem <- TRUE
-if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
-text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
-}else{
-text <- paste0(text, " AND ")
-}
-text <- paste0(text, "THE ", data.name, " OBJECT MUST BE MADE OF NON NEGATIVE NUMERIC VALUES")
-}
+    if(any(data < 0, na.rm = TRUE)){ # Warning: na.rm = TRUE required here for any()
+        problem <- TRUE
+        if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
+            text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
+        }else{
+            text <- paste0(text, " AND ")
+        }
+        text <- paste0(text, "THE ", data.name, " OBJECT MUST BE MADE OF NON NEGATIVE NUMERIC VALUES")
+    }
 }else if(neg.values == FALSE){
-problem <- TRUE
-if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
-text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
-}else{
-text <- paste0(text, " AND ")
-}
-text <- paste0(text, "THE ", data.name, " OBJECT MUST BE MADE OF NON NEGATIVE VALUES BUT IS ", ifelse(any(base::class(data) %in% "factor"), "A FACTOR", "NOT EVEN MODE NUMERIC"))
+    problem <- TRUE
+    if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
+        text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
+    }else{
+        text <- paste0(text, " AND ")
+    }
+    text <- paste0(text, "THE ", data.name, " OBJECT MUST BE MADE OF NON NEGATIVE VALUES BUT IS ", ifelse(any(base::class(data) %in% "factor"), "A FACTOR", "NOT EVEN MODE NUMERIC"))
 }
 if(print == TRUE & problem == TRUE){
-cat(paste0("\n\n================\n\n", text, "\n\n================\n\n"))
+    cat(paste0("\n\n================\n\n", text, "\n\n================\n\n"))
 }
 # output
 output <- list(problem = problem, text = text, object.name = data.name)
@@ -525,104 +525,104 @@ return(output)
 
 
 fun_secu <- function(pos = 1, name = NULL){
-# AIM
-# Verify that variables in the environment defined by the pos parameter are not present in the above environment (following R Scope). This can be used to avoid R scope preference of functions like get()
-# ARGUMENTS
-# pos: single integer indicating the position of the environment checked (argument n of parent.frame()). Value 1 means one step above the fun_secu() local environment (by default). This means that when fun_secu(pos = 1) is used inside a function A, it checks if variables in the local environment of this function A are also present in above environments (following R Scope). When fun_secu(pos = 1) is used in the Global environment, it checks the objects of this environment
-# name: single character string indicating the name of the function checked. If NULL, fun_secu() checks all the variables of the environment indicated by pos, as explained in the pos argument description. If non-null, fun_secu() checks all the variables presents in the local env of the function will be checked in the above envs (which includes the working environment (Global env)
-# RETURN
-# A character string of the local variables that match variables in the different environments of the R scope, or NULL if no match
-# REQUIRED PACKAGES
-# None
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# fun_secu()
-# fun_secu(pos = 2)
-# mean <- 0 ; fun1 <- function(){sd <- 1 ; fun_secu(name = as.character(sys.calls()[[length(sys.calls())]]))} ; fun2 <- function(){cor <- 2 ; fun1()} ; fun1() ; fun2() ; rm(mean) # sys.calls() gives the function name at top stack of the imbricated functions, sys.calls()[[length(sys.calls())]] the name of the just above function. This can also been used for the above function: as.character(sys.call(1))
-# test.pos <- 2 ; mean <- 0 ; fun1 <- function(){sd <- 1 ; fun_secu(pos = test.pos, name = if(length(sys.calls()) >= test.pos){as.character(sys.calls()[[length(sys.calls()) + 1 - test.pos]])}else{search()[ (1:length(search()))[test.pos - length(sys.calls())]]})} ; fun2 <- function(){cor <- 2 ; fun1()} ; fun1() ; fun2() ; rm(mean) # for argument name, here is a way to have the name of the tested environment according to test.pos value
-# DEBUGGING
-# pos = 1 ; name = NULL # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument primary checking
-# arg with no default values
-# end arg with no default values
-# using fun_check()
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = pos, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(name)){
-tempo <- fun_check(data = name, class = "vector", typeof = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end using fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument primary checking
-# second round of checking and data preparation
-# management of NA arguments
-tempo.arg <- names(arg.user.setting) # values provided by the user
-tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
-if(any(tempo.log) == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS", "THIS ARGUMENT"), " CANNOT JUST BE NA:", paste0(tempo.arg[tempo.log], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NA arguments
-# management of NULL arguments
-tempo.arg <- c(
-"pos"
-)
-tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
-if(any(tempo.log) == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS", "THIS ARGUMENT"), " CANNOT BE NULL:", paste0(tempo.arg[tempo.log], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NULL arguments
-# end second round of checking and data preparation
-# main code
-# match.list <- vector("list", length = (length(sys.calls()) - 1 + length(search()) + ifelse(length(sys.calls()) == 1L, -1, 0))) # match.list is a list of all the environment tested (local of functions and R envs), length(sys.calls()) - 1 to remove the level of the fun_secu() function, sys.calls() giving all the names of the imbricated functions, including fun_secu, ifelse(length(sys.calls()) == 1L, -1, 0) to remove Global env if this one is tested
-tempo.name <- rev(as.character(unlist(sys.calls()))) # get names of frames (i.e., enclosed env)
-tempo.frame <- rev(sys.frames())  # get frames (i.e., enclosed env)
-# dealing with source()
-# source() used in the Global env creates three frames above the Global env, which should be removed because not very interesting for variable duplications. Add a <<-(sys.frames()) in this code and source anova_contrasts code to see this. With ls(a[[4]]), we can see the content of each env, which are probably elements of source()
-if(any(sapply(tempo.frame, FUN = environmentName) %in% "R_GlobalEnv")){
-global.pos <- which(sapply(tempo.frame, FUN = environmentName) %in% "R_GlobalEnv")
-# remove the global env (because already in search(), and all the oabove env
-tempo.name <- tempo.name[-c(global.pos:length(tempo.frame))]
-tempo.frame <- tempo.frame[-c(global.pos:length(tempo.frame))]
-}
-# end dealing with source()
-# might have a problem if(length(tempo.name) == 0L){
-match.list <- vector("list", length = length(tempo.name) + length(search())) # match.list is a list of all the environment tested (local of functions and R envs), length(sys.calls()) - 1 to remove the level of the fun_secu() function, sys.calls() giving all the names of the imbricated functions, including fun_secu, ifelse(length(sys.calls()) == 1L, -1, 0) to remove Global env if this one is tested
-ls.names <- c(tempo.name, search()) # names of the functions + names of the search() environments
-ls.input <- c(tempo.frame, as.list(search())) # environements of the functions + names of the search() environments
-names(match.list) <- ls.names # 
-match.list <- match.list[-c(1:(pos + 1))] # because we check only above pos
-ls.tested <- ls.input[[pos + 1]]
-ls.input <- ls.input[-c(1:(pos + 1))]
-for(i1 in 1:length(match.list)){
-if(any(ls(name = ls.input[[i1]], all.names = TRUE) %in% ls(name = ls.tested, all.names = TRUE))){
-match.list[i1] <- list(ls(name = ls.input[[i1]], all.names = TRUE)[ls(name = ls.input[[i1]], all.names = TRUE) %in% ls(name = ls.tested, all.names = TRUE)])
-}
-}
-if( ! all(sapply(match.list, FUN = is.null))){
-output <- paste0("SOME VARIABLES ", ifelse(is.null(name), "OF THE CHECKED ENVIRONMENT", paste0("OF ", name)), " ARE ALSO PRESENT IN :\n", paste0(names(match.list[ ! sapply(match.list, FUN = is.null)]), ": ", sapply(match.list[ ! sapply(match.list, FUN = is.null)], FUN = paste0, collapse = " "), collapse = "\n"))
-}else{
-output <- NULL
-}
-return(output)
+    # AIM
+    # Verify that variables in the environment defined by the pos parameter are not present in the above environment (following R Scope). This can be used to avoid R scope preference of functions like get()
+    # ARGUMENTS
+    # pos: single integer indicating the position of the environment checked (argument n of parent.frame()). Value 1 means one step above the fun_secu() local environment (by default). This means that when fun_secu(pos = 1) is used inside a function A, it checks if variables in the local environment of this function A are also present in above environments (following R Scope). When fun_secu(pos = 1) is used in the Global environment, it checks the objects of this environment
+    # name: single character string indicating the name of the function checked. If NULL, fun_secu() checks all the variables of the environment indicated by pos, as explained in the pos argument description. If non-null, fun_secu() checks all the variables presents in the local env of the function will be checked in the above envs (which includes the working environment (Global env)
+    # RETURN
+    # A character string of the local variables that match variables in the different environments of the R scope, or NULL if no match
+    # REQUIRED PACKAGES
+    # None
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # fun_secu()
+    # fun_secu(pos = 2)
+    # mean <- 0 ; fun1 <- function(){sd <- 1 ; fun_secu(name = as.character(sys.calls()[[length(sys.calls())]]))} ; fun2 <- function(){cor <- 2 ; fun1()} ; fun1() ; fun2() ; rm(mean) # sys.calls() gives the function name at top stack of the imbricated functions, sys.calls()[[length(sys.calls())]] the name of the just above function. This can also been used for the above function: as.character(sys.call(1))
+    # test.pos <- 2 ; mean <- 0 ; fun1 <- function(){sd <- 1 ; fun_secu(pos = test.pos, name = if(length(sys.calls()) >= test.pos){as.character(sys.calls()[[length(sys.calls()) + 1 - test.pos]])}else{search()[ (1:length(search()))[test.pos - length(sys.calls())]]})} ; fun2 <- function(){cor <- 2 ; fun1()} ; fun1() ; fun2() ; rm(mean) # for argument name, here is a way to have the name of the tested environment according to test.pos value
+    # DEBUGGING
+    # pos = 1 ; name = NULL # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument primary checking
+    # arg with no default values
+    # end arg with no default values
+    # using fun_check()
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = pos, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(name)){
+        tempo <- fun_check(data = name, class = "vector", typeof = "character", length = 1, fun.name = function.name) ; eval(ee)
+    }
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end using fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument primary checking
+    # second round of checking and data preparation
+    # management of NA arguments
+    tempo.arg <- names(arg.user.setting) # values provided by the user
+    tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
+    if(any(tempo.log) == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS", "THIS ARGUMENT"), " CANNOT JUST BE NA:", paste0(tempo.arg[tempo.log], collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NA arguments
+    # management of NULL arguments
+    tempo.arg <- c(
+        "pos"
+    )
+    tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
+    if(any(tempo.log) == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS", "THIS ARGUMENT"), " CANNOT BE NULL:", paste0(tempo.arg[tempo.log], collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NULL arguments
+    # end second round of checking and data preparation
+    # main code
+    # match.list <- vector("list", length = (length(sys.calls()) - 1 + length(search()) + ifelse(length(sys.calls()) == 1L, -1, 0))) # match.list is a list of all the environment tested (local of functions and R envs), length(sys.calls()) - 1 to remove the level of the fun_secu() function, sys.calls() giving all the names of the imbricated functions, including fun_secu, ifelse(length(sys.calls()) == 1L, -1, 0) to remove Global env if this one is tested
+    tempo.name <- rev(as.character(unlist(sys.calls()))) # get names of frames (i.e., enclosed env)
+    tempo.frame <- rev(sys.frames())  # get frames (i.e., enclosed env)
+    # dealing with source()
+    # source() used in the Global env creates three frames above the Global env, which should be removed because not very interesting for variable duplications. Add a <<-(sys.frames()) in this code and source anova_contrasts code to see this. With ls(a[[4]]), we can see the content of each env, which are probably elements of source()
+    if(any(sapply(tempo.frame, FUN = environmentName) %in% "R_GlobalEnv")){
+        global.pos <- which(sapply(tempo.frame, FUN = environmentName) %in% "R_GlobalEnv")
+        # remove the global env (because already in search(), and all the oabove env
+        tempo.name <- tempo.name[-c(global.pos:length(tempo.frame))]
+        tempo.frame <- tempo.frame[-c(global.pos:length(tempo.frame))]
+    }
+    # end dealing with source()
+    # might have a problem if(length(tempo.name) == 0L){
+    match.list <- vector("list", length = length(tempo.name) + length(search())) # match.list is a list of all the environment tested (local of functions and R envs), length(sys.calls()) - 1 to remove the level of the fun_secu() function, sys.calls() giving all the names of the imbricated functions, including fun_secu, ifelse(length(sys.calls()) == 1L, -1, 0) to remove Global env if this one is tested
+    ls.names <- c(tempo.name, search()) # names of the functions + names of the search() environments
+    ls.input <- c(tempo.frame, as.list(search())) # environements of the functions + names of the search() environments
+    names(match.list) <- ls.names # 
+    match.list <- match.list[-c(1:(pos + 1))] # because we check only above pos
+    ls.tested <- ls.input[[pos + 1]]
+    ls.input <- ls.input[-c(1:(pos + 1))]
+    for(i1 in 1:length(match.list)){
+        if(any(ls(name = ls.input[[i1]], all.names = TRUE) %in% ls(name = ls.tested, all.names = TRUE))){
+            match.list[i1] <- list(ls(name = ls.input[[i1]], all.names = TRUE)[ls(name = ls.input[[i1]], all.names = TRUE) %in% ls(name = ls.tested, all.names = TRUE)])
+        }
+    }
+    if( ! all(sapply(match.list, FUN = is.null))){
+        output <- paste0("SOME VARIABLES ", ifelse(is.null(name), "OF THE CHECKED ENVIRONMENT", paste0("OF ", name)), " ARE ALSO PRESENT IN :\n", paste0(names(match.list[ ! sapply(match.list, FUN = is.null)]), ": ", sapply(match.list[ ! sapply(match.list, FUN = is.null)], FUN = paste0, collapse = " "), collapse = "\n"))
+    }else{
+        output <- NULL
+    }
+    return(output)
 }
 
 
@@ -638,273 +638,273 @@ return(output)
 # -> transferred into the cute package
 # Do not modify this function in cute_little_R_function anymore. See the cute repo
 fun_info <- function(
-data, 
-n = NULL, 
-warn.print = TRUE
+    data, 
+    n = NULL, 
+    warn.print = TRUE
 ){
-# AIM
-# Provide a broad description of an object
-# WARNINGS
-# None
-# ARGUMENTS
-# data: object to analyse
-# n: positive integer value indicating the n first number of elements to display per compartment of the output list (i.e., head(..., n)). Write NULL to return all the elements. Does not apply for the $STRUCTURE compartment output
-# warn.print: logical. Print potential warnings at the end of the execution? If FALSE the warning messages are added in the output list as an additional compartment (or NULL if no message).
-# RETURN
-# A list containing information, depending on the class and type of data. The backbone is generally:
-# $NAME: name of the object
-# $CLASS: class of the object (class() value)
-# $TYPE: type of the object (typeof() value)
-# $LENGTH: length of the object (length() value)
-# $NA.NB: number of NA and NaN (only for type "logical", "integer", "double", "complex", "character" or "list")
-# $HEAD: head of the object (head() value)
-# $TAIL: tail of the object (tail() value)
-# $DIMENSION: dimension (only for object with dimensions)
-# $SUMMARY: object summary (summary() value)
-# $STRUCTURE: object structure (str() value)
-# $WARNING: warning messages (only if the warn.print argument is FALSE)
-# If data is made of numerics, provide also:
-# $INF.NB: number of Inf and -Inf
-# $RANGE: range after removing Inf and NA
-# $SUM: sum after removing Inf and NA
-# $MEAN: mean after removing Inf and NA
-# If data is a 2D object, provide also:
-# $ROW_NAMES: row names
-# $COL_NAMES: column names
-# If data is a data frame, provide also:
-# $COLUMN_TYPE: type of each column (typeof() value)
-# If data is a list, provide also:
-# $COMPARTMENT_NAMES: names of the comprtments
-# $COMPARTMENT_TYPE: type of each compartment (typeof() value)
-# REQUIRED PACKAGES
-# None
-# REQUIRED FUNCTIONS FROM THE cute PACKAGE
-# fun_check()
-# fun_get_message()
-# EXAMPLE
-# fun_info(data = 1:3)
-# see http
-# DEBUGGING
-# mat1 <- matrix(1:3) ; data = env1 ; n = NULL ; warn.print = TRUE # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
-arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
-# end function name
-# required function checking
-req.function <- c(
-"fun_check", 
-"fun_get_message"
-)
-tempo <- NULL
-for(i1 in req.function){
-if(length(find(i1, mode = "function")) == 0L){
-tempo <- c(tempo, i1)
-}
-}
-if( ! is.null(tempo)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# reserved words
-# end reserved words
-# arg with no default values
-mandat.args <- c(
-"data"
-)
-tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
-if(any(tempo)){ # normally no NA for missing() output
-tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end arg with no default values
-# argument primary checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-if( ! is.null(n)){
-tempo <- fun_check(data = n, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = n, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){ # normally no NA
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between == #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument primary checking
-# second round of checking and data preparation
-# management of NA arguments
-tempo.arg <- names(arg.user.setting) # values provided by the user
-tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
-if(any(tempo.log) == TRUE){ # normally no NA because is.na() used here
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT JUST BE NA")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NA arguments
-# management of NULL arguments
-tempo.arg <-c(
-"data", 
-# "n", # because can be NULL
-"warn.print"
-)
-tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
-if(any(tempo.log) == TRUE){# normally no NA with is.null()
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NULL arguments
-# code that protects set.seed() in the global environment
-# end code that protects set.seed() in the global environment
-# warning initiation
-ini.warning.length <- options()$warning.length
-options(warning.length = 8170)
-warn <- NULL
-# warn.count <- 0 # not required
-# end warning initiation
-# other checkings
-if( ! is.null(n)){
-if(n < 1){
-tempo.cat <- paste0("ERROR IN ", function.name, ": n ARGUMENT MUST BE A POSITIVE AND NON NULL INTEGER")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(is.finite(n)){
-# warn.count <- warn.count + 1
-tempo.warn <- paste0("SOME COMPARTMENTS CAN BE TRUNCATED (n ARGUMENT IS ", n, ")")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# end other checkings
-# reserved word checking
-# end reserved word checking
-# end second round of checking and data preparation
-# package checking
-# end package checking
-# main code
-# new environment
-env.name <- paste0("env", as.numeric(Sys.time()))
-if(exists(env.name, where = -1)){ # verify if still ok when fun_info() is inside a function
-tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-assign(env.name, new.env())
-assign("data", data, envir = get(env.name, env = sys.nframe(), inherit = FALSE)) # data assigned in a new envir for test
-}
-# end new environment
-data.name <- deparse(substitute(data))
-output <- list("NAME" = data.name)
-tempo.try.error <- fun_get_message(data = "class(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
-if(is.null(tempo.try.error)){
-tempo <- list("CLASS" = class(data))
-output <- c(output, tempo)
-}
-tempo.try.error <- fun_get_message(data = "typeof(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
-if(is.null(tempo.try.error)){
-tempo <- list("TYPE" = typeof(data))
-output <- c(output, tempo)
-}
-tempo.try.error <- fun_get_message(data = "length(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
-if(is.null(tempo.try.error)){
-tempo <- list("LENGTH" = length(data))
-output <- c(output, tempo)
-}
-if(all(typeof(data) %in% c("integer", "numeric", "double")) & ! any(class(data) %in% "factor")){ # all() without na.rm -> ok because typeof(NA) is "logical" # any() without na.rm -> ok because class(NA) is "logical"
-tempo <- list("INF.NB" = sum(is.infinite(data)))
-output <- c(output, tempo)
-tempo <- list("RANGE" = range(data[ ! is.infinite(data)], na.rm = TRUE))
-output <- c(output, tempo)
-tempo <- list("SUM" = sum(data[ ! is.infinite(data)], na.rm = TRUE))
-output <- c(output, tempo)
-tempo <- list("MEAN" = mean(data[ ! is.infinite(data)], na.rm = TRUE))
-output <- c(output, tempo)
-}
-if(all(typeof(data) %in% c("logical", "integer", "double", "complex", "character", "list"))){ # all() without na.rm -> ok because typeof(NA) is "logical"
-tempo.try.error <- fun_get_message(data = "is.na(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
-if(is.null(tempo.try.error)){
-tempo <- list("NA.NB" = sum(is.na(data)))
-output <- c(output, tempo)
-}
-}
-tempo.try.error <- fun_get_message(data = "head(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
-if(is.null(tempo.try.error)){
-tempo <- list("HEAD" = head(data))
-output <- c(output, tempo)
-tempo <- list("TAIL" = tail(data)) # no reason that tail() does not work if head() works
-output <- c(output, tempo)
-}
-tempo.try.error <- fun_get_message(data = "dim(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
-if(is.null(tempo.try.error)){
-if(length(dim(data)) > 0){
-tempo <- list("DIMENSION" = dim(data))
-if(length(tempo[[1]]) == 2L){
-names(tempo[[1]]) <- c("NROW", "NCOL")
-}
-output <- c(output, tempo)
-}
-}
-if(all(class(data) == "data.frame") | all(class(data) %in% c("matrix", "array")) | all(class(data) == "table")){ # all() without na.rm -> ok because typeof(NA) is "logical"
-if(length(dim(data)) > 1){ # to avoid 1D table
-tempo <- list("ROW_NAMES" = dimnames(data)[[1]])
-output <- c(output, tempo)
-tempo <- list("COLUM_NAMES" = dimnames(data)[[2]])
-output <- c(output, tempo)
-}
-}
-tempo.try.error <- fun_get_message(data = "summary(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
-if(is.null(tempo.try.error)){
-tempo <- list("SUMMARY" = summary(data))
-output <- c(output, tempo)
-}
-tempo.try.error <- fun_get_message(data = "noquote(matrix(capture.output(str(data))))", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
-if(is.null(tempo.try.error)){
-tempo <- capture.output(str(data))
-tempo <- list("STRUCTURE" = noquote(matrix(tempo, dimnames = list(rep("", length(tempo)), "")))) # str() print automatically, ls.str() not but does not give the order of the data.frame
-output <- c(output, tempo)
-}
-if(all(class(data) == "data.frame")){ # all() without na.rm -> ok because class(NA) is "logical"
-tempo <- list("COLUMN_TYPE" = sapply(data, FUN = "typeof"))
-if(any(sapply(data, FUN = "class") %in% "factor")){ # if an ordered factor is present, then sapply(data, FUN = "class") return a list but works with any(sapply(data, FUN = "class") %in% "factor") # any() without na.rm -> ok because class(NA) is "logical"
-tempo.class <- sapply(data, FUN = "class")
-if(any(unlist(tempo.class) %in% "ordered")){ # any() without na.rm -> ok because class(NA) is "logical"
-tempo2 <- sapply(tempo.class, paste, collapse = " ") # paste the "ordered" factor" in "ordered factor"
-}else{
-tempo2 <- unlist(tempo.class)
-}
-tempo[["COLUMN_TYPE"]][grepl(x = tempo2, pattern = "factor")] <- tempo2[grepl(x = tempo2, pattern = "factor")]
-}
-output <- c(output, tempo)
-}
-if(all(class(data) == "list")){ # all() without na.rm -> ok because class(NA) is "logical"
-tempo <- list("COMPARTMENT_NAMES" = names(data))
-output <- c(output, tempo)
-tempo <- list("COMPARTMENT_TYPE" = sapply(data, FUN = "typeof"))
-if(any(unlist(sapply(data, FUN = "class")) %in% "factor")){ # if an ordered factor is present, then sapply(data, FUN = "class") return a list but works with any(sapply(data, FUN = "class") %in% "factor")  # any() without na.rm -> ok because class(NA) is "logical"
-tempo.class <- sapply(data, FUN = "class")
-if(any(unlist(tempo.class) %in% "ordered")){ # any() without na.rm -> ok because class(NA) is "logical"
-tempo2 <- sapply(tempo.class, paste, collapse = " ") # paste the "ordered" factor" in "ordered factor"
-}else{
-tempo2 <- unlist(tempo.class)
-}
-tempo[["COMPARTMENT_TYPE"]][grepl(x = tempo2, pattern = "factor")] <- tempo2[grepl(x = tempo2, pattern = "factor")]
-}
-output <- c(output, tempo)
-}
-if( ! is.null(n)){
-output[names(output) != "STRUCTURE"] <- lapply(X = output[names(output) != "STRUCTURE"], FUN = head, n = n, simplify = FALSE)
-}
-# output
-if(warn.print == FALSE){
-output <- c(output, WARNING = warn)
-}else if(warn.print == TRUE & ! is.null(warn)){
-on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
-}
-on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
-return(output)
-# end output
-# end main code
+    # AIM
+    # Provide a broad description of an object
+    # WARNINGS
+    # None
+    # ARGUMENTS
+    # data: object to analyse
+    # n: positive integer value indicating the n first number of elements to display per compartment of the output list (i.e., head(..., n)). Write NULL to return all the elements. Does not apply for the $STRUCTURE compartment output
+    # warn.print: logical. Print potential warnings at the end of the execution? If FALSE the warning messages are added in the output list as an additional compartment (or NULL if no message).
+    # RETURN
+    # A list containing information, depending on the class and type of data. The backbone is generally:
+    # $NAME: name of the object
+    # $CLASS: class of the object (class() value)
+    # $TYPE: type of the object (typeof() value)
+    # $LENGTH: length of the object (length() value)
+    # $NA.NB: number of NA and NaN (only for type "logical", "integer", "double", "complex", "character" or "list")
+    # $HEAD: head of the object (head() value)
+    # $TAIL: tail of the object (tail() value)
+    # $DIMENSION: dimension (only for object with dimensions)
+    # $SUMMARY: object summary (summary() value)
+    # $STRUCTURE: object structure (str() value)
+    # $WARNING: warning messages (only if the warn.print argument is FALSE)
+    # If data is made of numerics, provide also:
+    # $INF.NB: number of Inf and -Inf
+    # $RANGE: range after removing Inf and NA
+    # $SUM: sum after removing Inf and NA
+    # $MEAN: mean after removing Inf and NA
+    # If data is a 2D object, provide also:
+    # $ROW_NAMES: row names
+    # $COL_NAMES: column names
+    # If data is a data frame, provide also:
+    # $COLUMN_TYPE: type of each column (typeof() value)
+    # If data is a list, provide also:
+    # $COMPARTMENT_NAMES: names of the comprtments
+    # $COMPARTMENT_TYPE: type of each compartment (typeof() value)
+    # REQUIRED PACKAGES
+    # None
+    # REQUIRED FUNCTIONS FROM THE cute PACKAGE
+    # fun_check()
+    # fun_get_message()
+    # EXAMPLE
+    # fun_info(data = 1:3)
+    # see http
+    # DEBUGGING
+    # mat1 <- matrix(1:3) ; data = env1 ; n = NULL ; warn.print = TRUE # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
+    arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
+    # end function name
+    # required function checking
+    req.function <- c(
+        "fun_check", 
+        "fun_get_message"
+    )
+    tempo <- NULL
+    for(i1 in req.function){
+        if(length(find(i1, mode = "function")) == 0L){
+            tempo <- c(tempo, i1)
+        }
+    }
+    if( ! is.null(tempo)){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # reserved words
+    # end reserved words
+    # arg with no default values
+    mandat.args <- c(
+        "data"
+    )
+    tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
+    if(any(tempo)){ # normally no NA for missing() output
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end arg with no default values
+    # argument primary checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    if( ! is.null(n)){
+        tempo <- fun_check(data = n, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = n, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){ # normally no NA
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between == #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument primary checking
+    # second round of checking and data preparation
+    # management of NA arguments
+    tempo.arg <- names(arg.user.setting) # values provided by the user
+    tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
+    if(any(tempo.log) == TRUE){ # normally no NA because is.na() used here
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT JUST BE NA")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NA arguments
+    # management of NULL arguments
+    tempo.arg <-c(
+        "data", 
+        # "n", # because can be NULL
+        "warn.print"
+    )
+    tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
+    if(any(tempo.log) == TRUE){# normally no NA with is.null()
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NULL arguments
+    # code that protects set.seed() in the global environment
+    # end code that protects set.seed() in the global environment
+    # warning initiation
+    ini.warning.length <- options()$warning.length
+    options(warning.length = 8170)
+    warn <- NULL
+    # warn.count <- 0 # not required
+    # end warning initiation
+    # other checkings
+    if( ! is.null(n)){
+        if(n < 1){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": n ARGUMENT MUST BE A POSITIVE AND NON NULL INTEGER")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else if(is.finite(n)){
+            # warn.count <- warn.count + 1
+            tempo.warn <- paste0("SOME COMPARTMENTS CAN BE TRUNCATED (n ARGUMENT IS ", n, ")")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    # end other checkings
+    # reserved word checking
+    # end reserved word checking
+    # end second round of checking and data preparation
+    # package checking
+    # end package checking
+    # main code
+    # new environment
+    env.name <- paste0("env", as.numeric(Sys.time()))
+    if(exists(env.name, where = -1)){ # verify if still ok when fun_info() is inside a function
+        tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else{
+        assign(env.name, new.env())
+        assign("data", data, envir = get(env.name, env = sys.nframe(), inherit = FALSE)) # data assigned in a new envir for test
+    }
+    # end new environment
+    data.name <- deparse(substitute(data))
+    output <- list("NAME" = data.name)
+    tempo.try.error <- fun_get_message(data = "class(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
+    if(is.null(tempo.try.error)){
+        tempo <- list("CLASS" = class(data))
+        output <- c(output, tempo)
+    }
+    tempo.try.error <- fun_get_message(data = "typeof(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
+    if(is.null(tempo.try.error)){
+        tempo <- list("TYPE" = typeof(data))
+        output <- c(output, tempo)
+    }
+    tempo.try.error <- fun_get_message(data = "length(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
+    if(is.null(tempo.try.error)){
+        tempo <- list("LENGTH" = length(data))
+        output <- c(output, tempo)
+    }
+    if(all(typeof(data) %in% c("integer", "numeric", "double")) & ! any(class(data) %in% "factor")){ # all() without na.rm -> ok because typeof(NA) is "logical" # any() without na.rm -> ok because class(NA) is "logical"
+        tempo <- list("INF.NB" = sum(is.infinite(data)))
+        output <- c(output, tempo)
+        tempo <- list("RANGE" = range(data[ ! is.infinite(data)], na.rm = TRUE))
+        output <- c(output, tempo)
+        tempo <- list("SUM" = sum(data[ ! is.infinite(data)], na.rm = TRUE))
+        output <- c(output, tempo)
+        tempo <- list("MEAN" = mean(data[ ! is.infinite(data)], na.rm = TRUE))
+        output <- c(output, tempo)
+    }
+    if(all(typeof(data) %in% c("logical", "integer", "double", "complex", "character", "list"))){ # all() without na.rm -> ok because typeof(NA) is "logical"
+        tempo.try.error <- fun_get_message(data = "is.na(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
+        if(is.null(tempo.try.error)){
+            tempo <- list("NA.NB" = sum(is.na(data)))
+            output <- c(output, tempo)
+        }
+    }
+    tempo.try.error <- fun_get_message(data = "head(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
+    if(is.null(tempo.try.error)){
+        tempo <- list("HEAD" = head(data))
+        output <- c(output, tempo)
+        tempo <- list("TAIL" = tail(data)) # no reason that tail() does not work if head() works
+        output <- c(output, tempo)
+    }
+    tempo.try.error <- fun_get_message(data = "dim(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
+    if(is.null(tempo.try.error)){
+        if(length(dim(data)) > 0){
+            tempo <- list("DIMENSION" = dim(data))
+            if(length(tempo[[1]]) == 2L){
+                names(tempo[[1]]) <- c("NROW", "NCOL")
+            }
+            output <- c(output, tempo)
+        }
+    }
+    if(all(class(data) == "data.frame") | all(class(data) %in% c("matrix", "array")) | all(class(data) == "table")){ # all() without na.rm -> ok because typeof(NA) is "logical"
+        if(length(dim(data)) > 1){ # to avoid 1D table
+            tempo <- list("ROW_NAMES" = dimnames(data)[[1]])
+            output <- c(output, tempo)
+            tempo <- list("COLUM_NAMES" = dimnames(data)[[2]])
+            output <- c(output, tempo)
+        }
+    }
+    tempo.try.error <- fun_get_message(data = "summary(data)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
+    if(is.null(tempo.try.error)){
+        tempo <- list("SUMMARY" = summary(data))
+        output <- c(output, tempo)
+    }
+    tempo.try.error <- fun_get_message(data = "noquote(matrix(capture.output(str(data))))", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))
+    if(is.null(tempo.try.error)){
+        tempo <- capture.output(str(data))
+        tempo <- list("STRUCTURE" = noquote(matrix(tempo, dimnames = list(rep("", length(tempo)), "")))) # str() print automatically, ls.str() not but does not give the order of the data.frame
+        output <- c(output, tempo)
+    }
+    if(all(class(data) == "data.frame")){ # all() without na.rm -> ok because class(NA) is "logical"
+        tempo <- list("COLUMN_TYPE" = sapply(data, FUN = "typeof"))
+        if(any(sapply(data, FUN = "class") %in% "factor")){ # if an ordered factor is present, then sapply(data, FUN = "class") return a list but works with any(sapply(data, FUN = "class") %in% "factor") # any() without na.rm -> ok because class(NA) is "logical"
+            tempo.class <- sapply(data, FUN = "class")
+            if(any(unlist(tempo.class) %in% "ordered")){ # any() without na.rm -> ok because class(NA) is "logical"
+                tempo2 <- sapply(tempo.class, paste, collapse = " ") # paste the "ordered" factor" in "ordered factor"
+            }else{
+                tempo2 <- unlist(tempo.class)
+            }
+            tempo[["COLUMN_TYPE"]][grepl(x = tempo2, pattern = "factor")] <- tempo2[grepl(x = tempo2, pattern = "factor")]
+        }
+        output <- c(output, tempo)
+    }
+    if(all(class(data) == "list")){ # all() without na.rm -> ok because class(NA) is "logical"
+        tempo <- list("COMPARTMENT_NAMES" = names(data))
+        output <- c(output, tempo)
+        tempo <- list("COMPARTMENT_TYPE" = sapply(data, FUN = "typeof"))
+        if(any(unlist(sapply(data, FUN = "class")) %in% "factor")){ # if an ordered factor is present, then sapply(data, FUN = "class") return a list but works with any(sapply(data, FUN = "class") %in% "factor")  # any() without na.rm -> ok because class(NA) is "logical"
+            tempo.class <- sapply(data, FUN = "class")
+            if(any(unlist(tempo.class) %in% "ordered")){ # any() without na.rm -> ok because class(NA) is "logical"
+                tempo2 <- sapply(tempo.class, paste, collapse = " ") # paste the "ordered" factor" in "ordered factor"
+            }else{
+                tempo2 <- unlist(tempo.class)
+            }
+            tempo[["COMPARTMENT_TYPE"]][grepl(x = tempo2, pattern = "factor")] <- tempo2[grepl(x = tempo2, pattern = "factor")]
+        }
+        output <- c(output, tempo)
+    }
+    if( ! is.null(n)){
+        output[names(output) != "STRUCTURE"] <- lapply(X = output[names(output) != "STRUCTURE"], FUN = head, n = n, simplify = FALSE)
+    }
+    # output
+    if(warn.print == FALSE){
+        output <- c(output, WARNING = warn)
+    }else if(warn.print == TRUE & ! is.null(warn)){
+        on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
+    }
+    on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
+    return(output)
+    # end output
+    # end main code
 }
 
 
@@ -912,62 +912,62 @@ return(output)
 
 
 fun_head <- function(
-data1, 
-n = 6, 
-side = "l"
+    data1, 
+    n = 6, 
+    side = "l"
 ){
-# AIM
-# as head() but display the left or right head of big 2D objects
-# ARGUMENTS
-# data1: any object but more dedicated for matrix, data frame or table
-# n: as in head() but for for matrix, data frame or table, number of dimension to print (10 means 10 rows and columns)
-# side: either "l" or "r" for the left or right side of the 2D object (only for matrix, data frame or table)
-# BEWARE: other arguments of head() not used
-# RETURN
-# the head
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# obs1 = matrix(1:30, ncol = 5, dimnames = list(letters[1:6], LETTERS[1:5])) ; obs1 ; fun_head(obs1, 3)
-# DEBUGGING
-# data1 = matrix(1:30, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = n, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = side, options = c("l", "r"), length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-if( ! (any(class(data1) %in% c("data.frame", "table")) | all(class(data1) %in% c("matrix", "array")))){ # before R4.0.0, it was  ! any(class(data1) %in% c("matrix", "data.frame", "table"))
-return(head(data1, n))
-}else{
-obs.dim <- dim(data1)
-row <- 1:ifelse(obs.dim[1] < n, obs.dim[1], n)
-if(side == "l"){
-col <- 1:ifelse(obs.dim[2] < n, obs.dim[2], n)
-}
-if(side == "r"){
-col <- ifelse(obs.dim[2] < n, 1, obs.dim[2] - n + 1):obs.dim[2]
-}
-return(data1[row, col])
-}
+    # AIM
+    # as head() but display the left or right head of big 2D objects
+    # ARGUMENTS
+    # data1: any object but more dedicated for matrix, data frame or table
+    # n: as in head() but for for matrix, data frame or table, number of dimension to print (10 means 10 rows and columns)
+    # side: either "l" or "r" for the left or right side of the 2D object (only for matrix, data frame or table)
+    # BEWARE: other arguments of head() not used
+    # RETURN
+    # the head
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # obs1 = matrix(1:30, ncol = 5, dimnames = list(letters[1:6], LETTERS[1:5])) ; obs1 ; fun_head(obs1, 3)
+    # DEBUGGING
+    # data1 = matrix(1:30, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = n, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = side, options = c("l", "r"), length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    if( ! (any(class(data1) %in% c("data.frame", "table")) | all(class(data1) %in% c("matrix", "array")))){ # before R4.0.0, it was  ! any(class(data1) %in% c("matrix", "data.frame", "table"))
+        return(head(data1, n))
+    }else{
+        obs.dim <- dim(data1)
+        row <- 1:ifelse(obs.dim[1] < n, obs.dim[1], n)
+        if(side == "l"){
+            col <- 1:ifelse(obs.dim[2] < n, obs.dim[2], n)
+        }
+        if(side == "r"){
+            col <- ifelse(obs.dim[2] < n, 1, obs.dim[2] - n + 1):obs.dim[2]
+        }
+        return(data1[row, col])
+    }
 }
 
 
@@ -975,62 +975,62 @@ return(data1[row, col])
 
 
 fun_tail <- function(
-data1, 
-n = 6, 
-side = "l"
+    data1, 
+    n = 6, 
+    side = "l"
 ){
-# AIM
-# as tail() but display the left or right head of big 2D objects
-# ARGUMENTS
-# data1: any object but more dedicated for matrix, data frame or table
-# n: as in tail() but for for matrix, data frame or table, number of dimension to print (10 means 10 rows and columns)
-# side: either "l" or "r" for the left or right side of the 2D object (only for matrix, data frame or table)
-# BEWARE: other arguments of tail() not used
-# RETURN
-# the tail
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# obs1 = matrix(1:30, ncol = 5, dimnames = list(letters[1:6], LETTERS[1:5])) ; obs1 ; fun_tail(obs1, 3, "r")
-# DEBUGGING
-# data1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = n, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = side, options = c("l", "r"), length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-if( ! (any(class(data1) %in% c("data.frame", "table")) | all(class(data1) %in% c("matrix", "array")))){ # before R4.0.0, it was  ! any(class(data1) %in% c("matrix", "data.frame", "table"))
-return(tail(data1, n))
-}else{
-obs.dim <- dim(data1)
-row <- ifelse(obs.dim[1] < n, 1, obs.dim[1] - n + 1):obs.dim[1]
-if(side == "l"){
-col <- 1:ifelse(obs.dim[2] < n, obs.dim[2], n)
-}
-if(side == "r"){
-col <- ifelse(obs.dim[2] < n, 1, obs.dim[2] - n + 1):obs.dim[2]
-}
-return(data1[row, col])
-}
+    # AIM
+    # as tail() but display the left or right head of big 2D objects
+    # ARGUMENTS
+    # data1: any object but more dedicated for matrix, data frame or table
+    # n: as in tail() but for for matrix, data frame or table, number of dimension to print (10 means 10 rows and columns)
+    # side: either "l" or "r" for the left or right side of the 2D object (only for matrix, data frame or table)
+    # BEWARE: other arguments of tail() not used
+    # RETURN
+    # the tail
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # obs1 = matrix(1:30, ncol = 5, dimnames = list(letters[1:6], LETTERS[1:5])) ; obs1 ; fun_tail(obs1, 3, "r")
+    # DEBUGGING
+    # data1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = n, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = side, options = c("l", "r"), length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    if( ! (any(class(data1) %in% c("data.frame", "table")) | all(class(data1) %in% c("matrix", "array")))){ # before R4.0.0, it was  ! any(class(data1) %in% c("matrix", "data.frame", "table"))
+        return(tail(data1, n))
+    }else{
+        obs.dim <- dim(data1)
+        row <- ifelse(obs.dim[1] < n, 1, obs.dim[1] - n + 1):obs.dim[1]
+        if(side == "l"){
+            col <- 1:ifelse(obs.dim[2] < n, obs.dim[2], n)
+        }
+        if(side == "r"){
+            col <- ifelse(obs.dim[2] < n, 1, obs.dim[2] - n + 1):obs.dim[2]
+        }
+        return(data1[row, col])
+    }
 }
 
 
@@ -1038,241 +1038,241 @@ return(data1[row, col])
 
 
 fun_comp_1d <- function(data1, data2){
-# AIM
-# compare two 1D datasets (vector or factor or 1D table, or 1D matrix or 1D array) of the same class or not. Check and report in a list if the 2 datasets have:
-# same class
-# common elements
-# common element names (except factors)
-# common levels (factors only)
-# ARGUMENTS
-# data1: vector or factor or 1D table, or 1D matrix or 1D array
-# data2: vector or factor or 1D table, or 1D matrix or 1D array
-# RETURN
-# a list containing:
-# $same.class: logical. Are class identical?
-# $class: class of the 2 datasets (NULL otherwise)
-# $same.length: logical. Are number of elements identical?
-# $length: number of elements in the 2 datasets (NULL otherwise)
-# $same.levels: logical. Are levels identical? NULL if data1 and data2 are not factors
-# $levels: levels of the 2 datasets if identical (NULL otherwise or NULL if data1 and data2 are not factors)
-# $any.id.levels: logical. Is there any identical levels? (NULL if data1 and data2 are not factors)
-# $same.levels.pos1: positions, in data1, of the levels identical in data2 (NULL otherwise or NULL if data1 and data2 are not factors)
-# $same.levels.pos2: positions, in data2, of the levels identical in data1 (NULL otherwise or NULL if data1 and data2 are not factors)
-# $same.levels.match1: positions, in data2, of the levels that match the levels in data1, as given by match(data1, data2) (NULL otherwise or NULL if data1 and data2 are not factors)
-# $same.levels.match2: positions, in data1, of the levels that match the levels in data2, as given by match(data1, data2) (NULL otherwise or NULL if data1 and data2 are not factors)
-# $common.levels: common levels between data1 and data2 (can be a subset of $levels or not). NULL if no common levels or if data1 and data2 are not factors
-# $same.names: logical. Are element names identical? NULL if data1 and data2 have no names
-# $name: name of elements of the 2 datasets if identical (NULL otherwise)
-# $any.id.name: logical. Is there any element names identical ?
-# $same.names.pos1: positions, in data1, of the element names identical in data2. NULL if no identical names
-# $same.names.pos2: positions, in data2, of the elements names identical in data1. NULL if no identical names
-# $same.names.match1: positions, in data2, of the names that match the names in data1, as given by match(data1, data2) (NULL otherwise)
-# $same.names.match2: positions, in data1, of the names that match the names in data2, as given by match(data1, data2) (NULL otherwise)
-# $common.names: common element names between data1 and data2 (can be a subset of $name or not). NULL if no common element names
-# $any.id.element: logical. is there any identical elements ?
-# $same.elements.pos1: positions, in data1, of the elements identical in data2. NULL if no identical elements
-# $same.elements.pos2: positions, in data2, of the elements identical in data1. NULL if no identical elements
-# $same.elements.match1: positions, in data2, of the elements that match the elements in data1, as given by match(data1, data2) (NULL otherwise)
-# $same.elements.match2: positions, in data1, of the elements that match the elements in data2, as given by match(data1, data2) (NULL otherwise)
-# $common.elements: common elements between data1 and data2. NULL if no common elements
-# $same.order: logical. Are all elements in the same order? TRUE or FALSE if elements of data1 and data2 are identical but not necessary in the same order. NULL otherwise (different length for instance)
-# $order1: order of all elements of data1. NULL if $same.order is FALSE
-# $order2: order of all elements of data2. NULL if $same.order is FALSE
-# $identical.object: logical. Are objects identical (kind of object, element names, content, including content order)?
-# $identical.content: logical. Are content objects identical (identical elements, including order, excluding kind of object and element names)?
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# none
-# EXAMPLES
-# obs1 = 1:5 ; obs2 = 1:5 ; names(obs1) <- LETTERS[1:5] ; names(obs2) <- LETTERS[1:5] ; fun_comp_1d(obs1, obs2)
-# obs1 = 1:5 ; obs2 = 1:5 ; names(obs1) <- LETTERS[1:5] ; fun_comp_1d(obs1, obs2)
-# obs1 = 1:5 ; obs2 = 3:6 ; names(obs1) <- LETTERS[1:5] ; names(obs2) <- LETTERS[1:4] ; fun_comp_1d(obs1, obs2)
-# obs1 = factor(LETTERS[1:5]) ; obs2 = factor(LETTERS[1:5]) ; fun_comp_1d(obs1, obs2)
-# obs1 = factor(LETTERS[1:5]) ; obs2 = factor(LETTERS[10:11]) ; fun_comp_1d(obs1, obs2)
-# obs1 = factor(LETTERS[1:5]) ; obs2 = factor(LETTERS[4:7]) ; fun_comp_1d(obs1, obs2)
-# obs1 = factor(c(LETTERS[1:4], "E")) ; obs2 = factor(c(LETTERS[1:4], "F")) ; fun_comp_1d(obs1, obs2)
-# obs1 = 1:5 ; obs2 = factor(LETTERS[1:5]) ; fun_comp_1d(obs1, obs2)
-# obs1 = 1:5 ; obs2 = 1.1:6.1 ; fun_comp_1d(obs1, obs2)
-# obs1 = as.table(1:5); obs2 = as.table(1:5) ; fun_comp_1d(obs1, obs2)
-# obs1 = as.table(1:5); obs2 = 1:5 ; fun_comp_1d(obs1, obs2)
-# DEBUGGING
-# data1 = 1:5 ; data2 = 1:5 ; names(data1) <- LETTERS[1:5] ; names(data2) <- LETTERS[1:5] # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# argument checking
-if( ! any(class(data1) %in% c("logical", "integer", "numeric", "character", "factor", "table"))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 ARGUMENT MUST BE A NON NULL VECTOR, FACTOR OR 1D TABLE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(all(class(data1) %in% "table")){
-if(length(dim(data1)) > 1){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 ARGUMENT MUST BE A 1D TABLE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if( ! any(class(data2) %in% c("logical", "integer", "numeric", "character", "factor", "table"))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data2 ARGUMENT MUST BE A NON NULL VECTOR, FACTOR OR 1D TABLE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(all(class(data2) %in% "table")){
-if(length(dim(data2)) > 1){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data2 ARGUMENT MUST BE A 1D TABLE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) # activate this line and use the function to check arguments status
-# end argument checking
-# main code
-same.class <- FALSE
-class <- NULL
-same.length <- FALSE
-length <- NULL
-same.levels <- NULL # not FALSE to deal with no factors
-levels <- NULL
-any.id.levels <- FALSE
-same.levels.pos1 <- NULL
-same.levels.pos2 <- NULL
-same.levels.match1 <- NULL
-same.levels.match2 <- NULL
-common.levels <- NULL
-same.names <- NULL # not FALSE to deal with absence of name
-name <- NULL
-any.id.name <- FALSE
-same.names.pos1 <- NULL
-same.names.pos2 <- NULL
-same.names.match1 <- NULL
-same.names.match2 <- NULL
-common.names <- NULL
-any.id.element <- FALSE
-same.elements.pos1 <- NULL
-same.elements.pos2 <- NULL
-same.elements.match1 <- NULL
-same.elements.match2 <- NULL
-common.elements <- NULL
-same.order <- NULL
-order1 <- NULL
-order2 <- NULL
-identical.object <- FALSE
-identical.content <- FALSE
-if(identical(data1, data2)){
-same.class <- TRUE
-class <- class(data1)
-same.length <- TRUE
-length <- length(data1)
-if(any(class(data1) %in% "factor")){
-same.levels <- TRUE
-levels <- levels(data1)
-any.id.levels <- TRUE
-same.levels.pos1 <- 1:length(levels(data1))
-same.levels.pos2 <- 1:length(levels(data2))
-same.levels.match1 <- 1:length(levels(data1))
-same.levels.match2 <- 1:length(levels(data2))
-common.levels <- levels(data1)
-}
-if( ! is.null(names(data1))){
-same.names <- TRUE
-name <- names(data1)
-any.id.name <- TRUE
-same.names.pos1 <- 1:length(data1)
-same.names.pos2 <- 1:length(data2)
-same.names.match1 <- 1:length(data1)
-same.names.match2 <- 1:length(data2)
-common.names <- names(data1)
-}
-any.id.element <- TRUE
-same.elements.pos1 <- 1:length(data1)
-same.elements.pos2 <- 1:length(data2)
-same.elements.match1 <- 1:length(data1)
-same.elements.match2 <- 1:length(data2)
-common.elements <- data1
-same.order <- TRUE
-order1 <- order(data1)
-order2 <- order(data2)
-identical.object <- TRUE
-identical.content <- TRUE
-}else{
-if(identical(class(data1), class(data2))){
-same.class <- TRUE
-class <- class(data1)
-}
-if(identical(length(data1), length(data2))){
-same.length<- TRUE
-length <- length(data1)
-}
-if(any(class(data1) %in% "factor") & any(class(data2) %in% "factor")){
-if(identical(levels(data1), levels(data2))){
-same.levels <- TRUE
-levels <- levels(data1)
-}else{
-same.levels <- FALSE
-}
-if(any(levels(data1) %in% levels(data2))){
-any.id.levels <- TRUE
-same.levels.pos1 <- which(levels(data1) %in% levels(data2))
-same.levels.match1 <- match(levels(data1), levels(data2))
-}
-if(any(levels(data2) %in% levels(data1))){
-any.id.levels <- TRUE
-same.levels.pos2 <- which(levels(data2) %in% levels(data1))
-same.levels.match2 <- match(levels(data2), levels(data1))
-}
-if(any.id.levels == TRUE){
-common.levels <- unique(c(levels(data1)[same.levels.pos1], levels(data2)[same.levels.pos2]))
-}
-}
-if(any(class(data1) %in% "factor")){ # to compare content
-data1 <- as.character(data1)
-}
-if(any(class(data2) %in% "factor")){ # to compare content
-data2 <- as.character(data2)
-}
-if( ! (is.null(names(data1)) & is.null(names(data2)))){
-if(identical(names(data1), names(data2))){
-same.names <- TRUE
-name <- names(data1)
-}else{
-same.names <- FALSE
-}
-if(any(names(data1) %in% names(data2))){
-any.id.name <- TRUE
-same.names.pos1 <- which(names(data1) %in% names(data2))
-same.names.match1 <- match(names(data1), names(data2))
-}
-if(any(names(data2) %in% names(data1))){
-any.id.name <- TRUE
-same.names.pos2 <- which(names(data2) %in% names(data1))
-same.names.match2 <- match(names(data2), names(data1))
-}
-if(any.id.name == TRUE){
-common.names <- unique(c(names(data1)[same.names.pos1], names(data2)[same.names.pos2]))
-}
-}
-names(data1) <- NULL # names solved -> to do not be disturbed by names
-names(data2) <- NULL # names solved -> to do not be disturbed by names
-if(any(data1 %in% data2)){
-any.id.element <- TRUE
-same.elements.pos1 <- which(data1 %in% data2)
-same.elements.match1 <- match(data1, data2)
-}
-if(any(data2 %in% data1)){
-any.id.element <- TRUE
-same.elements.pos2 <- which(data2 %in% data1)
-same.elements.match2 <- match(data2, data1)
-}
-if(any.id.element == TRUE){
-common.elements <- unique(c(data1[same.elements.pos1], data2[same.elements.pos2]))
-}
-if(identical(data1, data2)){
-identical.content <- TRUE
-same.order <- TRUE
-}else if(identical(sort(data1), sort(data2))){
-same.order <- FALSE
-order1 <- order(data1)
-order2 <- order(data2)
-}
-}
-output <- list(same.class = same.class, class = class, same.length = same.length, length = length, same.levels = same.levels, levels = levels, any.id.levels = any.id.levels, same.levels.pos1 = same.levels.pos1, same.levels.pos2 = same.levels.pos2, same.levels.match1 = same.levels.match1, same.levels.match2 = same.levels.match2, common.levels = common.levels, same.names = same.names, name = name, any.id.name = any.id.name, same.names.pos1 = same.names.pos1, same.names.pos2 = same.names.pos2, same.names.match1 = same.names.match1, same.names.match2 = same.names.match2, common.names = common.names, any.id.element = any.id.element, same.elements.pos1 = same.elements.pos1, same.elements.pos2 = same.elements.pos2, same.elements.match1 = same.elements.match1, same.elements.match2 = same.elements.match2, common.elements = common.elements, same.order = same.order, order1 = order1, order2 = order2, identical.object = identical.object, identical.content = identical.content)
-return(output)
+    # AIM
+    # compare two 1D datasets (vector or factor or 1D table, or 1D matrix or 1D array) of the same class or not. Check and report in a list if the 2 datasets have:
+    # same class
+    # common elements
+    # common element names (except factors)
+    # common levels (factors only)
+    # ARGUMENTS
+    # data1: vector or factor or 1D table, or 1D matrix or 1D array
+    # data2: vector or factor or 1D table, or 1D matrix or 1D array
+    # RETURN
+    # a list containing:
+    # $same.class: logical. Are class identical?
+    # $class: class of the 2 datasets (NULL otherwise)
+    # $same.length: logical. Are number of elements identical?
+    # $length: number of elements in the 2 datasets (NULL otherwise)
+    # $same.levels: logical. Are levels identical? NULL if data1 and data2 are not factors
+    # $levels: levels of the 2 datasets if identical (NULL otherwise or NULL if data1 and data2 are not factors)
+    # $any.id.levels: logical. Is there any identical levels? (NULL if data1 and data2 are not factors)
+    # $same.levels.pos1: positions, in data1, of the levels identical in data2 (NULL otherwise or NULL if data1 and data2 are not factors)
+    # $same.levels.pos2: positions, in data2, of the levels identical in data1 (NULL otherwise or NULL if data1 and data2 are not factors)
+    # $same.levels.match1: positions, in data2, of the levels that match the levels in data1, as given by match(data1, data2) (NULL otherwise or NULL if data1 and data2 are not factors)
+    # $same.levels.match2: positions, in data1, of the levels that match the levels in data2, as given by match(data1, data2) (NULL otherwise or NULL if data1 and data2 are not factors)
+    # $common.levels: common levels between data1 and data2 (can be a subset of $levels or not). NULL if no common levels or if data1 and data2 are not factors
+    # $same.names: logical. Are element names identical? NULL if data1 and data2 have no names
+    # $name: name of elements of the 2 datasets if identical (NULL otherwise)
+    # $any.id.name: logical. Is there any element names identical ?
+    # $same.names.pos1: positions, in data1, of the element names identical in data2. NULL if no identical names
+    # $same.names.pos2: positions, in data2, of the elements names identical in data1. NULL if no identical names
+    # $same.names.match1: positions, in data2, of the names that match the names in data1, as given by match(data1, data2) (NULL otherwise)
+    # $same.names.match2: positions, in data1, of the names that match the names in data2, as given by match(data1, data2) (NULL otherwise)
+    # $common.names: common element names between data1 and data2 (can be a subset of $name or not). NULL if no common element names
+    # $any.id.element: logical. is there any identical elements ?
+    # $same.elements.pos1: positions, in data1, of the elements identical in data2. NULL if no identical elements
+    # $same.elements.pos2: positions, in data2, of the elements identical in data1. NULL if no identical elements
+    # $same.elements.match1: positions, in data2, of the elements that match the elements in data1, as given by match(data1, data2) (NULL otherwise)
+    # $same.elements.match2: positions, in data1, of the elements that match the elements in data2, as given by match(data1, data2) (NULL otherwise)
+    # $common.elements: common elements between data1 and data2. NULL if no common elements
+    # $same.order: logical. Are all elements in the same order? TRUE or FALSE if elements of data1 and data2 are identical but not necessary in the same order. NULL otherwise (different length for instance)
+    # $order1: order of all elements of data1. NULL if $same.order is FALSE
+    # $order2: order of all elements of data2. NULL if $same.order is FALSE
+    # $identical.object: logical. Are objects identical (kind of object, element names, content, including content order)?
+    # $identical.content: logical. Are content objects identical (identical elements, including order, excluding kind of object and element names)?
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # none
+    # EXAMPLES
+    # obs1 = 1:5 ; obs2 = 1:5 ; names(obs1) <- LETTERS[1:5] ; names(obs2) <- LETTERS[1:5] ; fun_comp_1d(obs1, obs2)
+    # obs1 = 1:5 ; obs2 = 1:5 ; names(obs1) <- LETTERS[1:5] ; fun_comp_1d(obs1, obs2)
+    # obs1 = 1:5 ; obs2 = 3:6 ; names(obs1) <- LETTERS[1:5] ; names(obs2) <- LETTERS[1:4] ; fun_comp_1d(obs1, obs2)
+    # obs1 = factor(LETTERS[1:5]) ; obs2 = factor(LETTERS[1:5]) ; fun_comp_1d(obs1, obs2)
+    # obs1 = factor(LETTERS[1:5]) ; obs2 = factor(LETTERS[10:11]) ; fun_comp_1d(obs1, obs2)
+    # obs1 = factor(LETTERS[1:5]) ; obs2 = factor(LETTERS[4:7]) ; fun_comp_1d(obs1, obs2)
+    # obs1 = factor(c(LETTERS[1:4], "E")) ; obs2 = factor(c(LETTERS[1:4], "F")) ; fun_comp_1d(obs1, obs2)
+    # obs1 = 1:5 ; obs2 = factor(LETTERS[1:5]) ; fun_comp_1d(obs1, obs2)
+    # obs1 = 1:5 ; obs2 = 1.1:6.1 ; fun_comp_1d(obs1, obs2)
+    # obs1 = as.table(1:5); obs2 = as.table(1:5) ; fun_comp_1d(obs1, obs2)
+    # obs1 = as.table(1:5); obs2 = 1:5 ; fun_comp_1d(obs1, obs2)
+    # DEBUGGING
+    # data1 = 1:5 ; data2 = 1:5 ; names(data1) <- LETTERS[1:5] ; names(data2) <- LETTERS[1:5] # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # argument checking
+    if( ! any(class(data1) %in% c("logical", "integer", "numeric", "character", "factor", "table"))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 ARGUMENT MUST BE A NON NULL VECTOR, FACTOR OR 1D TABLE")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else if(all(class(data1) %in% "table")){
+        if(length(dim(data1)) > 1){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 ARGUMENT MUST BE A 1D TABLE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if( ! any(class(data2) %in% c("logical", "integer", "numeric", "character", "factor", "table"))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": THE data2 ARGUMENT MUST BE A NON NULL VECTOR, FACTOR OR 1D TABLE")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else if(all(class(data2) %in% "table")){
+        if(length(dim(data2)) > 1){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": THE data2 ARGUMENT MUST BE A 1D TABLE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) # activate this line and use the function to check arguments status
+    # end argument checking
+    # main code
+    same.class <- FALSE
+    class <- NULL
+    same.length <- FALSE
+    length <- NULL
+    same.levels <- NULL # not FALSE to deal with no factors
+    levels <- NULL
+    any.id.levels <- FALSE
+    same.levels.pos1 <- NULL
+    same.levels.pos2 <- NULL
+    same.levels.match1 <- NULL
+    same.levels.match2 <- NULL
+    common.levels <- NULL
+    same.names <- NULL # not FALSE to deal with absence of name
+    name <- NULL
+    any.id.name <- FALSE
+    same.names.pos1 <- NULL
+    same.names.pos2 <- NULL
+    same.names.match1 <- NULL
+    same.names.match2 <- NULL
+    common.names <- NULL
+    any.id.element <- FALSE
+    same.elements.pos1 <- NULL
+    same.elements.pos2 <- NULL
+    same.elements.match1 <- NULL
+    same.elements.match2 <- NULL
+    common.elements <- NULL
+    same.order <- NULL
+    order1 <- NULL
+    order2 <- NULL
+    identical.object <- FALSE
+    identical.content <- FALSE
+    if(identical(data1, data2)){
+        same.class <- TRUE
+        class <- class(data1)
+        same.length <- TRUE
+        length <- length(data1)
+        if(any(class(data1) %in% "factor")){
+            same.levels <- TRUE
+            levels <- levels(data1)
+            any.id.levels <- TRUE
+            same.levels.pos1 <- 1:length(levels(data1))
+            same.levels.pos2 <- 1:length(levels(data2))
+            same.levels.match1 <- 1:length(levels(data1))
+            same.levels.match2 <- 1:length(levels(data2))
+            common.levels <- levels(data1)
+        }
+        if( ! is.null(names(data1))){
+            same.names <- TRUE
+            name <- names(data1)
+            any.id.name <- TRUE
+            same.names.pos1 <- 1:length(data1)
+            same.names.pos2 <- 1:length(data2)
+            same.names.match1 <- 1:length(data1)
+            same.names.match2 <- 1:length(data2)
+            common.names <- names(data1)
+        }
+        any.id.element <- TRUE
+        same.elements.pos1 <- 1:length(data1)
+        same.elements.pos2 <- 1:length(data2)
+        same.elements.match1 <- 1:length(data1)
+        same.elements.match2 <- 1:length(data2)
+        common.elements <- data1
+        same.order <- TRUE
+        order1 <- order(data1)
+        order2 <- order(data2)
+        identical.object <- TRUE
+        identical.content <- TRUE
+    }else{
+        if(identical(class(data1), class(data2))){
+            same.class <- TRUE
+            class <- class(data1)
+        }
+        if(identical(length(data1), length(data2))){
+            same.length<- TRUE
+            length <- length(data1)
+        }
+        if(any(class(data1) %in% "factor") & any(class(data2) %in% "factor")){
+            if(identical(levels(data1), levels(data2))){
+                same.levels <- TRUE
+                levels <- levels(data1)
+            }else{
+                same.levels <- FALSE
+            }
+            if(any(levels(data1) %in% levels(data2))){
+                any.id.levels <- TRUE
+                same.levels.pos1 <- which(levels(data1) %in% levels(data2))
+                same.levels.match1 <- match(levels(data1), levels(data2))
+            }
+            if(any(levels(data2) %in% levels(data1))){
+                any.id.levels <- TRUE
+                same.levels.pos2 <- which(levels(data2) %in% levels(data1))
+                same.levels.match2 <- match(levels(data2), levels(data1))
+            }
+            if(any.id.levels == TRUE){
+                common.levels <- unique(c(levels(data1)[same.levels.pos1], levels(data2)[same.levels.pos2]))
+            }
+        }
+        if(any(class(data1) %in% "factor")){ # to compare content
+            data1 <- as.character(data1)
+        }
+        if(any(class(data2) %in% "factor")){ # to compare content
+            data2 <- as.character(data2)
+        }
+        if( ! (is.null(names(data1)) & is.null(names(data2)))){
+            if(identical(names(data1), names(data2))){
+                same.names <- TRUE
+                name <- names(data1)
+            }else{
+                same.names <- FALSE
+            }
+            if(any(names(data1) %in% names(data2))){
+                any.id.name <- TRUE
+                same.names.pos1 <- which(names(data1) %in% names(data2))
+                same.names.match1 <- match(names(data1), names(data2))
+            }
+            if(any(names(data2) %in% names(data1))){
+                any.id.name <- TRUE
+                same.names.pos2 <- which(names(data2) %in% names(data1))
+                same.names.match2 <- match(names(data2), names(data1))
+            }
+            if(any.id.name == TRUE){
+                common.names <- unique(c(names(data1)[same.names.pos1], names(data2)[same.names.pos2]))
+            }
+        }
+        names(data1) <- NULL # names solved -> to do not be disturbed by names
+        names(data2) <- NULL # names solved -> to do not be disturbed by names
+        if(any(data1 %in% data2)){
+            any.id.element <- TRUE
+            same.elements.pos1 <- which(data1 %in% data2)
+            same.elements.match1 <- match(data1, data2)
+        }
+        if(any(data2 %in% data1)){
+            any.id.element <- TRUE
+            same.elements.pos2 <- which(data2 %in% data1)
+            same.elements.match2 <- match(data2, data1)
+        }
+        if(any.id.element == TRUE){
+            common.elements <- unique(c(data1[same.elements.pos1], data2[same.elements.pos2]))
+        }
+        if(identical(data1, data2)){
+            identical.content <- TRUE
+            same.order <- TRUE
+        }else if(identical(sort(data1), sort(data2))){
+            same.order <- FALSE
+            order1 <- order(data1)
+            order2 <- order(data2)
+        }
+    }
+    output <- list(same.class = same.class, class = class, same.length = same.length, length = length, same.levels = same.levels, levels = levels, any.id.levels = any.id.levels, same.levels.pos1 = same.levels.pos1, same.levels.pos2 = same.levels.pos2, same.levels.match1 = same.levels.match1, same.levels.match2 = same.levels.match2, common.levels = common.levels, same.names = same.names, name = name, any.id.name = any.id.name, same.names.pos1 = same.names.pos1, same.names.pos2 = same.names.pos2, same.names.match1 = same.names.match1, same.names.match2 = same.names.match2, common.names = common.names, any.id.element = any.id.element, same.elements.pos1 = same.elements.pos1, same.elements.pos2 = same.elements.pos2, same.elements.match1 = same.elements.match1, same.elements.match2 = same.elements.match2, common.elements = common.elements, same.order = same.order, order1 = order1, order2 = order2, identical.object = identical.object, identical.content = identical.content)
+    return(output)
 }
 
 
@@ -1280,1052 +1280,1052 @@ return(output)
 
 
 fun_comp_2d <- function(data1, data2){
-# AIM
-# compare two 2D datasets of the same class or not. Check and report in a list if the 2 datasets have:
-# same class
-# common row names
-# common column names
-# same row number
-# same column number
-# potential identical rows between the 2 datasets
-# potential identical columns between the 2 datasets
-# WARNINGS
-# For data frames: content are compared after conversion of content into characters. This means that the comparison of the content of data frame, either row to row, or column to column, does not take into account the mode in the different columns. This concern the results in $any.id.row, $same.row.pos1, $same.row.pos2, $same.row.match1, $same.row.match2, $any.id.col, $same.row.col1, $same.row.col2, $same.col.match1, $same.col.match2 and $identical.content result
-# "TOO BIG FOR EVALUATION" returned in $same.row.pos1, $same.row.pos2, $same.row.match1 and $same.row.match2 when nrow(data1) * nrow(data2) > 1e6 and $any.id.row remains NULL
-# "TOO BIG FOR EVALUATION" returned in $same.row.col1, $same.row.col2, $same.col.match1 and $same.col.match2 when ncol(data1) * ncol(data2) > 1e6 and $any.id.col remains NULL
-# ARGUMENTS
-# data1: matrix, data frame or table
-# data2: matrix, data frame or table
-# RETURN
-# a list containing:
-# $same.class: logical. Are class identical ?
-# $class: classes of the 2 datasets (NULL otherwise)
-# $same.dim: logical. Are dimension identical ?
-# $dim: dimension of the 2 datasets (NULL otherwise)
-# $same.row.nb: logical. Are number of rows identical ?
-# $row.nb: nb of rows of the 2 datasets if identical (NULL otherwise)
-# $same.col.nb: logical. Are number of columns identical ?
-# $col.nb: nb of columns of the 2 datasets if identical (NULL otherwise)
-# $same.row.name: logical. Are row names identical ? NULL if no row names in the two 2D datasets
-# $row.name: name of rows of the 2 datasets if identical (NULL otherwise)
-# $any.id.row.name: logical. Is there any row names identical ? NULL if no row names in the two 2D datasets
-# $same.row.names.pos1: positions, in data1, of the row names identical in data2
-# $same.row.names.pos2: positions, in data2, of the row names identical in data1
-# $same.row.names.match1: positions, in data2, of the row names that match the row names in data1, as given by match(data1, data2) (NULL otherwise)
-# $same.row.names.match2: positions, in data1, of the row names that match the row names in data2, as given by match(data1, data2) (NULL otherwise)
-# $common.row.names: common row names between data1 and data2 (can be a subset of $name or not). NULL if no common row names
-# $same.col.name: logical. Are column names identical ? NULL if no col names in the two 2D datasets
-# $col.name: name of columns of the 2 datasets if identical (NULL otherwise)
-# $any.id.col.name: logical. Is there any column names identical ? NULL if no col names in the two 2D datasets
-# $same.col.names.pos1: positions, in data1, of the column names identical in data2
-# $same.col.names.pos2: positions, in data2, of the column names identical in data1
-# $same.col.names.match1: positions, in data2, of the column names that match the column names in data1, as given by match(data1, data2) (NULL otherwise)
-# $same.col.names.match2: positions, in data1, of the column names that match the column names in data2, as given by match(data1, data2) (NULL otherwise)
-# $common.col.names: common column names between data1 and data2 (can be a subset of $name or not). NULL if no common column names
-# $any.id.row: logical. is there identical rows (not considering row names)? NULL if nrow(data1) * nrow(data2) > 1e10
-# $same.row.pos1: positions, in data1, of the rows identical in data2 (not considering row names). Return "TOO BIG FOR EVALUATION" if nrow(data1) * nrow(data2) > 1e10
-# $same.row.pos2: positions, in data2, of the rows identical in data1 (not considering row names). Return "TOO BIG FOR EVALUATION" if nrow(data1) * nrow(data2) > 1e10
-# $same.row.match1: positions, in data2, of the rows that match the rows in data1, as given by match(data1, data2) (NULL otherwise)
-# $same.row.match2: positions, in data1, of the rows that match the rows in data2, as given by match(data1, data2) (NULL otherwise)
-# $any.id.col: logical. is there identical columns (not considering column names)? NULL if ncol(data1) * ncol(data2) > 1e10
-# $same.col.pos1: position in data1 of the cols identical in data2 (not considering column names). Return "TOO BIG FOR EVALUATION" if ncol(data1) * ncol(data2) > 1e10
-# $same.col.pos2: position in data2 of the cols identical in data1 (not considering column names). Return "TOO BIG FOR EVALUATION" if ncol(data1) * ncol(data2) > 1e10
-# $same.col.match1: positions, in data2, of the columns that match the columns in data1, as given by match(data1, data2) (NULL otherwise)
-# $same.row.match2: positions, in data1, of the columns that match the columns in data2, as given by match(data1, data2) (NULL otherwise)
-# $identical.object: logical. Are objects identical (including row & column names)?
-# $identical.content: logical. Are content objects identical (identical excluding row & column names)?
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# none
-# EXAMPLES
-# obs1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs2 = as.data.frame(matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])), stringsAsFactors = TRUE) ; obs1 ; obs2 ; fun_comp_2d(obs1, obs2)
-# obs1 = matrix(101:110, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs2 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs1 ; obs2 ; fun_comp_2d(obs1, obs2)
-# large matrices
-# obs1 = matrix(1:1e6, ncol = 5, dimnames = list(NULL, LETTERS[1:5])) ; obs2 = matrix(as.integer((1:1e6)+1e6/5), ncol = 5, dimnames = list(NULL, LETTERS[1:5])) ; head(obs1) ; head(obs2) ; fun_comp_2d(obs1, obs2)
-# WARNING: when comparing content (rows, columns, or total), double and integer data are considered as different -> double(1) != integer(1)
-# obs1 = matrix(1:1e6, ncol = 5, dimnames = list(NULL, LETTERS[1:5])) ; obs2 = matrix((1:1e6)+1e6/5, ncol = 5, dimnames = list(NULL, LETTERS[1:5])) ; head(obs1) ; head(obs2) ; fun_comp_2d(obs1, obs2)
-# Matrices: same row conten tand same row names
-# obs1 = matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs2 = matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("a", "z", "b"), c(LETTERS[1:2], "k", LETTERS[5:4]))) ; obs1 ; obs2 ; fun_comp_2d(obs1, obs2)
-# Matrices: same row content but not same row names -> works: same content is identified
-# obs1 = matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs2 = matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("x", "z", "y"), c(LETTERS[1:2], "k", LETTERS[5:4]))) ; obs1 ; obs2 ; fun_comp_2d(obs1, obs2)
-# obs1 = t(matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5]))) ; obs2 = t(matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("a", "z", "b"), c(LETTERS[1:2], "k", LETTERS[5:4])))) ; obs1 ; obs2 ; fun_comp_2d(obs1, obs2)
-# Data frames: same row content and same row names, not same mode between columns
-# obs1 = as.data.frame(matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5]))) ; obs2 = as.data.frame(matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("a", "z", "b"), c(LETTERS[1:2], "k", LETTERS[5:4])))) ; obs1[, 5] <- as.character(obs1[, 5]) ; obs2[, 5] <- as.character(obs2[, 5]) ; obs1 ; obs2 ; str(obs1) ; str(obs2) ; fun_comp_2d(obs1, obs2)
-# Data frames: same row content but not same row names -> works: same content is identified
-# obs1 = as.data.frame(matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5]))) ; obs2 = as.data.frame(matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("x", "z", "y"), c(LETTERS[1:2], "k", LETTERS[5:4])))) ; obs1[, 5] <- as.character(obs1[, 5]) ; obs2[, 5] <- as.character(obs2[, 5]) ; obs1 ; obs2 ; str(obs1) ; str(obs2) ; fun_comp_2d(obs1, obs2)
-# DEBUGGING
-# data1 = matrix(1:10, ncol = 5) ; data2 = matrix(1:10, ncol = 5) # for function debugging
-# data1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; data2 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
-# data1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; data2 = matrix(1:10, ncol = 5) # for function debugging
-# data1 = matrix(1:15, byrow = TRUE, ncol = 5, dimnames = list(letters[1:3], LETTERS[1:5])) ; data2 = matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
-# data1 = matrix(1:15, ncol = 5, dimnames = list(letters[1:3], LETTERS[1:5])) ; data2 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
-# data1 = matrix(1:15, ncol = 5, dimnames = list(paste0("A", letters[1:3]), LETTERS[1:5])) ; data2 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
-# data1 = matrix(1:15, ncol = 5, dimnames = list(letters[1:3], LETTERS[1:5])) ; data2 = matrix(1:12, ncol = 4, dimnames = list(letters[1:3], LETTERS[1:4])) # for function debugging
-# data1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; data2 = matrix(101:110, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
-# data1 = data.frame(a = 1:3, b= letters[1:3], row.names = LETTERS[1:3], stringsAsFactors = TRUE) ; data2 = data.frame(A = 1:3, B= letters[1:3], stringsAsFactors = TRUE) # for function debugging
-# data1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; data2 = as.data.frame(matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])), stringsAsFactors = TRUE) # for function debugging
-# data1 = matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; data2 = matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("a", "z", "b"), c(LETTERS[1:2], "k", LETTERS[5:4]))) # for function debugging
-# data1 = table(Exp1 = c("A", "A", "A", "B", "B", "B"), Exp2 = c("A1", "B1", "A1", "C1", "C1", "B1")) ; data2 = data.frame(A = 1:3, B= letters[1:3], stringsAsFactors = TRUE) # for function debugging
-# data1 = matrix(1:1e6, ncol = 5, dimnames = list(NULL, LETTERS[1:5])) ; data2 = matrix((1:1e6)+1e6/5, ncol = 5, dimnames = list(NULL, LETTERS[1:5]))
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# argument checking
-if( ! (any(class(data1) %in% c("data.frame", "table")) | all(class(data1) %in% c("matrix", "array")))){ # before R4.0.0, it was  ! any(class(data1) %in% c("matrix", "data.frame", "table"))
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 ARGUMENT MUST BE A MATRIX, DATA FRAME OR TABLE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    # AIM
+    # compare two 2D datasets of the same class or not. Check and report in a list if the 2 datasets have:
+    # same class
+    # common row names
+    # common column names
+    # same row number
+    # same column number
+    # potential identical rows between the 2 datasets
+    # potential identical columns between the 2 datasets
+    # WARNINGS
+    # For data frames: content are compared after conversion of content into characters. This means that the comparison of the content of data frame, either row to row, or column to column, does not take into account the mode in the different columns. This concern the results in $any.id.row, $same.row.pos1, $same.row.pos2, $same.row.match1, $same.row.match2, $any.id.col, $same.row.col1, $same.row.col2, $same.col.match1, $same.col.match2 and $identical.content result
+    # "TOO BIG FOR EVALUATION" returned in $same.row.pos1, $same.row.pos2, $same.row.match1 and $same.row.match2 when nrow(data1) * nrow(data2) > 1e6 and $any.id.row remains NULL
+    # "TOO BIG FOR EVALUATION" returned in $same.row.col1, $same.row.col2, $same.col.match1 and $same.col.match2 when ncol(data1) * ncol(data2) > 1e6 and $any.id.col remains NULL
+    # ARGUMENTS
+    # data1: matrix, data frame or table
+    # data2: matrix, data frame or table
+    # RETURN
+    # a list containing:
+    # $same.class: logical. Are class identical ?
+    # $class: classes of the 2 datasets (NULL otherwise)
+    # $same.dim: logical. Are dimension identical ?
+    # $dim: dimension of the 2 datasets (NULL otherwise)
+    # $same.row.nb: logical. Are number of rows identical ?
+    # $row.nb: nb of rows of the 2 datasets if identical (NULL otherwise)
+    # $same.col.nb: logical. Are number of columns identical ?
+    # $col.nb: nb of columns of the 2 datasets if identical (NULL otherwise)
+    # $same.row.name: logical. Are row names identical ? NULL if no row names in the two 2D datasets
+    # $row.name: name of rows of the 2 datasets if identical (NULL otherwise)
+    # $any.id.row.name: logical. Is there any row names identical ? NULL if no row names in the two 2D datasets
+    # $same.row.names.pos1: positions, in data1, of the row names identical in data2
+    # $same.row.names.pos2: positions, in data2, of the row names identical in data1
+    # $same.row.names.match1: positions, in data2, of the row names that match the row names in data1, as given by match(data1, data2) (NULL otherwise)
+    # $same.row.names.match2: positions, in data1, of the row names that match the row names in data2, as given by match(data1, data2) (NULL otherwise)
+    # $common.row.names: common row names between data1 and data2 (can be a subset of $name or not). NULL if no common row names
+    # $same.col.name: logical. Are column names identical ? NULL if no col names in the two 2D datasets
+    # $col.name: name of columns of the 2 datasets if identical (NULL otherwise)
+    # $any.id.col.name: logical. Is there any column names identical ? NULL if no col names in the two 2D datasets
+    # $same.col.names.pos1: positions, in data1, of the column names identical in data2
+    # $same.col.names.pos2: positions, in data2, of the column names identical in data1
+    # $same.col.names.match1: positions, in data2, of the column names that match the column names in data1, as given by match(data1, data2) (NULL otherwise)
+    # $same.col.names.match2: positions, in data1, of the column names that match the column names in data2, as given by match(data1, data2) (NULL otherwise)
+    # $common.col.names: common column names between data1 and data2 (can be a subset of $name or not). NULL if no common column names
+    # $any.id.row: logical. is there identical rows (not considering row names)? NULL if nrow(data1) * nrow(data2) > 1e10
+    # $same.row.pos1: positions, in data1, of the rows identical in data2 (not considering row names). Return "TOO BIG FOR EVALUATION" if nrow(data1) * nrow(data2) > 1e10
+    # $same.row.pos2: positions, in data2, of the rows identical in data1 (not considering row names). Return "TOO BIG FOR EVALUATION" if nrow(data1) * nrow(data2) > 1e10
+    # $same.row.match1: positions, in data2, of the rows that match the rows in data1, as given by match(data1, data2) (NULL otherwise)
+    # $same.row.match2: positions, in data1, of the rows that match the rows in data2, as given by match(data1, data2) (NULL otherwise)
+    # $any.id.col: logical. is there identical columns (not considering column names)? NULL if ncol(data1) * ncol(data2) > 1e10
+    # $same.col.pos1: position in data1 of the cols identical in data2 (not considering column names). Return "TOO BIG FOR EVALUATION" if ncol(data1) * ncol(data2) > 1e10
+    # $same.col.pos2: position in data2 of the cols identical in data1 (not considering column names). Return "TOO BIG FOR EVALUATION" if ncol(data1) * ncol(data2) > 1e10
+    # $same.col.match1: positions, in data2, of the columns that match the columns in data1, as given by match(data1, data2) (NULL otherwise)
+    # $same.row.match2: positions, in data1, of the columns that match the columns in data2, as given by match(data1, data2) (NULL otherwise)
+    # $identical.object: logical. Are objects identical (including row & column names)?
+    # $identical.content: logical. Are content objects identical (identical excluding row & column names)?
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # none
+    # EXAMPLES
+    # obs1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs2 = as.data.frame(matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])), stringsAsFactors = TRUE) ; obs1 ; obs2 ; fun_comp_2d(obs1, obs2)
+    # obs1 = matrix(101:110, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs2 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs1 ; obs2 ; fun_comp_2d(obs1, obs2)
+    # large matrices
+    # obs1 = matrix(1:1e6, ncol = 5, dimnames = list(NULL, LETTERS[1:5])) ; obs2 = matrix(as.integer((1:1e6)+1e6/5), ncol = 5, dimnames = list(NULL, LETTERS[1:5])) ; head(obs1) ; head(obs2) ; fun_comp_2d(obs1, obs2)
+    # WARNING: when comparing content (rows, columns, or total), double and integer data are considered as different -> double(1) != integer(1)
+    # obs1 = matrix(1:1e6, ncol = 5, dimnames = list(NULL, LETTERS[1:5])) ; obs2 = matrix((1:1e6)+1e6/5, ncol = 5, dimnames = list(NULL, LETTERS[1:5])) ; head(obs1) ; head(obs2) ; fun_comp_2d(obs1, obs2)
+    # Matrices: same row conten tand same row names
+    # obs1 = matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs2 = matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("a", "z", "b"), c(LETTERS[1:2], "k", LETTERS[5:4]))) ; obs1 ; obs2 ; fun_comp_2d(obs1, obs2)
+    # Matrices: same row content but not same row names -> works: same content is identified
+    # obs1 = matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs2 = matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("x", "z", "y"), c(LETTERS[1:2], "k", LETTERS[5:4]))) ; obs1 ; obs2 ; fun_comp_2d(obs1, obs2)
+    # obs1 = t(matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5]))) ; obs2 = t(matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("a", "z", "b"), c(LETTERS[1:2], "k", LETTERS[5:4])))) ; obs1 ; obs2 ; fun_comp_2d(obs1, obs2)
+    # Data frames: same row content and same row names, not same mode between columns
+    # obs1 = as.data.frame(matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5]))) ; obs2 = as.data.frame(matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("a", "z", "b"), c(LETTERS[1:2], "k", LETTERS[5:4])))) ; obs1[, 5] <- as.character(obs1[, 5]) ; obs2[, 5] <- as.character(obs2[, 5]) ; obs1 ; obs2 ; str(obs1) ; str(obs2) ; fun_comp_2d(obs1, obs2)
+    # Data frames: same row content but not same row names -> works: same content is identified
+    # obs1 = as.data.frame(matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5]))) ; obs2 = as.data.frame(matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("x", "z", "y"), c(LETTERS[1:2], "k", LETTERS[5:4])))) ; obs1[, 5] <- as.character(obs1[, 5]) ; obs2[, 5] <- as.character(obs2[, 5]) ; obs1 ; obs2 ; str(obs1) ; str(obs2) ; fun_comp_2d(obs1, obs2)
+    # DEBUGGING
+    # data1 = matrix(1:10, ncol = 5) ; data2 = matrix(1:10, ncol = 5) # for function debugging
+    # data1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; data2 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
+    # data1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; data2 = matrix(1:10, ncol = 5) # for function debugging
+    # data1 = matrix(1:15, byrow = TRUE, ncol = 5, dimnames = list(letters[1:3], LETTERS[1:5])) ; data2 = matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
+    # data1 = matrix(1:15, ncol = 5, dimnames = list(letters[1:3], LETTERS[1:5])) ; data2 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
+    # data1 = matrix(1:15, ncol = 5, dimnames = list(paste0("A", letters[1:3]), LETTERS[1:5])) ; data2 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
+    # data1 = matrix(1:15, ncol = 5, dimnames = list(letters[1:3], LETTERS[1:5])) ; data2 = matrix(1:12, ncol = 4, dimnames = list(letters[1:3], LETTERS[1:4])) # for function debugging
+    # data1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; data2 = matrix(101:110, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) # for function debugging
+    # data1 = data.frame(a = 1:3, b= letters[1:3], row.names = LETTERS[1:3], stringsAsFactors = TRUE) ; data2 = data.frame(A = 1:3, B= letters[1:3], stringsAsFactors = TRUE) # for function debugging
+    # data1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; data2 = as.data.frame(matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])), stringsAsFactors = TRUE) # for function debugging
+    # data1 = matrix(1:10, byrow = TRUE, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; data2 = matrix(c(1:5, 101:105, 6:10), byrow = TRUE, ncol = 5, dimnames = list(c("a", "z", "b"), c(LETTERS[1:2], "k", LETTERS[5:4]))) # for function debugging
+    # data1 = table(Exp1 = c("A", "A", "A", "B", "B", "B"), Exp2 = c("A1", "B1", "A1", "C1", "C1", "B1")) ; data2 = data.frame(A = 1:3, B= letters[1:3], stringsAsFactors = TRUE) # for function debugging
+    # data1 = matrix(1:1e6, ncol = 5, dimnames = list(NULL, LETTERS[1:5])) ; data2 = matrix((1:1e6)+1e6/5, ncol = 5, dimnames = list(NULL, LETTERS[1:5]))
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # argument checking
+    if( ! (any(class(data1) %in% c("data.frame", "table")) | all(class(data1) %in% c("matrix", "array")))){ # before R4.0.0, it was  ! any(class(data1) %in% c("matrix", "data.frame", "table"))
+        tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 ARGUMENT MUST BE A MATRIX, DATA FRAME OR TABLE")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! (any(class(data2) %in% c("data.frame", "table")) | all(class(data2) %in% c("matrix", "array")))){ # before R4.0.0, it was  ! any(class(data2) %in% c("matrix", "data.frame", "table"))
+        tempo.cat <- paste0("ERROR IN ", function.name, ": THE data2 ARGUMENT MUST BE A MATRIX, DATA FRAME OR TABLE")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) # activate this line and use the function to check arguments status
+    # end argument checking
+    # main code
+    same.class <- NULL
+    class <- NULL
+    same.dim <- NULL
+    dim <- NULL
+    same.row.nb <- NULL
+    row.nb <- NULL
+    same.col.nb <- NULL
+    col.nb <- NULL
+    same.row.name <- NULL
+    row.name <- NULL
+    any.id.row.name <- NULL
+    same.row.names.pos1 <- NULL
+    same.row.names.pos2 <- NULL
+    same.row.names.match1 <- NULL
+    same.row.names.match2 <- NULL
+    common.row.names <- NULL
+    same.col.name <- NULL
+    any.id.col.name <- NULL
+    same.col.names.pos1 <- NULL
+    same.col.names.pos2 <- NULL
+    same.col.names.match1 <- NULL
+    same.col.names.match2 <- NULL
+    common.col.names <- NULL
+    col.name <- NULL
+    any.id.row <- NULL
+    same.row.pos1 <- NULL
+    same.row.pos2 <- NULL
+    same.row.match1 <- NULL
+    same.row.match2 <- NULL
+    any.id.col <- NULL
+    same.col.pos1 <- NULL
+    same.col.pos2 <- NULL
+    same.col.match1 <- NULL
+    same.col.match2 <- NULL
+    identical.object <- NULL
+    identical.content <- NULL
+    if(identical(data1, data2) & (any(class(data1) %in% c("data.frame", "table")) | all(class(data1) %in% c("matrix", "array")))){ # before R4.0.0, it was  ! any(class(data1) %in% c("matrix", "data.frame", "table"))
+        same.class <- TRUE
+        class <- class(data1)
+        same.dim <- TRUE
+        dim <- dim(data1)
+        same.row.nb <- TRUE
+        row.nb <- nrow(data1)
+        same.col.nb <- TRUE
+        col.nb <- ncol(data1)
+        same.row.name <- TRUE
+        row.name <- dimnames(data1)[[1]]
+        any.id.row.name <- TRUE
+        same.row.names.pos1 <- 1:row.nb
+        same.row.names.pos2 <- 1:row.nb
+        same.row.names.match1 <- 1:row.nb
+        same.row.names.match2 <- 1:row.nb
+        common.row.names <- dimnames(data1)[[1]]
+        same.col.name <- TRUE
+        col.name <- dimnames(data1)[[2]]
+        any.id.col.name <- TRUE
+        same.col.names.pos1 <- 1:col.nb
+        same.col.names.pos2 <- 1:col.nb
+        same.col.names.match1 <- 1:col.nb
+        same.col.names.match2 <- 1:col.nb
+        common.col.names <- dimnames(data1)[[2]]
+        any.id.row <- TRUE
+        same.row.pos1 <- 1:row.nb
+        same.row.pos2 <- 1:row.nb
+        same.row.match1 <- 1:row.nb
+        same.row.match2 <- 1:row.nb
+        any.id.col <- TRUE
+        same.col.pos1 <- 1:col.nb
+        same.col.pos2 <- 1:col.nb
+        same.col.match1 <- 1:col.nb
+        same.col.match2 <- 1:col.nb
+        identical.object <- TRUE
+        identical.content <- TRUE
+    }else{
+        identical.object <- FALSE
+        if(all(class(data1) == "table") & length(dim(data1)) == 1L){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 ARGUMENT IS A 1D TABLE. USE THE fun_comp_1d FUNCTION")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(all(class(data2) == "table") & length(dim(data2)) == 1L){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": THE data2 ARGUMENT IS A 1D TABLE. USE THE fun_comp_1d FUNCTION")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if( ! identical(class(data1), class(data2))){
+            same.class <- FALSE
+        }else if( ! (any(class(data1) %in% c("data.frame", "table")) | all(class(data1) %in% c("matrix", "array")))){ # before R4.0.0, it was  ! any(class(data1) %in% c("matrix", "data.frame", "table"))
+            tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 AND data2 ARGUMENTS MUST BE EITHER MATRIX, DATA FRAME OR TABLE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            same.class <- TRUE
+            class <- class(data1)
+        }
+        if( ! identical(dim(data1), dim(data2))){
+            same.dim <- FALSE
+        }else{
+            same.dim <- TRUE
+            dim <- dim(data1)
+        }
+        if( ! identical(nrow(data1), nrow(data2))){
+            same.row.nb <- FALSE
+        }else{
+            same.row.nb <- TRUE
+            row.nb <- nrow(data1)
+        }
+        if( ! identical(ncol(data1), ncol(data2))){
+            same.col.nb <- FALSE
+        }else{
+            same.col.nb <- TRUE
+            col.nb <- ncol(data1)
+        }
+        # row and col names
+        if(is.null(dimnames(data1)) & is.null(dimnames(data2))){
+            same.row.name <- NULL # but already NULL
+            same.col.name <- NULL # but already NULL
+            # other row names param remain NULL
+        }else if((is.null(dimnames(data1)) & ! is.null(dimnames(data2))) | ( ! is.null(dimnames(data1)) & is.null(dimnames(data2)))){
+            same.row.name <- FALSE
+            same.col.name <- FALSE
+            any.id.row.name <- FALSE
+            any.id.col.name <- FALSE
+            # other row names param remain NULL
+        }else{
+            # row names
+            if(is.null(dimnames(data1)[[1]]) & is.null(dimnames(data2)[[1]])){
+                same.row.name <- NULL # but already NULL
+                # other row names param remain NULL
+            }else if((is.null(dimnames(data1)[[1]]) & ! is.null(dimnames(data2)[[1]])) | ( ! is.null(dimnames(data1)[[1]]) & is.null(dimnames(data2)[[1]]))){
+                same.row.name <- FALSE
+                any.id.row.name <- FALSE
+                # other row names param remain NULL
+            }else if(identical(dimnames(data1)[[1]], dimnames(data2)[[1]])){
+                same.row.name <- TRUE
+                row.name <- dimnames(data1)[[1]]
+                any.id.row.name <- TRUE
+                same.row.names.pos1 <- 1:nrow(data1)
+                same.row.names.pos2 <- 1:nrow(data1)
+                same.row.names.match1 <- 1:nrow(data1)
+                same.row.names.match2 <- 1:nrow(data1)
+                common.row.names <- dimnames(data1)[[1]]
+            }else{
+                same.row.name <- FALSE
+                any.id.row.name <- FALSE
+                if(any(dimnames(data1)[[1]] %in% dimnames(data2)[[1]])){
+                    any.id.row.name <- TRUE
+                    same.row.names.pos1 <- which(dimnames(data1)[[1]] %in% dimnames(data2)[[1]])
+                    same.row.names.match1 <- match(dimnames(data1)[[1]], dimnames(data2)[[1]])
+                }
+                if(any(dimnames(data2)[[1]] %in% dimnames(data1)[[1]])){
+                    any.id.row.name <- TRUE
+                    same.row.names.pos2 <- which(dimnames(data2)[[1]] %in% dimnames(data1)[[1]])
+                    same.row.names.match2 <- match(dimnames(data2)[[1]], dimnames(data1)[[1]])
+                }
+                if(any.id.row.name == TRUE){
+                    common.row.names <- unique(c(dimnames(data1)[[1]][same.row.names.pos1], dimnames(data2)[[1]][same.row.names.pos2]))
+                }
+            }
+            # col names
+            if(is.null(dimnames(data1)[[2]]) & is.null(dimnames(data2)[[2]])){
+                same.col.name <- NULL # but already NULL
+                # other col names param remain NULL
+            }else if((is.null(dimnames(data1)[[2]]) & ! is.null(dimnames(data2)[[2]])) | ( ! is.null(dimnames(data1)[[2]]) & is.null(dimnames(data2)[[2]]))){
+                same.col.name <- FALSE
+                any.id.col.name <- FALSE
+                # other col names param remain NULL
+            }else if(identical(dimnames(data1)[[2]], dimnames(data2)[[2]])){
+                same.col.name <- TRUE
+                col.name <- dimnames(data1)[[2]]
+                any.id.col.name <- TRUE
+                same.col.names.pos1 <- 1:ncol(data1)
+                same.col.names.pos2 <- 1:ncol(data1)
+                same.col.names.match1 <- 1:ncol(data1)
+                same.col.names.match2 <- 1:ncol(data1)
+                common.col.names <- dimnames(data1)[[2]]
+            }else{
+                same.col.name <- FALSE
+                any.id.col.name <- FALSE
+                if(any(dimnames(data1)[[2]] %in% dimnames(data2)[[2]])){
+                    any.id.col.name <- TRUE
+                    same.col.names.pos1 <- which(dimnames(data1)[[2]] %in% dimnames(data2)[[2]])
+                    same.col.names.match1 <- match(dimnames(data1)[[2]], dimnames(data2)[[2]])
+                }
+                if(any(dimnames(data2)[[2]] %in% dimnames(data1)[[2]])){
+                    any.id.col.name <- TRUE
+                    same.col.names.pos2 <- which(dimnames(data2)[[2]] %in% dimnames(data1)[[2]])
+                    same.col.names.match2 <- match(dimnames(data2)[[2]], dimnames(data1)[[2]])
+                }
+                if(any.id.col.name == TRUE){
+                    common.col.names <- unique(c(dimnames(data1)[[2]][same.col.names.pos1], dimnames(data2)[[2]][same.col.names.pos2]))
+                }
+            }
+        }
+        # identical row and col content
+        if(all(class(data1) == "table")){
+            data1 <- as.data.frame(matrix(data1, ncol = ncol(data1)), stringsAsFactors = FALSE) # conversion of table into data frame to facilitate inter class comparison
+        }else if(all(class(data1) %in% c("matrix", "array"))){
+            data1 <- as.data.frame(data1, stringsAsFactors = FALSE) # conversion of matrix into data frame to facilitate inter class comparison
+        }else if(all(class(data1) == "data.frame")){
+            # data1 <- data.frame(lapply(data1, as.character), stringsAsFactors = FALSE) # conversion of columns into characters
+        }
+        if(all(class(data2) == "table")){
+            data2 <- as.data.frame(matrix(data2, ncol = ncol(data2)), stringsAsFactors = FALSE) # conversion of table into data frame to facilitate inter class comparison
+        }else if(all(class(data2) %in% c("matrix", "array"))){
+            data2 <- as.data.frame(data2, stringsAsFactors = FALSE) # conversion of matrix into data frame to facilitate inter class comparison
+        }else if(all(class(data2) == "data.frame")){
+            # data2 <- data.frame(lapply(data2, as.character), stringsAsFactors = FALSE) # conversion of columns into characters
+        }
+        row.names(data1) <- paste0("A", 1:nrow(data1))
+        row.names(data2) <- paste0("A", 1:nrow(data2))
+        if(same.col.nb == TRUE){ # because if not the same col nb, the row cannot be identical
+            if(all(sapply(data1, FUN = typeof) == "integer") & all(sapply(data2, FUN = typeof) == "integer") & as.double(nrow(data1)) * nrow(data2) <= 1e10){ # fast method for integers (thus not data frames). as.double(nrow(data1)) to prevent integer overflow because R is 32 bits for integers
+                tempo1 <- c(as.data.frame(t(data1), stringsAsFactors = FALSE)) # conversion into list. This work fast with only integers (because 32 bits)
+                tempo2 <- c(as.data.frame(t(data2), stringsAsFactors = FALSE)) # conversion into list. This work fast with only integers (because 32 bits)
+                same.row.pos1 <- which(tempo1 %in% tempo2)
+                same.row.pos2 <- which(tempo2 %in% tempo1)
+                same.row.match1 <- match(tempo1, tempo2)
+                same.row.match2 <- match(tempo2, tempo1)
+            }else if(as.double(nrow(data1)) * nrow(data2) <= 1e6){ # as.double(nrow(data1)) to prevent integer overflow because R is 32 bits for integers
+                # inactivated because I would like to keep the mode during comparisons
+                # if(col.nb <= 10){ # if ncol is not to big, the t() should not be that long
+                # tempo1 <- c(as.data.frame(t(data1), stringsAsFactors = FALSE)) # conversion into list. This work fast with only integers (because 32 bits)
+                # tempo2 <- c(as.data.frame(t(data2), stringsAsFactors = FALSE)) # conversion into list. 
+                # same.row.pos1 <- which(tempo1 %in% tempo2)
+                # same.row.pos2 <- which(tempo2 %in% tempo1)
+                # same.row.match1 <- match(tempo1, tempo2)
+                # same.row.match2 <- match(tempo2, tempo1)
+                # }else{
+                # very long computation
+                same.row.pos1 <- logical(length = nrow(data1)) # FALSE by default
+                same.row.pos1[] <- FALSE # security
+                same.row.pos2 <- logical(length = nrow(data2)) # FALSE by default
+                same.row.pos2[] <- FALSE # security
+                same.row.match1 <- rep(NA, nrow(data1))
+                same.row.match2 <- rep(NA, nrow(data2))
+                for(i3 in 1:nrow(data1)){
+                    for(i4 in 1:nrow(data2)){
+                        tempo1 <- data1[i3, ]
+                        tempo2 <- data2[i4, ]
+                        rownames(tempo1) <- NULL # to have same row and column names
+                        colnames(tempo1) <- NULL # to have same row and column names
+                        rownames(tempo2) <- NULL # to have same row and column names
+                        colnames(tempo2) <- NULL # to have same row and column names
+                        if(identical(tempo1, tempo2)){
+                            same.row.pos1[i3] <- TRUE
+                            same.row.pos2[i4] <- TRUE
+                            same.row.match1[i3] <- i4
+                            same.row.match2[i4] <- i3
+                        }
+                    }
+                }
+                same.row.pos1 <- which(same.row.pos1)
+                same.row.pos2 <- which(same.row.pos2)
+                # }
+            }else{
+                same.row.pos1 <- "TOO BIG FOR EVALUATION"
+                same.row.pos2 <- "TOO BIG FOR EVALUATION"
+                same.row.match1 <- "TOO BIG FOR EVALUATION"
+                same.row.match2 <- "TOO BIG FOR EVALUATION"
+            }
+            
+            names(same.row.pos1) <- NULL
+            names(same.row.pos2) <- NULL
+            if(all(is.na(same.row.pos1))){
+                same.row.pos1 <- NULL
+            }else{
+                same.row.pos1 <- same.row.pos1[ ! is.na(same.row.pos1)]
+                any.id.row <- TRUE
+            }
+            if(all(is.na(same.row.pos2))){
+                same.row.pos2 <- NULL
+            }else{
+                same.row.pos2 <- same.row.pos2[ ! is.na(same.row.pos2)]
+                any.id.row <- TRUE
+            }
+            if(is.null(same.row.pos1) & is.null(same.row.pos2)){
+                any.id.row <- FALSE
+            }else if(length(same.row.pos1) == 0L & length(same.row.pos2) == 0L){
+                any.id.row <- FALSE
+            }else if(all(same.row.pos1 == "TOO BIG FOR EVALUATION") & all(same.row.pos2 == "TOO BIG FOR EVALUATION")){
+                any.id.row <- NULL
+            }
+        }else{
+            any.id.row <- FALSE
+            # same.row.pos1 and 2 remain NULL
+        }
+        if(same.row.nb == TRUE){ # because if not the same row nb, the col cannot be identical
+            if(as.double(ncol(data1)) * ncol(data2) <= 1e10){ # comparison of data frame columns is much easier than rows because no need to use t() before converting to list for fast comparison. as.double(ncol(data1)) to prevent integer overflow because R is 32 bits for integers
+                # if(all(sapply(data1, FUN = typeof) == "integer") & all(sapply(data2, FUN = typeof) == "integer") & as.double(ncol(data1)) * ncol(data2) <= 1e10){ # fast method for integers (thus not data frames). as.double(ncol(data1)) to prevent integer overflow because R is 32 bits for integers
+                tempo1 <- c(data1)
+                tempo2 <- c(data2)
+                same.col.pos1 <- which(tempo1 %in% tempo2)
+                same.col.pos2 <- which(tempo2 %in% tempo1)
+                same.col.match1 <- match(tempo1, tempo2)
+                same.col.match2 <- match(tempo2, tempo1)
+                # }else if(as.double(ncol(data1)) * ncol(data2) <= 1e6){ # as.double(ncol(data1)) to prevent integer overflow because R is 32 bits for integers
+                # same.col.pos1 <- logical(length = ncol(data1)) # FALSE by default
+                # same.col.pos1[] <- FALSE # security
+                # same.col.pos2 <- logical(length = ncol(data2)) # FALSE by default
+                # same.col.pos2[] <- FALSE # security
+                # same.col.match1 <- rep(NA, ncol(data1))
+                # same.col.match2 <- rep(NA, ncol(data2))
+                # for(i3 in 1:ncol(data1)){
+                # for(i4 in 1:ncol(data2)){
+                # if(identical(data1[ , i3], data2[ , i4])){
+                # same.col.pos1[i3] <- TRUE
+                # same.col.pos2[i4] <- TRUE
+                # same.col.match1[i3] <- i4
+                # same.col.match2[i4] <- i3
+                # }
+                # }
+                # }
+                # same.col.pos1 <- which(same.col.pos1)
+                # same.col.pos2 <- which(same.col.pos2)
+            }else{
+                same.col.pos1 <- "TOO BIG FOR EVALUATION"
+                same.col.pos2 <- "TOO BIG FOR EVALUATION"
+            }
+            names(same.col.pos1) <- NULL
+            names(same.col.pos2) <- NULL
+            if(all(is.na(same.col.pos1))){
+                same.col.pos1 <- NULL
+            }else{
+                same.col.pos1 <- same.col.pos1[ ! is.na(same.col.pos1)]
+                any.id.col <- TRUE
+            }
+            if(all(is.na(same.col.pos2))){
+                same.col.pos2 <- NULL
+            }else{
+                same.col.pos2 <- same.col.pos2[ ! is.na(same.col.pos2)]
+                any.id.col <- TRUE
+            }
+            if(is.null(same.col.pos1) & is.null(same.col.pos2)){
+                any.id.col <- FALSE
+            }else if(length(same.col.pos1) == 0L & length(same.col.pos2) == 0L){
+                any.id.col <- FALSE
+            }else if(all(same.col.pos1 == "TOO BIG FOR EVALUATION") & all(same.col.pos2 == "TOO BIG FOR EVALUATION")){
+                any.id.col <- NULL
+            }
+        }else{
+            any.id.col <- FALSE
+            # same.col.pos1 and 2 remain NULL
+        }
+        if(same.dim == TRUE){
+            names(data1) <- NULL
+            row.names(data1) <- NULL
+            names(data2) <- NULL
+            row.names(data2) <- NULL
+            if(identical(data1, data2)){
+                identical.content <- TRUE
+            }else{
+                identical.content <- FALSE
+            }
+        }else{
+            identical.content <- FALSE
+        }
+    }
+    output <- list(same.class = same.class, class = class, same.dim = same.dim, dim = dim, same.row.nb = same.row.nb, row.nb = row.nb, same.col.nb = same.col.nb , col.nb = col.nb, same.row.name = same.row.name, row.name = row.name, any.id.row.name = any.id.row.name, same.row.names.pos1 = same.row.names.pos1, same.row.names.pos2 = same.row.names.pos2, same.row.names.match1 = same.row.names.match1, same.row.names.match2 = same.row.names.match2, common.row.names = common.row.names, same.col.name = same.col.name, col.name = col.name,any.id.col.name = any.id.col.name, same.col.names.pos1 = same.col.names.pos1, same.col.names.pos2 = same.col.names.pos2, same.col.names.match1 = same.col.names.match1, same.col.names.match2 = same.col.names.match2, common.col.names = common.col.names, any.id.row = any.id.row, same.row.pos1 = same.row.pos1, same.row.pos2 = same.row.pos2, same.row.match1 = same.row.match1, same.row.match2 = same.row.match2, any.id.col = any.id.col, same.col.pos1 = same.col.pos1, same.col.pos2 = same.col.pos2, same.col.match1 = same.col.match1, same.col.match2 = same.col.match2, identical.object = identical.object, identical.content = identical.content)
+    return(output)
 }
-if( ! (any(class(data2) %in% c("data.frame", "table")) | all(class(data2) %in% c("matrix", "array")))){ # before R4.0.0, it was  ! any(class(data2) %in% c("matrix", "data.frame", "table"))
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data2 ARGUMENT MUST BE A MATRIX, DATA FRAME OR TABLE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+
+
+######## fun_comp_list() #### comparison of two lists
+
+
+fun_comp_list <- function(data1, data2){
+    # AIM
+    # compare two lists. Check and report in a list if the 2 datasets have:
+    # same length
+    # common names
+    # common compartments
+    # ARGUMENTS
+    # data1: list
+    # data2: list
+    # RETURN
+    # a list containing:
+    # $same.length: logical. Are number of elements identical?
+    # $length: number of elements in the 2 datasets (NULL otherwise)
+    # $same.names: logical. Are element names identical ?
+    # $name: name of elements of the 2 datasets if identical (NULL otherwise)
+    # $any.id.name: logical. Is there any element names identical ?
+    # $same.names.pos1: positions, in data1, of the element names identical in data2
+    # $same.names.pos2: positions, in data2, of the compartment names identical in data1
+    # $any.id.compartment: logical. is there any identical compartments ?
+    # $same.compartment.pos1: positions, in data1, of the compartments identical in data2
+    # $same.compartment.pos2: positions, in data2, of the compartments identical in data1
+    # $identical.object: logical. Are objects identical (kind of object, compartment names and content)?
+    # $identical.content: logical. Are content objects identical (identical compartments excluding compartment names)?
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # none
+    # EXAMPLES
+    # obs1 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; obs2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; fun_comp_list(obs1, obs2)
+    # obs1 = list(1:5, LETTERS[1:2]) ; obs2 = list(a = 1:5, b = LETTERS[1:2]) ; fun_comp_list(obs1, obs2)
+    # obs1 = list(b = 1:5, c = LETTERS[1:2]) ; obs2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; fun_comp_list(obs1, obs2)
+    # obs1 = list(b = 1:5, c = LETTERS[1:2]) ; obs2 = list(LETTERS[5:9], matrix(1:6), 1:5) ; fun_comp_list(obs1, obs2)
+    # DEBUGGING
+    # data1 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; data2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) # for function debugging
+    # data1 = list(a = 1:5, b = LETTERS[1:2]) ; data2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # argument checking
+    if( ! any(class(data1) %in% "list")){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 ARGUMENT MUST BE A LIST")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! any(class(data2) %in% "list")){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": THE data2 ARGUMENT MUST BE A LIST")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) # activate this line and use the function to check arguments status
+    # end argument checking
+    # main code
+    same.length <- NULL
+    length <- NULL
+    same.names <- NULL
+    name <- NULL
+    any.id.name <- NULL
+    same.names.pos1 <- NULL
+    same.names.pos2 <- NULL
+    any.id.compartment <- NULL
+    same.compartment.pos1 <- NULL
+    same.compartment.pos2 <- NULL
+    identical.object <- NULL
+    identical.content <- NULL
+    if(identical(data1, data2)){
+        same.length <- TRUE
+        length <- length(data1)
+        if( ! is.null(names(data1))){
+            same.names <- TRUE
+            name <- names(data1)
+            any.id.name <- TRUE
+            same.names.pos1 <- 1:length(data1)
+            same.names.pos2 <- 1:length(data2)
+        }
+        any.id.compartment <- TRUE
+        same.compartment.pos1 <- 1:length(data1)
+        same.compartment.pos2 <- 1:length(data2)
+        identical.object <- TRUE
+        identical.content <- TRUE
+    }else{
+        identical.object <- FALSE
+        if( ! identical(length(data1), length(data2))){
+            same.length<- FALSE
+        }else{
+            same.length<- TRUE
+            length <- length(data1)
+        }
+        if( ! (is.null(names(data1)) & is.null(names(data2)))){
+            if( ! identical(names(data1), names(data2))){
+                same.names <- FALSE
+            }else{
+                same.names <- TRUE
+                name <- names(data1)
+            }
+            any.id.name <- FALSE
+            if(any(names(data1) %in% names(data2))){
+                any.id.name <- TRUE
+                same.names.pos1 <- which(names(data1) %in% names(data2))
+            }
+            if(any(names(data2) %in% names(data1))){
+                any.id.name <- TRUE
+                same.names.pos2 <- which(names(data2) %in% names(data1))
+            }
+        }
+        names(data1) <- NULL
+        names(data2) <- NULL
+        any.id.compartment <- FALSE
+        if(any(data1 %in% data2)){
+            any.id.compartment <- TRUE
+            same.compartment.pos1 <- which(data1 %in% data2)
+        }
+        if(any(data2 %in% data1)){
+            any.id.compartment <- TRUE
+            same.compartment.pos2 <- which(data2 %in% data1)
+        }
+        if(same.length == TRUE & ! all(is.null(same.compartment.pos1), is.null(same.compartment.pos2))){
+            if(identical(same.compartment.pos1, same.compartment.pos2)){
+                identical.content <- TRUE
+            }else{
+                identical.content <- FALSE
+            }
+        }else{
+            identical.content <- FALSE
+        }
+    }
+    output <- list(same.length = same.length, length = length, same.names = same.names, name = name, any.id.name = any.id.name, same.names.pos1 = same.names.pos1, same.names.pos2 = same.names.pos2, any.id.compartment = any.id.compartment, same.compartment.pos1 = same.compartment.pos1, same.compartment.pos2 = same.compartment.pos2, identical.object = identical.object, identical.content = identical.content)
+    return(output)
 }
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) # activate this line and use the function to check arguments status
-# end argument checking
-# main code
-same.class <- NULL
-class <- NULL
-same.dim <- NULL
-dim <- NULL
-same.row.nb <- NULL
-row.nb <- NULL
-same.col.nb <- NULL
-col.nb <- NULL
-same.row.name <- NULL
-row.name <- NULL
-any.id.row.name <- NULL
-same.row.names.pos1 <- NULL
-same.row.names.pos2 <- NULL
-same.row.names.match1 <- NULL
-same.row.names.match2 <- NULL
-common.row.names <- NULL
-same.col.name <- NULL
-any.id.col.name <- NULL
-same.col.names.pos1 <- NULL
-same.col.names.pos2 <- NULL
-same.col.names.match1 <- NULL
-same.col.names.match2 <- NULL
-common.col.names <- NULL
-col.name <- NULL
-any.id.row <- NULL
-same.row.pos1 <- NULL
-same.row.pos2 <- NULL
-same.row.match1 <- NULL
-same.row.match2 <- NULL
-any.id.col <- NULL
-same.col.pos1 <- NULL
-same.col.pos2 <- NULL
-same.col.match1 <- NULL
-same.col.match2 <- NULL
-identical.object <- NULL
-identical.content <- NULL
-if(identical(data1, data2) & (any(class(data1) %in% c("data.frame", "table")) | all(class(data1) %in% c("matrix", "array")))){ # before R4.0.0, it was  ! any(class(data1) %in% c("matrix", "data.frame", "table"))
-same.class <- TRUE
-class <- class(data1)
-same.dim <- TRUE
-dim <- dim(data1)
-same.row.nb <- TRUE
-row.nb <- nrow(data1)
-same.col.nb <- TRUE
-col.nb <- ncol(data1)
-same.row.name <- TRUE
-row.name <- dimnames(data1)[[1]]
-any.id.row.name <- TRUE
-same.row.names.pos1 <- 1:row.nb
-same.row.names.pos2 <- 1:row.nb
-same.row.names.match1 <- 1:row.nb
-same.row.names.match2 <- 1:row.nb
-common.row.names <- dimnames(data1)[[1]]
-same.col.name <- TRUE
-col.name <- dimnames(data1)[[2]]
-any.id.col.name <- TRUE
-same.col.names.pos1 <- 1:col.nb
-same.col.names.pos2 <- 1:col.nb
-same.col.names.match1 <- 1:col.nb
-same.col.names.match2 <- 1:col.nb
-common.col.names <- dimnames(data1)[[2]]
-any.id.row <- TRUE
-same.row.pos1 <- 1:row.nb
-same.row.pos2 <- 1:row.nb
-same.row.match1 <- 1:row.nb
-same.row.match2 <- 1:row.nb
-any.id.col <- TRUE
-same.col.pos1 <- 1:col.nb
-same.col.pos2 <- 1:col.nb
-same.col.match1 <- 1:col.nb
-same.col.match2 <- 1:col.nb
-identical.object <- TRUE
-identical.content <- TRUE
-}else{
-identical.object <- FALSE
-if(all(class(data1) == "table") & length(dim(data1)) == 1L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 ARGUMENT IS A 1D TABLE. USE THE fun_comp_1d FUNCTION")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+
+
+######## fun_test() #### test combinations of argument values of a function and return errors (and graphs)
+
+
+# add traceback https://stackoverflow.com/questions/47414119/how-to-read-a-traceback-in-r
+
+fun_test <- function(
+    fun, 
+    arg, 
+    val, 
+    expect.error = NULL, 
+    parall = FALSE, 
+    thread.nb = NULL, 
+    print.count = 10, 
+    plot.fun = FALSE, 
+    export = FALSE, 
+    res.path = NULL, 
+    lib.path = NULL, 
+    cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
+){
+    # AIM
+    # test combinations of argument values of a function
+    # WARNINGS
+    # Limited to 43 arguments with at least 2 values each. The total number of arguments tested can be more if the additional arguments have a single value. The limit is due to nested "for" loops (https://stat.ethz.ch/pipermail/r-help/2008-March/157341.html), but it should not be a problem since the number of tests would be 2^43 > 8e12
+    # ARGUMENTS
+    # fun: character string indicating the name of the function tested (without brackets)
+    # arg: vector of character strings of arguments of fun. At least arguments that do not have default values must be present in this vector
+    # val: list with number of compartments equal to length of arg, each compartment containing values of the corresponding argument in arg. Each different value must be in a list or in a vector. For instance, argument 3 in arg is a logical argument (values accepted TRUE, FALSE, NA). Thus, compartment 3 of val can be either list(TRUE, FALSE, NA), or c(TRUE, FALSE, NA). NULL value alone must be written list(NULL)
+    # expect.error: list of exactly the same structure as val argument, but containing FALSE or TRUE, depending on whether error is expected (TRUE) or not (FALSE) for each corresponding value of val. A message is returned depending on discrepancies between the expected and observed errors. BEWARE: not always possible to write the expected errors for all the combination of argument values. Ignored if NULL
+    # parall: logical. Force parallelization ?
+    # thread.nb: numeric value indicating the number of threads to use if ever parallelization is required. If NULL, all the available threads will be used. Ignored if parall is FALSE
+    # print.count: interger value. Print a working progress message every print.count during loops. BEWARE: can increase substentially the time to complete the process using a small value, like 10 for instance. Use Inf is no loop message desired
+    # plot.fun: logical. Plot the plotting function tested for each test?
+    # export: logical. Export the results into a .RData file and into a .txt file? If FALSE, return a list into the console (see below). BEWARE: will be automatically set to TRUE if parall is TRUE. This means that when using parallelization, the results are systematically exported, not returned into the console
+    # res.path: character string indicating the absolute pathway of folder where the txt results and pdfs, containing all the plots, will be saved. Several txt and pdf, one per thread, if parallelization. Ignored if export is FALSE. Must be specified if parall is TRUE or if export is TRUE
+    # lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
+    # cute.path: character string indicating the absolute path of the cute.R file. Will be remove when cute will be a package. Ignored if parall is FALSE
+    # REQUIRED PACKAGES
+    # lubridate
+    # parallel if parall arguemtn is TRUE (included in the R installation packages but not automatically loaded)
+    # pdftools if parall arguemtn is TRUE (included in the R installation packages but not automatically loaded)
+    # If the tested function is in a package, this package must be imported first (no parallelization) or must be in the classical R package folder indicated by the lib.path argument (parallelization)
+    # RETURN
+    # if export is FALSE a list containing:
+    # $fun: the tested function
+    # $instruction: the initial instruction
+    # $sys.info: system and packages info
+    # $data: a data frame of all the combination tested, containing the following columns:
+    # the different values tested, named by arguments
+    # $kind: a vector of character strings indicating the kind of test result: either "ERROR", or "WARNING", or "OK"
+    # $problem: a logical vector indicating if error or not
+    # $expected.error: optional logical vector indicating the expected error specified in the expect.error argument
+    # $message: either NULL if $kind is always "OK", or the messages
+    # if export is TRUE 1) the same list object into a .RData file, 2) also the $data data frame into a .txt file, and 3) if expect.error is non NULL and if any discrepancy, the $data data frame into a .txt file but containing only the rows with discrepancies between expected and observed errors
+    # one or several pdf if a plotting function is tested and if the plot.fun argument is TRUE
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # fun_get_message()
+    # fun_pack()
+    # EXAMPLES
+    # fun_test(fun = "unique", arg = c("x", "incomparables"), val = list(x = list(1:10, c(1,1,2,8), NA), incomparable = c(TRUE, FALSE, NA)))
+    # fun_test(fun = "fun_round", arg = c("data", "dec.nb", "after.lead.zero"), val = list(L1 = list(c(1, 1.0002256, 1.23568), "a", NA), L2 = list(2, c(1,3), NA), L3 = c(TRUE, FALSE, NA)))
+    # fun_test(fun = "plot", arg = c("x", "y"), val = list(x = list(1:10, 12:13, NA, (1:10)^2), y = list(1:10, NA, NA)),  expect.error = list(x = list(FALSE, TRUE, TRUE, FALSE), y = list(FALSE, TRUE, TRUE)), parall = FALSE, thread.nb = NULL, plot.fun = TRUE, res.path = "C:\\Users\\Gael\\Desktop\\", lib.path = NULL)
+    # fun_test(fun = "plot", arg = c("x", "y"), val = list(x = list(1:10, 12:13, NA, (1:10)^2), y = list(1:10, NA, NA)), parall = FALSE, thread.nb = 4, plot.fun = TRUE, res.path = "C:\\Users\\Gael\\Desktop\\", lib.path = "C:\\Program Files\\R\\R-4.0.2\\library\\")
+    # set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; fun_test(fun = "fun_gg_boxplot", arg = c("data1", "y", "categ"), val = list(L1 = list(L1 = obs1), L2 = list(L1 = "Time"), L3 = list(L1 = "Group1")))
+    # set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; fun_test(fun = "fun_gg_boxplot", arg = c("data1", "y", "categ"), val = list(L1 = list(obs1), L2 = "Time", L3 = "Group1"), parall = FALSE, thread.nb = NULL, plot.fun = TRUE, res.path = "C:\\Users\\Gael\\Desktop\\", lib.path = "C:\\Program Files\\R\\R-4.0.2\\library\\")
+    # library(ggplot2) ; fun_test(fun = "geom_histogram", arg = c("data", "mapping"), val = list(x = list(data.frame(X = "a", stringsAsFactors = TRUE)), y = list(ggplot2::aes(x = X))), parall = FALSE, thread.nb = NULL, plot.fun = TRUE, res.path = "C:\\Users\\Gael\\Desktop\\", lib.path = "C:\\Program Files\\R\\R-4.0.2\\library\\") # BEWARE: ggplot2::geom_histogram does not work
+    # DEBUGGING
+    # fun = "unique" ; arg = "x" ; val = list(x = list(1:10, c(1,1,2,8), NA)) ; expect.error = list(x = list(FALSE, FALSE, TRUE)) ; parall = FALSE ; thread.nb = NULL ; plot.fun = FALSE ; export = FALSE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL ; print.count = 1 ; cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R" # for function debugging
+    # fun = "unique" ; arg = c("x", "incomparables") ; val = list(x = list(1:10, c(1,1,2,8), NA), incomparable = c(TRUE, FALSE, NA)) ; expect.error = NULL ; parall = FALSE ; thread.nb = 2 ; plot.fun = FALSE ; export = TRUE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL ; print.count = 10 ; cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R" # for function debugging
+    # fun = "plot" ; arg = c("x", "y") ; val = list(x = list(1:10, 12:13, NA), y = list(1:10, NA, NA)) ; expect.error = list(x = list(FALSE, FALSE, TRUE, FALSE), y = list(FALSE, TRUE, TRUE)) ; print.count = 10 ; parall = FALSE ; thread.nb = NULL ; plot.fun = TRUE ; export = TRUE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL # for function debugging
+    # set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; fun = "fun_gg_boxplot" ; arg = c("data1", "y", "categ") ; val = list(L1 = list(L1 = obs1), L2 = list(L1 = "Time"), L3 = list(L1 = "Group1")) ; expect.error = NULL ; print.count = 10 ; parall = FALSE ; thread.nb = NULL ; plot.fun = TRUE ; export = TRUE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL # for function debugging
+    # fun = "unique" ; arg = "x" ; val = list(list(1:3, mean)) ; expect.error = list(TRUE, TRUE) ; parall = FALSE ; thread.nb = NULL ; plot.fun = FALSE ; export = FALSE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL ; print.count = 1 ; cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R" # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
+    arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
+    # end function name
+    # required function checking
+    req.function <- c(
+        "fun_check", 
+        "fun_get_message", 
+        "fun_pack"
+    )
+    tempo <- NULL
+    for(i1 in req.function){
+        if(length(find(i1, mode = "function")) == 0L){
+            tempo <- c(tempo, i1)
+        }
+    }
+    if( ! is.null(tempo)){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # reserved words
+    # end reserved words
+    # arg with no default values
+    mandat.args <- c(
+        "fun", 
+        "arg", 
+        "val"
+    )
+    tempo <- eval(parse(text = paste0("missing(", paste0(mandat.args, collapse = ") | missing("), "))")))
+    print(tempo)
+    if(any(tempo)){ # normally no NA for missing() output
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end arg with no default values
+    # argument primary checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = fun, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = arg, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = val, class = "list", fun.name = function.name) ; eval(ee)
+    if( ! is.null(expect.error)){
+        tempo <- fun_check(data = expect.error, class = "list", fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = parall, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if(parall == TRUE){
+        if( ! is.null(thread.nb)){
+            tempo <- fun_check(data = thread.nb, typeof = "integer", double.as.integer.allowed = TRUE, neg.values = FALSE, length = 1, fun.name = function.name) ; eval(ee)
+            if(tempo$problem == FALSE & thread.nb < 1){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": thread.nb PARAMETER MUST EQUAL OR GREATER THAN 1: ", thread.nb)
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }
+    tempo <- fun_check(data = print.count, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = plot.fun, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = export, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(res.path)){
+        tempo <- fun_check(data = res.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(lib.path)){
+        tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = cute.path, class = "vector", typeof = "character", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end using fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument primary checking
+    # second round of checking and data preparation
+    # new environment
+    env.name <- paste0("env", as.numeric(Sys.time()))
+    if(exists(env.name, where = -1)){ # verify if still ok when fun_info() is inside a function
+        tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else{
+        assign(env.name, new.env())
+        assign("data", data, envir = get(env.name, env = sys.nframe(), inherit = FALSE)) # data assigned in a new envir for test
+    }
+    # end new environment
+    # management of NA arguments
+    tempo.arg <- names(arg.user.setting) # values provided by the user
+    tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
+    if(any(tempo.log) == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS", "THIS ARGUMENT"), " CANNOT JUST BE NA:", paste0(tempo.arg[tempo.log], collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NA arguments
+    # management of NULL arguments
+    tempo.arg <-c(
+        "fun", 
+        "arg", 
+        "val", 
+        # "expect.erro", # because can be NULL
+        "parall", 
+        # "thread.nb", # because can be NULL
+        "print.count", 
+        "plot.fun", 
+        "export", 
+        # "res.path", # because can be NULL
+        # "lib.path", # because can be NULL
+        "cute.path"
+    )
+    tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
+    if(any(tempo.log) == TRUE){# normally no NA with is.null()
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NULL arguments
+    # code that protects set.seed() in the global environment
+    # end code that protects set.seed() in the global environment
+    # warning initiation
+    # end warning initiation
+    # other checkings
+    if(grepl(x = fun, pattern = "()$")){ # remove ()
+        fun <- sub(x = fun, pattern = "()$", replacement = "")
+    }
+    if( ! exists(fun)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": CHARACTER STRING IN fun ARGUMENT DOES NOT EXIST IN THE R WORKING ENVIRONMENT: ", paste(fun, collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+    }else if( ! all(base::class(get(fun)) == "function")){ # here no env = sys.nframe(), inherit = FALSE for get() because fun is a function in the classical scope
+        tempo.cat <- paste0("ERROR IN ", function.name, ": fun ARGUMENT IS NOT CLASS \"function\" BUT: ", paste(base::class(get(fun)), collapse = "\n"), "\nCHECK IF ANY CREATED OBJECT WOULD HAVE THE NAME OF THE TESTED FUNCTION")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+    }
+    if(tempo$problem == FALSE & base::length(arg) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": arg ARGUMENT CANNOT BE LENGTH 0")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+    }
+    for(i2 in 1:base::length(val)){
+        tempo1 <- fun_check(data = val[[i2]], class = "vector", na.contain = TRUE, fun.name = function.name)
+        tempo2 <- fun_check(data = val[[i2]], class = "list", na.contain = TRUE, fun.name = function.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": COMPARTMENT ", i2, " OF val ARGUMENT MUST BE A VECTOR OR A LIST")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+        }else if(tempo1$problem == FALSE){ # vector split into list compartments
+            val[[i2]] <- split(x = val[[i2]], f = 1:base::length(val[[i2]]))
+        }
+    }
+    if(base::length(arg) != base::length(val)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": LENGTH OF arg ARGUMENT MUST BE IDENTICAL TO LENGTH OF val ARGUMENT:\nHERE IT IS: ", base::length(arg), " VERSUS ", base::length(val))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+    }
+    args <- names(formals(get(fun))) # here no env = sys.nframe(), inherit = FALSE for get() because fun is a function in the classical scope
+    if( ! all(arg %in% args)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": SOME OF THE STRINGS IN arg ARE NOT ARGUMENTS OF fun\nfun ARGUMENTS: ", paste(args, collapse = " "),"\nPROBLEMATIC STRINGS IN arg: ", paste(arg[ ! arg %in% args], collapse = " "))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+    }
+    if(sum(sapply(val, FUN = length) > 1) > 43){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": CANNOT TEST MORE THAN 43 ARGUMENTS IF THEY ALL HAVE AT LEAST 2 VALUES EACH\nHERE THE NUMBER IS: ", sum(sapply(val, FUN = length) > 1))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+    }
+    if( ! is.null(expect.error)){
+        if(base::length(val) != base::length(expect.error)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": LENGTH OF val ARGUMENT MUST BE IDENTICAL TO LENGTH OF expect.error ARGUMENT:\nHERE IT IS: ", base::length(val), " VERSUS ", base::length(expect.error))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+        }
+        for(i3 in 1:base::length(expect.error)){
+            tempo1 <- fun_check(data = expect.error[[i3]], class = "vector",  mode = "logical", fun.name = function.name)
+            tempo2 <- fun_check(data =  expect.error[[i3]], class = "list", fun.name = function.name)
+            if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": COMPARTMENT ", i3, " OF expect.error ARGUMENT MUST BE TRUE OR FALSE")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+            }else if(tempo1$problem == FALSE){ # vector split into list compartments
+                expect.error[[i3]] <- split(x = expect.error[[i3]], f = 1:base::length(expect.error[[i3]]))
+            }
+        }
+    }
+    if( ! is.null(res.path)){
+        if( ! all(dir.exists(res.path))){ # separation to avoid the problem of tempo$problem == FALSE and res.path == NA
+            tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE res.path ARGUMENT DOES NOT EXISTS:\n", paste(res.path, collapse = "\n"))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+        }
+    }
+    if(parall == TRUE & is.null(res.path)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": res.path ARGUMENT MUST BE SPECIFIED IF parall ARGUMENT IS TRUE")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+    }
+    if(is.null(res.path) & export == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": res.path ARGUMENT MUST BE SPECIFIED IF export ARGUMENT TRUE")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+    }
+    if(parall == TRUE & export == FALSE){
+        export <- TRUE
+        tempo.cat <- paste0("WARNING FROM ", function.name, ": export ARGUMENT CONVERTED TO TRUE BECAUSE thread.nb ARGUMENT IS NOT NULL")
+        warning(paste0("\n", tempo.cat, "\n"), call. = FALSE)
+    }
+    if( ! is.null(lib.path)){
+        if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
+            tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+        }
+    }
+    if(parall == TRUE){
+        if(grepl(x = cute.path, pattern = "^http")){
+            tempo.error1 <- any(grepl(x = fun_get_message(data = "source(cute.path)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE)), pattern = "^[Ee]rror"))
+            tempo.error2 <- FALSE
+        }else{
+            tempo.error1 <- FALSE
+            tempo.error2 <- ! file.exists(cute.path)
+        }
+        if(tempo.error1 | tempo.error2){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(grepl(x = cute.path, pattern = "^http"), "URL", "FILE"), " PATH INDICATED IN THE cute.path PARAMETER DOES NOT EXISTS:\n", cute.path)
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+        }
+    }
+    # end other checkings
+    # reserved word checking
+    # end reserved word checking
+    # end second round of checking and data preparation
+    # package checking
+    fun_pack(req.package = c("lubridate"), lib.path = lib.path)
+    if(parall == TRUE){
+        fun_pack(req.package = c("parallel", "pdftools"), lib.path = lib.path)
+    }
+    # end package checking
+    # declaration of special plot functions
+    sp.plot.fun <- c("fun_gg_scatter", "fun_gg_bar", "fun_gg_boxplot")
+    # end declaration of special plot functions
+    # main code
+    ini.warning.length <- base::options()$warning.length
+    options(warning.length = 8170)
+    warn <- NULL
+    warn.count <- 0
+    cat("\nfun_test JOB IGNITION\n")
+    ini.date <- Sys.time()
+    ini.time <- as.numeric(ini.date) # time of process begin, converted into seconds
+    if(export == TRUE){
+        res.path <- paste0(res.path, "/fun_test_res_", trunc(ini.time))
+        if(dir.exists(res.path)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": FOLDER ALREADY EXISTS\n", res.path, "\nPLEASE RERUN ONCE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            dir.create(res.path)
+        }
+    }
+    total.comp.nb <- prod(sapply(val, FUN = "length"))
+    cat(paste0("\nTHE TOTAL NUMBER OF TESTS IS: ", total.comp.nb, "\n"))
+    # creation of the txt instruction that includes several loops
+    loop.string <- NULL
+    end.loop.string <- NULL
+    fun.args <- NULL
+    fun.args2 <- NULL
+    error.values <- NULL
+    arg.values <- "list("
+    for(i1 in 1:base::length(arg)){
+        if(parall == FALSE){
+            if(base::length(val[[i1]]) > 1){ # loop only if more than one value in base::length(val[[i1]])
+                loop.string <- paste0(loop.string, "for(i", i1, " in 1:", base::length(val[[i1]]), "){")
+                end.loop.string <- paste0(end.loop.string, "}")
+            }
+        }else{
+            loop.string <- "for(i in x){"
+            end.loop.string <- "}"
+        }
+        fun.args <- paste0(
+            fun.args, 
+            ifelse(i1 == 1L, "", ", "), 
+            arg[i1], 
+            " = val[[", 
+            i1, 
+            "]][[", 
+            if(parall == FALSE){
+                if(base::length(val[[i1]]) > 1){
+                    paste0("i", i1)
+                }else{
+                    "1" # a unique element in val[[i1]]
+                }
+            }else{
+                paste0("i.list[[", i1, "]][i]")
+            }, 
+            "]]"
+        )
+        fun.args2 <- paste0(
+            fun.args2, 
+            ifelse(i1 == 1L, "", ", "), 
+            arg[i1], 
+            " = val[[", 
+            i1, 
+            "]][[', ", 
+            if(parall == FALSE){
+                if(base::length(val[[i1]]) > 1){
+                    paste0("i", i1)
+                }else{
+                    "1" # a unique element in val[[i1]]
+                }
+            }else{
+                paste0("i.list[[", i1, "]][i]")
+            }, 
+            ", ']]"
+        )
+        arg.values <- paste0(
+            arg.values, 
+            "val[[", i1, "]][[", 
+            if(parall == FALSE){
+                if(base::length(val[[i1]]) > 1){
+                    paste0("i", i1)
+                }else{
+                    "1" # a unique element in val[[i1]]
+                }
+            }else{
+                paste0("i.list[[", i1, "]][i]")
+            }, 
+            "]]", 
+            ifelse(i1 == base::length(arg), "", ", ")
+        )
+        error.values <- paste0(
+            error.values, 
+            ifelse(i1 == 1L, "", " | "), 
+            "expect.error[[", i1, "]][[", 
+            if(parall == FALSE){
+                if(base::length(expect.error[[i1]]) > 1){
+                    paste0("i", i1)
+                }else{
+                    "1" # a unique element in expect.error[[i1]]
+                }
+            }else{
+                paste0("i.list[[", i1, "]][i]")
+            }, 
+            "]]"
+        )
+    }
+    arg.values <- paste0(arg.values, ")")
+    fun.test <- paste0(fun, "(", fun.args, ")")
+    fun.test2 <- paste0("paste0('", fun, "(", fun.args2, ")')")
+    # plot title for special plot functions
+    if(plot.fun == TRUE){
+        plot.kind <- "classic"
+        if(fun %in% sp.plot.fun){
+            plot.kind <- "special"
+            if(any(arg %in% "title")){ # this is for the special functions
+                tempo.match <- regmatches(x = fun.test, m = regexpr(text = fun.test, pattern = "title = .+[,)]"))
+                tempo.match <- substring(tempo.match , 1, nchar(tempo.match) - 1)
+                fun.test <- sub(x = fun.test, pattern = tempo.match, replacement = paste0(tempo.match, "\ntempo.title"))
+            }else{
+                fun.test <- sub(x = fun.test, pattern = ")$", replacement = ", title = tempo.title)")
+            }
+        }
+    }
+    # end plot title for special plot functions
+    kind <- character()
+    problem <- logical()
+    expected.error <- logical()
+    res <- character()
+    count <- 0
+    print.count.loop <- 0
+    plot.count <- 0
+    if(base::length(arg) == 1L){
+        data <- data.frame()
+    }else{ # base::length(arg) == 0L already tested above
+        data <- data.frame(t(vector("character", base::length(arg))), stringsAsFactors = FALSE)[-1, ] # -1 to remove the single row created and to have an empty data frame with base::length(arg) columns
+    }
+    code <- paste(
+        loop.string, '
+count <- count + 1
+print.count.loop <- print.count.loop + 1
+arg.values.print <- eval(parse(text = arg.values)) # recover the list of the i1 compartment
+for(j3 in 1:base::length(arg.values.print)){ # WARNING: do not use i1, i2 etc., here because already in loop.string
+tempo.capt <- capture.output(tempo.error <- fun_get_message(data =  paste0("paste(arg.values.print[[", j3, "]])"), kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))) # collapsing arg.values sometimes does not work (with function for instance)
+if( ! is.null(tempo.error)){
+arg.values.print[[j3]] <- paste0("SPECIAL VALUE OF CLASS ", base::class(arg.values.print[[j3]]), " AND TYPE ", base::typeof(arg.values.print[[j3]]))
 }
-if(all(class(data2) == "table") & length(dim(data2)) == 1L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data2 ARGUMENT IS A 1D TABLE. USE THE fun_comp_1d FUNCTION")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
 }
-if( ! identical(class(data1), class(data2))){
-same.class <- FALSE
-}else if( ! (any(class(data1) %in% c("data.frame", "table")) | all(class(data1) %in% c("matrix", "array")))){ # before R4.0.0, it was  ! any(class(data1) %in% c("matrix", "data.frame", "table"))
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 AND data2 ARGUMENTS MUST BE EITHER MATRIX, DATA FRAME OR TABLE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-same.class <- TRUE
-class <- class(data1)
+data <- rbind(data, as.character(sapply(arg.values.print, FUN = "paste", collapse = " ")), stringsAsFactors = FALSE) # each colum is a test
+tempo.capt <- capture.output(tempo.try.error <- fun_get_message(data = eval(parse(text = fun.test2)), kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))) # data argument needs a character string but eval(parse(text = fun.test2)) provides it (eval parse replace the i1, i2, etc., by the correct values, meaning that only val is required in the env.name environment)
+tempo.capt <- capture.output(tempo.try.warning <- fun_get_message(data = eval(parse(text = fun.test2)), kind = "warning", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE), print.no = TRUE)) # data argument needs a character string but eval(parse(text = fun.test2)) provides it (eval parse replace the i1, i2, etc., by the correct values, meaning that only val is required in the env.name environment)
+if( ! is.null(expect.error)){
+expected.error <- c(expected.error, eval(parse(text = error.values)))
 }
-if( ! identical(dim(data1), dim(data2))){
-same.dim <- FALSE
-}else{
-same.dim <- TRUE
-dim <- dim(data1)
-}
-if( ! identical(nrow(data1), nrow(data2))){
-same.row.nb <- FALSE
-}else{
-same.row.nb <- TRUE
-row.nb <- nrow(data1)
-}
-if( ! identical(ncol(data1), ncol(data2))){
-same.col.nb <- FALSE
-}else{
-same.col.nb <- TRUE
-col.nb <- ncol(data1)
-}
-# row and col names
-if(is.null(dimnames(data1)) & is.null(dimnames(data2))){
-same.row.name <- NULL # but already NULL
-same.col.name <- NULL # but already NULL
-# other row names param remain NULL
-}else if((is.null(dimnames(data1)) & ! is.null(dimnames(data2))) | ( ! is.null(dimnames(data1)) & is.null(dimnames(data2)))){
-same.row.name <- FALSE
-same.col.name <- FALSE
-any.id.row.name <- FALSE
-any.id.col.name <- FALSE
-# other row names param remain NULL
-}else{
-# row names
-if(is.null(dimnames(data1)[[1]]) & is.null(dimnames(data2)[[1]])){
-same.row.name <- NULL # but already NULL
-# other row names param remain NULL
-}else if((is.null(dimnames(data1)[[1]]) & ! is.null(dimnames(data2)[[1]])) | ( ! is.null(dimnames(data1)[[1]]) & is.null(dimnames(data2)[[1]]))){
-same.row.name <- FALSE
-any.id.row.name <- FALSE
-# other row names param remain NULL
-}else if(identical(dimnames(data1)[[1]], dimnames(data2)[[1]])){
-same.row.name <- TRUE
-row.name <- dimnames(data1)[[1]]
-any.id.row.name <- TRUE
-same.row.names.pos1 <- 1:nrow(data1)
-same.row.names.pos2 <- 1:nrow(data1)
-same.row.names.match1 <- 1:nrow(data1)
-same.row.names.match2 <- 1:nrow(data1)
-common.row.names <- dimnames(data1)[[1]]
-}else{
-same.row.name <- FALSE
-any.id.row.name <- FALSE
-if(any(dimnames(data1)[[1]] %in% dimnames(data2)[[1]])){
-any.id.row.name <- TRUE
-same.row.names.pos1 <- which(dimnames(data1)[[1]] %in% dimnames(data2)[[1]])
-same.row.names.match1 <- match(dimnames(data1)[[1]], dimnames(data2)[[1]])
-}
-if(any(dimnames(data2)[[1]] %in% dimnames(data1)[[1]])){
-any.id.row.name <- TRUE
-same.row.names.pos2 <- which(dimnames(data2)[[1]] %in% dimnames(data1)[[1]])
-same.row.names.match2 <- match(dimnames(data2)[[1]], dimnames(data1)[[1]])
-}
-if(any.id.row.name == TRUE){
-common.row.names <- unique(c(dimnames(data1)[[1]][same.row.names.pos1], dimnames(data2)[[1]][same.row.names.pos2]))
-}
-}
-# col names
-if(is.null(dimnames(data1)[[2]]) & is.null(dimnames(data2)[[2]])){
-same.col.name <- NULL # but already NULL
-# other col names param remain NULL
-}else if((is.null(dimnames(data1)[[2]]) & ! is.null(dimnames(data2)[[2]])) | ( ! is.null(dimnames(data1)[[2]]) & is.null(dimnames(data2)[[2]]))){
-same.col.name <- FALSE
-any.id.col.name <- FALSE
-# other col names param remain NULL
-}else if(identical(dimnames(data1)[[2]], dimnames(data2)[[2]])){
-same.col.name <- TRUE
-col.name <- dimnames(data1)[[2]]
-any.id.col.name <- TRUE
-same.col.names.pos1 <- 1:ncol(data1)
-same.col.names.pos2 <- 1:ncol(data1)
-same.col.names.match1 <- 1:ncol(data1)
-same.col.names.match2 <- 1:ncol(data1)
-common.col.names <- dimnames(data1)[[2]]
-}else{
-same.col.name <- FALSE
-any.id.col.name <- FALSE
-if(any(dimnames(data1)[[2]] %in% dimnames(data2)[[2]])){
-any.id.col.name <- TRUE
-same.col.names.pos1 <- which(dimnames(data1)[[2]] %in% dimnames(data2)[[2]])
-same.col.names.match1 <- match(dimnames(data1)[[2]], dimnames(data2)[[2]])
-}
-if(any(dimnames(data2)[[2]] %in% dimnames(data1)[[2]])){
-any.id.col.name <- TRUE
-same.col.names.pos2 <- which(dimnames(data2)[[2]] %in% dimnames(data1)[[2]])
-same.col.names.match2 <- match(dimnames(data2)[[2]], dimnames(data1)[[2]])
-}
-if(any.id.col.name == TRUE){
-common.col.names <- unique(c(dimnames(data1)[[2]][same.col.names.pos1], dimnames(data2)[[2]][same.col.names.pos2]))
-}
-}
-}
-# identical row and col content
-if(all(class(data1) == "table")){
-data1 <- as.data.frame(matrix(data1, ncol = ncol(data1)), stringsAsFactors = FALSE) # conversion of table into data frame to facilitate inter class comparison
-}else if(all(class(data1) %in% c("matrix", "array"))){
-data1 <- as.data.frame(data1, stringsAsFactors = FALSE) # conversion of matrix into data frame to facilitate inter class comparison
-}else if(all(class(data1) == "data.frame")){
-# data1 <- data.frame(lapply(data1, as.character), stringsAsFactors = FALSE) # conversion of columns into characters
-}
-if(all(class(data2) == "table")){
-data2 <- as.data.frame(matrix(data2, ncol = ncol(data2)), stringsAsFactors = FALSE) # conversion of table into data frame to facilitate inter class comparison
-}else if(all(class(data2) %in% c("matrix", "array"))){
-data2 <- as.data.frame(data2, stringsAsFactors = FALSE) # conversion of matrix into data frame to facilitate inter class comparison
-}else if(all(class(data2) == "data.frame")){
-# data2 <- data.frame(lapply(data2, as.character), stringsAsFactors = FALSE) # conversion of columns into characters
-}
-row.names(data1) <- paste0("A", 1:nrow(data1))
-row.names(data2) <- paste0("A", 1:nrow(data2))
-if(same.col.nb == TRUE){ # because if not the same col nb, the row cannot be identical
-if(all(sapply(data1, FUN = typeof) == "integer") & all(sapply(data2, FUN = typeof) == "integer") & as.double(nrow(data1)) * nrow(data2) <= 1e10){ # fast method for integers (thus not data frames). as.double(nrow(data1)) to prevent integer overflow because R is 32 bits for integers
-tempo1 <- c(as.data.frame(t(data1), stringsAsFactors = FALSE)) # conversion into list. This work fast with only integers (because 32 bits)
-tempo2 <- c(as.data.frame(t(data2), stringsAsFactors = FALSE)) # conversion into list. This work fast with only integers (because 32 bits)
-same.row.pos1 <- which(tempo1 %in% tempo2)
-same.row.pos2 <- which(tempo2 %in% tempo1)
-same.row.match1 <- match(tempo1, tempo2)
-same.row.match2 <- match(tempo2, tempo1)
-}else if(as.double(nrow(data1)) * nrow(data2) <= 1e6){ # as.double(nrow(data1)) to prevent integer overflow because R is 32 bits for integers
-# inactivated because I would like to keep the mode during comparisons
-# if(col.nb <= 10){ # if ncol is not to big, the t() should not be that long
-# tempo1 <- c(as.data.frame(t(data1), stringsAsFactors = FALSE)) # conversion into list. This work fast with only integers (because 32 bits)
-# tempo2 <- c(as.data.frame(t(data2), stringsAsFactors = FALSE)) # conversion into list. 
-# same.row.pos1 <- which(tempo1 %in% tempo2)
-# same.row.pos2 <- which(tempo2 %in% tempo1)
-# same.row.match1 <- match(tempo1, tempo2)
-# same.row.match2 <- match(tempo2, tempo1)
-# }else{
-# very long computation
-same.row.pos1 <- logical(length = nrow(data1)) # FALSE by default
-same.row.pos1[] <- FALSE # security
-same.row.pos2 <- logical(length = nrow(data2)) # FALSE by default
-same.row.pos2[] <- FALSE # security
-same.row.match1 <- rep(NA, nrow(data1))
-same.row.match2 <- rep(NA, nrow(data2))
-for(i3 in 1:nrow(data1)){
-for(i4 in 1:nrow(data2)){
-tempo1 <- data1[i3, ]
-tempo2 <- data2[i4, ]
-rownames(tempo1) <- NULL # to have same row and column names
-colnames(tempo1) <- NULL # to have same row and column names
-rownames(tempo2) <- NULL # to have same row and column names
-colnames(tempo2) <- NULL # to have same row and column names
-if(identical(tempo1, tempo2)){
-same.row.pos1[i3] <- TRUE
-same.row.pos2[i4] <- TRUE
-same.row.match1[i3] <- i4
-same.row.match2[i4] <- i3
-}
-}
-}
-same.row.pos1 <- which(same.row.pos1)
-same.row.pos2 <- which(same.row.pos2)
-# }
-}else{
-same.row.pos1 <- "TOO BIG FOR EVALUATION"
-same.row.pos2 <- "TOO BIG FOR EVALUATION"
-same.row.match1 <- "TOO BIG FOR EVALUATION"
-same.row.match2 <- "TOO BIG FOR EVALUATION"
-}
-
-names(same.row.pos1) <- NULL
-names(same.row.pos2) <- NULL
-if(all(is.na(same.row.pos1))){
-same.row.pos1 <- NULL
-}else{
-same.row.pos1 <- same.row.pos1[ ! is.na(same.row.pos1)]
-any.id.row <- TRUE
-}
-if(all(is.na(same.row.pos2))){
-same.row.pos2 <- NULL
-}else{
-same.row.pos2 <- same.row.pos2[ ! is.na(same.row.pos2)]
-any.id.row <- TRUE
-}
-if(is.null(same.row.pos1) & is.null(same.row.pos2)){
-any.id.row <- FALSE
-}else if(length(same.row.pos1) == 0L & length(same.row.pos2) == 0L){
-any.id.row <- FALSE
-}else if(all(same.row.pos1 == "TOO BIG FOR EVALUATION") & all(same.row.pos2 == "TOO BIG FOR EVALUATION")){
-any.id.row <- NULL
-}
-}else{
-any.id.row <- FALSE
-# same.row.pos1 and 2 remain NULL
-}
-if(same.row.nb == TRUE){ # because if not the same row nb, the col cannot be identical
-if(as.double(ncol(data1)) * ncol(data2) <= 1e10){ # comparison of data frame columns is much easier than rows because no need to use t() before converting to list for fast comparison. as.double(ncol(data1)) to prevent integer overflow because R is 32 bits for integers
-# if(all(sapply(data1, FUN = typeof) == "integer") & all(sapply(data2, FUN = typeof) == "integer") & as.double(ncol(data1)) * ncol(data2) <= 1e10){ # fast method for integers (thus not data frames). as.double(ncol(data1)) to prevent integer overflow because R is 32 bits for integers
-tempo1 <- c(data1)
-tempo2 <- c(data2)
-same.col.pos1 <- which(tempo1 %in% tempo2)
-same.col.pos2 <- which(tempo2 %in% tempo1)
-same.col.match1 <- match(tempo1, tempo2)
-same.col.match2 <- match(tempo2, tempo1)
-# }else if(as.double(ncol(data1)) * ncol(data2) <= 1e6){ # as.double(ncol(data1)) to prevent integer overflow because R is 32 bits for integers
-# same.col.pos1 <- logical(length = ncol(data1)) # FALSE by default
-# same.col.pos1[] <- FALSE # security
-# same.col.pos2 <- logical(length = ncol(data2)) # FALSE by default
-# same.col.pos2[] <- FALSE # security
-# same.col.match1 <- rep(NA, ncol(data1))
-# same.col.match2 <- rep(NA, ncol(data2))
-# for(i3 in 1:ncol(data1)){
-# for(i4 in 1:ncol(data2)){
-# if(identical(data1[ , i3], data2[ , i4])){
-# same.col.pos1[i3] <- TRUE
-# same.col.pos2[i4] <- TRUE
-# same.col.match1[i3] <- i4
-# same.col.match2[i4] <- i3
-# }
-# }
-# }
-# same.col.pos1 <- which(same.col.pos1)
-# same.col.pos2 <- which(same.col.pos2)
-}else{
-same.col.pos1 <- "TOO BIG FOR EVALUATION"
-same.col.pos2 <- "TOO BIG FOR EVALUATION"
-}
-names(same.col.pos1) <- NULL
-names(same.col.pos2) <- NULL
-if(all(is.na(same.col.pos1))){
-same.col.pos1 <- NULL
-}else{
-same.col.pos1 <- same.col.pos1[ ! is.na(same.col.pos1)]
-any.id.col <- TRUE
-}
-if(all(is.na(same.col.pos2))){
-same.col.pos2 <- NULL
-}else{
-same.col.pos2 <- same.col.pos2[ ! is.na(same.col.pos2)]
-any.id.col <- TRUE
-}
-if(is.null(same.col.pos1) & is.null(same.col.pos2)){
-any.id.col <- FALSE
-}else if(length(same.col.pos1) == 0L & length(same.col.pos2) == 0L){
-any.id.col <- FALSE
-}else if(all(same.col.pos1 == "TOO BIG FOR EVALUATION") & all(same.col.pos2 == "TOO BIG FOR EVALUATION")){
-any.id.col <- NULL
-}
-}else{
-any.id.col <- FALSE
-# same.col.pos1 and 2 remain NULL
-}
-if(same.dim == TRUE){
-names(data1) <- NULL
-row.names(data1) <- NULL
-names(data2) <- NULL
-row.names(data2) <- NULL
-if(identical(data1, data2)){
-identical.content <- TRUE
-}else{
-identical.content <- FALSE
-}
-}else{
-identical.content <- FALSE
-}
-}
-output <- list(same.class = same.class, class = class, same.dim = same.dim, dim = dim, same.row.nb = same.row.nb, row.nb = row.nb, same.col.nb = same.col.nb , col.nb = col.nb, same.row.name = same.row.name, row.name = row.name, any.id.row.name = any.id.row.name, same.row.names.pos1 = same.row.names.pos1, same.row.names.pos2 = same.row.names.pos2, same.row.names.match1 = same.row.names.match1, same.row.names.match2 = same.row.names.match2, common.row.names = common.row.names, same.col.name = same.col.name, col.name = col.name,any.id.col.name = any.id.col.name, same.col.names.pos1 = same.col.names.pos1, same.col.names.pos2 = same.col.names.pos2, same.col.names.match1 = same.col.names.match1, same.col.names.match2 = same.col.names.match2, common.col.names = common.col.names, any.id.row = any.id.row, same.row.pos1 = same.row.pos1, same.row.pos2 = same.row.pos2, same.row.match1 = same.row.match1, same.row.match2 = same.row.match2, any.id.col = any.id.col, same.col.pos1 = same.col.pos1, same.col.pos2 = same.col.pos2, same.col.match1 = same.col.match1, same.col.match2 = same.col.match2, identical.object = identical.object, identical.content = identical.content)
-return(output)
-}
-
-
-######## fun_comp_list() #### comparison of two lists
-
-
-fun_comp_list <- function(data1, data2){
-# AIM
-# compare two lists. Check and report in a list if the 2 datasets have:
-# same length
-# common names
-# common compartments
-# ARGUMENTS
-# data1: list
-# data2: list
-# RETURN
-# a list containing:
-# $same.length: logical. Are number of elements identical?
-# $length: number of elements in the 2 datasets (NULL otherwise)
-# $same.names: logical. Are element names identical ?
-# $name: name of elements of the 2 datasets if identical (NULL otherwise)
-# $any.id.name: logical. Is there any element names identical ?
-# $same.names.pos1: positions, in data1, of the element names identical in data2
-# $same.names.pos2: positions, in data2, of the compartment names identical in data1
-# $any.id.compartment: logical. is there any identical compartments ?
-# $same.compartment.pos1: positions, in data1, of the compartments identical in data2
-# $same.compartment.pos2: positions, in data2, of the compartments identical in data1
-# $identical.object: logical. Are objects identical (kind of object, compartment names and content)?
-# $identical.content: logical. Are content objects identical (identical compartments excluding compartment names)?
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# none
-# EXAMPLES
-# obs1 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; obs2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; fun_comp_list(obs1, obs2)
-# obs1 = list(1:5, LETTERS[1:2]) ; obs2 = list(a = 1:5, b = LETTERS[1:2]) ; fun_comp_list(obs1, obs2)
-# obs1 = list(b = 1:5, c = LETTERS[1:2]) ; obs2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; fun_comp_list(obs1, obs2)
-# obs1 = list(b = 1:5, c = LETTERS[1:2]) ; obs2 = list(LETTERS[5:9], matrix(1:6), 1:5) ; fun_comp_list(obs1, obs2)
-# DEBUGGING
-# data1 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) ; data2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) # for function debugging
-# data1 = list(a = 1:5, b = LETTERS[1:2]) ; data2 = list(a = 1:5, b = LETTERS[1:2], d = matrix(1:6)) # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# argument checking
-if( ! any(class(data1) %in% "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 ARGUMENT MUST BE A LIST")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! any(class(data2) %in% "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data2 ARGUMENT MUST BE A LIST")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) # activate this line and use the function to check arguments status
-# end argument checking
-# main code
-same.length <- NULL
-length <- NULL
-same.names <- NULL
-name <- NULL
-any.id.name <- NULL
-same.names.pos1 <- NULL
-same.names.pos2 <- NULL
-any.id.compartment <- NULL
-same.compartment.pos1 <- NULL
-same.compartment.pos2 <- NULL
-identical.object <- NULL
-identical.content <- NULL
-if(identical(data1, data2)){
-same.length <- TRUE
-length <- length(data1)
-if( ! is.null(names(data1))){
-same.names <- TRUE
-name <- names(data1)
-any.id.name <- TRUE
-same.names.pos1 <- 1:length(data1)
-same.names.pos2 <- 1:length(data2)
-}
-any.id.compartment <- TRUE
-same.compartment.pos1 <- 1:length(data1)
-same.compartment.pos2 <- 1:length(data2)
-identical.object <- TRUE
-identical.content <- TRUE
-}else{
-identical.object <- FALSE
-if( ! identical(length(data1), length(data2))){
-same.length<- FALSE
-}else{
-same.length<- TRUE
-length <- length(data1)
-}
-if( ! (is.null(names(data1)) & is.null(names(data2)))){
-if( ! identical(names(data1), names(data2))){
-same.names <- FALSE
-}else{
-same.names <- TRUE
-name <- names(data1)
-}
-any.id.name <- FALSE
-if(any(names(data1) %in% names(data2))){
-any.id.name <- TRUE
-same.names.pos1 <- which(names(data1) %in% names(data2))
-}
-if(any(names(data2) %in% names(data1))){
-any.id.name <- TRUE
-same.names.pos2 <- which(names(data2) %in% names(data1))
-}
-}
-names(data1) <- NULL
-names(data2) <- NULL
-any.id.compartment <- FALSE
-if(any(data1 %in% data2)){
-any.id.compartment <- TRUE
-same.compartment.pos1 <- which(data1 %in% data2)
-}
-if(any(data2 %in% data1)){
-any.id.compartment <- TRUE
-same.compartment.pos2 <- which(data2 %in% data1)
-}
-if(same.length == TRUE & ! all(is.null(same.compartment.pos1), is.null(same.compartment.pos2))){
-if(identical(same.compartment.pos1, same.compartment.pos2)){
-identical.content <- TRUE
-}else{
-identical.content <- FALSE
-}
-}else{
-identical.content <- FALSE
-}
-}
-output <- list(same.length = same.length, length = length, same.names = same.names, name = name, any.id.name = any.id.name, same.names.pos1 = same.names.pos1, same.names.pos2 = same.names.pos2, any.id.compartment = any.id.compartment, same.compartment.pos1 = same.compartment.pos1, same.compartment.pos2 = same.compartment.pos2, identical.object = identical.object, identical.content = identical.content)
-return(output)
-}
-
-
-######## fun_test() #### test combinations of argument values of a function and return errors (and graphs)
-
-
-# add traceback https://stackoverflow.com/questions/47414119/how-to-read-a-traceback-in-r
-
-fun_test <- function(
-fun, 
-arg, 
-val, 
-expect.error = NULL, 
-parall = FALSE, 
-thread.nb = NULL, 
-print.count = 10, 
-plot.fun = FALSE, 
-export = FALSE, 
-res.path = NULL, 
-lib.path = NULL, 
-cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
-){
-# AIM
-# test combinations of argument values of a function
-# WARNINGS
-# Limited to 43 arguments with at least 2 values each. The total number of arguments tested can be more if the additional arguments have a single value. The limit is due to nested "for" loops (https://stat.ethz.ch/pipermail/r-help/2008-March/157341.html), but it should not be a problem since the number of tests would be 2^43 > 8e12
-# ARGUMENTS
-# fun: character string indicating the name of the function tested (without brackets)
-# arg: vector of character strings of arguments of fun. At least arguments that do not have default values must be present in this vector
-# val: list with number of compartments equal to length of arg, each compartment containing values of the corresponding argument in arg. Each different value must be in a list or in a vector. For instance, argument 3 in arg is a logical argument (values accepted TRUE, FALSE, NA). Thus, compartment 3 of val can be either list(TRUE, FALSE, NA), or c(TRUE, FALSE, NA). NULL value alone must be written list(NULL)
-# expect.error: list of exactly the same structure as val argument, but containing FALSE or TRUE, depending on whether error is expected (TRUE) or not (FALSE) for each corresponding value of val. A message is returned depending on discrepancies between the expected and observed errors. BEWARE: not always possible to write the expected errors for all the combination of argument values. Ignored if NULL
-# parall: logical. Force parallelization ?
-# thread.nb: numeric value indicating the number of threads to use if ever parallelization is required. If NULL, all the available threads will be used. Ignored if parall is FALSE
-# print.count: interger value. Print a working progress message every print.count during loops. BEWARE: can increase substentially the time to complete the process using a small value, like 10 for instance. Use Inf is no loop message desired
-# plot.fun: logical. Plot the plotting function tested for each test?
-# export: logical. Export the results into a .RData file and into a .txt file? If FALSE, return a list into the console (see below). BEWARE: will be automatically set to TRUE if parall is TRUE. This means that when using parallelization, the results are systematically exported, not returned into the console
-# res.path: character string indicating the absolute pathway of folder where the txt results and pdfs, containing all the plots, will be saved. Several txt and pdf, one per thread, if parallelization. Ignored if export is FALSE. Must be specified if parall is TRUE or if export is TRUE
-# lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
-# cute.path: character string indicating the absolute path of the cute.R file. Will be remove when cute will be a package. Ignored if parall is FALSE
-# REQUIRED PACKAGES
-# lubridate
-# parallel if parall arguemtn is TRUE (included in the R installation packages but not automatically loaded)
-# pdftools if parall arguemtn is TRUE (included in the R installation packages but not automatically loaded)
-# If the tested function is in a package, this package must be imported first (no parallelization) or must be in the classical R package folder indicated by the lib.path argument (parallelization)
-# RETURN
-# if export is FALSE a list containing:
-# $fun: the tested function
-# $instruction: the initial instruction
-# $sys.info: system and packages info
-# $data: a data frame of all the combination tested, containing the following columns:
-# the different values tested, named by arguments
-# $kind: a vector of character strings indicating the kind of test result: either "ERROR", or "WARNING", or "OK"
-# $problem: a logical vector indicating if error or not
-# $expected.error: optional logical vector indicating the expected error specified in the expect.error argument
-# $message: either NULL if $kind is always "OK", or the messages
-# if export is TRUE 1) the same list object into a .RData file, 2) also the $data data frame into a .txt file, and 3) if expect.error is non NULL and if any discrepancy, the $data data frame into a .txt file but containing only the rows with discrepancies between expected and observed errors
-# one or several pdf if a plotting function is tested and if the plot.fun argument is TRUE
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# fun_get_message()
-# fun_pack()
-# EXAMPLES
-# fun_test(fun = "unique", arg = c("x", "incomparables"), val = list(x = list(1:10, c(1,1,2,8), NA), incomparable = c(TRUE, FALSE, NA)))
-# fun_test(fun = "fun_round", arg = c("data", "dec.nb", "after.lead.zero"), val = list(L1 = list(c(1, 1.0002256, 1.23568), "a", NA), L2 = list(2, c(1,3), NA), L3 = c(TRUE, FALSE, NA)))
-# fun_test(fun = "plot", arg = c("x", "y"), val = list(x = list(1:10, 12:13, NA, (1:10)^2), y = list(1:10, NA, NA)),  expect.error = list(x = list(FALSE, TRUE, TRUE, FALSE), y = list(FALSE, TRUE, TRUE)), parall = FALSE, thread.nb = NULL, plot.fun = TRUE, res.path = "C:\\Users\\Gael\\Desktop\\", lib.path = NULL)
-# fun_test(fun = "plot", arg = c("x", "y"), val = list(x = list(1:10, 12:13, NA, (1:10)^2), y = list(1:10, NA, NA)), parall = FALSE, thread.nb = 4, plot.fun = TRUE, res.path = "C:\\Users\\Gael\\Desktop\\", lib.path = "C:\\Program Files\\R\\R-4.0.2\\library\\")
-# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; fun_test(fun = "fun_gg_boxplot", arg = c("data1", "y", "categ"), val = list(L1 = list(L1 = obs1), L2 = list(L1 = "Time"), L3 = list(L1 = "Group1")))
-# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; fun_test(fun = "fun_gg_boxplot", arg = c("data1", "y", "categ"), val = list(L1 = list(obs1), L2 = "Time", L3 = "Group1"), parall = FALSE, thread.nb = NULL, plot.fun = TRUE, res.path = "C:\\Users\\Gael\\Desktop\\", lib.path = "C:\\Program Files\\R\\R-4.0.2\\library\\")
-# library(ggplot2) ; fun_test(fun = "geom_histogram", arg = c("data", "mapping"), val = list(x = list(data.frame(X = "a", stringsAsFactors = TRUE)), y = list(ggplot2::aes(x = X))), parall = FALSE, thread.nb = NULL, plot.fun = TRUE, res.path = "C:\\Users\\Gael\\Desktop\\", lib.path = "C:\\Program Files\\R\\R-4.0.2\\library\\") # BEWARE: ggplot2::geom_histogram does not work
-# DEBUGGING
-# fun = "unique" ; arg = "x" ; val = list(x = list(1:10, c(1,1,2,8), NA)) ; expect.error = list(x = list(FALSE, FALSE, TRUE)) ; parall = FALSE ; thread.nb = NULL ; plot.fun = FALSE ; export = FALSE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL ; print.count = 1 ; cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R" # for function debugging
-# fun = "unique" ; arg = c("x", "incomparables") ; val = list(x = list(1:10, c(1,1,2,8), NA), incomparable = c(TRUE, FALSE, NA)) ; expect.error = NULL ; parall = FALSE ; thread.nb = 2 ; plot.fun = FALSE ; export = TRUE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL ; print.count = 10 ; cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R" # for function debugging
-# fun = "plot" ; arg = c("x", "y") ; val = list(x = list(1:10, 12:13, NA), y = list(1:10, NA, NA)) ; expect.error = list(x = list(FALSE, FALSE, TRUE, FALSE), y = list(FALSE, TRUE, TRUE)) ; print.count = 10 ; parall = FALSE ; thread.nb = NULL ; plot.fun = TRUE ; export = TRUE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL # for function debugging
-# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; fun = "fun_gg_boxplot" ; arg = c("data1", "y", "categ") ; val = list(L1 = list(L1 = obs1), L2 = list(L1 = "Time"), L3 = list(L1 = "Group1")) ; expect.error = NULL ; print.count = 10 ; parall = FALSE ; thread.nb = NULL ; plot.fun = TRUE ; export = TRUE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL # for function debugging
-# fun = "unique" ; arg = "x" ; val = list(list(1:3, mean)) ; expect.error = list(TRUE, TRUE) ; parall = FALSE ; thread.nb = NULL ; plot.fun = FALSE ; export = FALSE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL ; print.count = 1 ; cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R" # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
-arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
-# end function name
-# required function checking
-req.function <- c(
-"fun_check", 
-"fun_get_message", 
-"fun_pack"
-)
-tempo <- NULL
-for(i1 in req.function){
-if(length(find(i1, mode = "function")) == 0L){
-tempo <- c(tempo, i1)
-}
-}
-if( ! is.null(tempo)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# reserved words
-# end reserved words
-# arg with no default values
-mandat.args <- c(
-"fun", 
-"arg", 
-"val"
-)
-tempo <- eval(parse(text = paste0("missing(", paste0(mandat.args, collapse = ") | missing("), "))")))
-print(tempo)
-if(any(tempo)){ # normally no NA for missing() output
-tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end arg with no default values
-# argument primary checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = fun, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = arg, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = val, class = "list", fun.name = function.name) ; eval(ee)
-if( ! is.null(expect.error)){
-tempo <- fun_check(data = expect.error, class = "list", fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = parall, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(parall == TRUE){
-if( ! is.null(thread.nb)){
-tempo <- fun_check(data = thread.nb, typeof = "integer", double.as.integer.allowed = TRUE, neg.values = FALSE, length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & thread.nb < 1){
-tempo.cat <- paste0("ERROR IN ", function.name, ": thread.nb PARAMETER MUST EQUAL OR GREATER THAN 1: ", thread.nb)
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}
-tempo <- fun_check(data = print.count, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = plot.fun, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = export, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(res.path)){
-tempo <- fun_check(data = res.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(lib.path)){
-tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = cute.path, class = "vector", typeof = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end using fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument primary checking
-# second round of checking and data preparation
-# new environment
-env.name <- paste0("env", as.numeric(Sys.time()))
-if(exists(env.name, where = -1)){ # verify if still ok when fun_info() is inside a function
-tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-assign(env.name, new.env())
-assign("data", data, envir = get(env.name, env = sys.nframe(), inherit = FALSE)) # data assigned in a new envir for test
-}
-# end new environment
-# management of NA arguments
-tempo.arg <- names(arg.user.setting) # values provided by the user
-tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
-if(any(tempo.log) == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS", "THIS ARGUMENT"), " CANNOT JUST BE NA:", paste0(tempo.arg[tempo.log], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NA arguments
-# management of NULL arguments
-tempo.arg <-c(
-"fun", 
-"arg", 
-"val", 
-# "expect.erro", # because can be NULL
-"parall", 
-# "thread.nb", # because can be NULL
-"print.count", 
-"plot.fun", 
-"export", 
-# "res.path", # because can be NULL
-# "lib.path", # because can be NULL
-"cute.path"
-)
-tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
-if(any(tempo.log) == TRUE){# normally no NA with is.null()
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NULL arguments
-# code that protects set.seed() in the global environment
-# end code that protects set.seed() in the global environment
-# warning initiation
-# end warning initiation
-# other checkings
-if(grepl(x = fun, pattern = "()$")){ # remove ()
-fun <- sub(x = fun, pattern = "()$", replacement = "")
-}
-if( ! exists(fun)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CHARACTER STRING IN fun ARGUMENT DOES NOT EXIST IN THE R WORKING ENVIRONMENT: ", paste(fun, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}else if( ! all(base::class(get(fun)) == "function")){ # here no env = sys.nframe(), inherit = FALSE for get() because fun is a function in the classical scope
-tempo.cat <- paste0("ERROR IN ", function.name, ": fun ARGUMENT IS NOT CLASS \"function\" BUT: ", paste(base::class(get(fun)), collapse = "\n"), "\nCHECK IF ANY CREATED OBJECT WOULD HAVE THE NAME OF THE TESTED FUNCTION")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-if(tempo$problem == FALSE & base::length(arg) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": arg ARGUMENT CANNOT BE LENGTH 0")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-for(i2 in 1:base::length(val)){
-tempo1 <- fun_check(data = val[[i2]], class = "vector", na.contain = TRUE, fun.name = function.name)
-tempo2 <- fun_check(data = val[[i2]], class = "list", na.contain = TRUE, fun.name = function.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": COMPARTMENT ", i2, " OF val ARGUMENT MUST BE A VECTOR OR A LIST")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}else if(tempo1$problem == FALSE){ # vector split into list compartments
-val[[i2]] <- split(x = val[[i2]], f = 1:base::length(val[[i2]]))
-}
-}
-if(base::length(arg) != base::length(val)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": LENGTH OF arg ARGUMENT MUST BE IDENTICAL TO LENGTH OF val ARGUMENT:\nHERE IT IS: ", base::length(arg), " VERSUS ", base::length(val))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-args <- names(formals(get(fun))) # here no env = sys.nframe(), inherit = FALSE for get() because fun is a function in the classical scope
-if( ! all(arg %in% args)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": SOME OF THE STRINGS IN arg ARE NOT ARGUMENTS OF fun\nfun ARGUMENTS: ", paste(args, collapse = " "),"\nPROBLEMATIC STRINGS IN arg: ", paste(arg[ ! arg %in% args], collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-if(sum(sapply(val, FUN = length) > 1) > 43){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CANNOT TEST MORE THAN 43 ARGUMENTS IF THEY ALL HAVE AT LEAST 2 VALUES EACH\nHERE THE NUMBER IS: ", sum(sapply(val, FUN = length) > 1))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-if( ! is.null(expect.error)){
-if(base::length(val) != base::length(expect.error)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": LENGTH OF val ARGUMENT MUST BE IDENTICAL TO LENGTH OF expect.error ARGUMENT:\nHERE IT IS: ", base::length(val), " VERSUS ", base::length(expect.error))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-for(i3 in 1:base::length(expect.error)){
-tempo1 <- fun_check(data = expect.error[[i3]], class = "vector",  mode = "logical", fun.name = function.name)
-tempo2 <- fun_check(data =  expect.error[[i3]], class = "list", fun.name = function.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": COMPARTMENT ", i3, " OF expect.error ARGUMENT MUST BE TRUE OR FALSE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}else if(tempo1$problem == FALSE){ # vector split into list compartments
-expect.error[[i3]] <- split(x = expect.error[[i3]], f = 1:base::length(expect.error[[i3]]))
-}
-}
-}
-if( ! is.null(res.path)){
-if( ! all(dir.exists(res.path))){ # separation to avoid the problem of tempo$problem == FALSE and res.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE res.path ARGUMENT DOES NOT EXISTS:\n", paste(res.path, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-}
-if(parall == TRUE & is.null(res.path)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": res.path ARGUMENT MUST BE SPECIFIED IF parall ARGUMENT IS TRUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-if(is.null(res.path) & export == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": res.path ARGUMENT MUST BE SPECIFIED IF export ARGUMENT TRUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-if(parall == TRUE & export == FALSE){
-export <- TRUE
-tempo.cat <- paste0("WARNING FROM ", function.name, ": export ARGUMENT CONVERTED TO TRUE BECAUSE thread.nb ARGUMENT IS NOT NULL")
-warning(paste0("\n", tempo.cat, "\n"), call. = FALSE)
-}
-if( ! is.null(lib.path)){
-if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-}
-if(parall == TRUE){
-if(grepl(x = cute.path, pattern = "^http")){
-tempo.error1 <- any(grepl(x = fun_get_message(data = "source(cute.path)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE)), pattern = "^[Ee]rror"))
-tempo.error2 <- FALSE
-}else{
-tempo.error1 <- FALSE
-tempo.error2 <- ! file.exists(cute.path)
-}
-if(tempo.error1 | tempo.error2){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(grepl(x = cute.path, pattern = "^http"), "URL", "FILE"), " PATH INDICATED IN THE cute.path PARAMETER DOES NOT EXISTS:\n", cute.path)
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-}
-# end other checkings
-# reserved word checking
-# end reserved word checking
-# end second round of checking and data preparation
-# package checking
-fun_pack(req.package = c("lubridate"), lib.path = lib.path)
-if(parall == TRUE){
-fun_pack(req.package = c("parallel", "pdftools"), lib.path = lib.path)
-}
-# end package checking
-# declaration of special plot functions
-sp.plot.fun <- c("fun_gg_scatter", "fun_gg_bar", "fun_gg_boxplot")
-# end declaration of special plot functions
-# main code
-ini.warning.length <- base::options()$warning.length
-options(warning.length = 8170)
-warn <- NULL
-warn.count <- 0
-cat("\nfun_test JOB IGNITION\n")
-ini.date <- Sys.time()
-ini.time <- as.numeric(ini.date) # time of process begin, converted into seconds
-if(export == TRUE){
-res.path <- paste0(res.path, "/fun_test_res_", trunc(ini.time))
-if(dir.exists(res.path)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": FOLDER ALREADY EXISTS\n", res.path, "\nPLEASE RERUN ONCE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-dir.create(res.path)
-}
-}
-total.comp.nb <- prod(sapply(val, FUN = "length"))
-cat(paste0("\nTHE TOTAL NUMBER OF TESTS IS: ", total.comp.nb, "\n"))
-# creation of the txt instruction that includes several loops
-loop.string <- NULL
-end.loop.string <- NULL
-fun.args <- NULL
-fun.args2 <- NULL
-error.values <- NULL
-arg.values <- "list("
-for(i1 in 1:base::length(arg)){
-if(parall == FALSE){
-if(base::length(val[[i1]]) > 1){ # loop only if more than one value in base::length(val[[i1]])
-loop.string <- paste0(loop.string, "for(i", i1, " in 1:", base::length(val[[i1]]), "){")
-end.loop.string <- paste0(end.loop.string, "}")
-}
-}else{
-loop.string <- "for(i in x){"
-end.loop.string <- "}"
-}
-fun.args <- paste0(
-fun.args, 
-ifelse(i1 == 1L, "", ", "), 
-arg[i1], 
-" = val[[", 
-i1, 
-"]][[", 
-if(parall == FALSE){
-if(base::length(val[[i1]]) > 1){
-paste0("i", i1)
-}else{
-"1" # a unique element in val[[i1]]
-}
-}else{
-paste0("i.list[[", i1, "]][i]")
-}, 
-"]]"
-)
-fun.args2 <- paste0(
-fun.args2, 
-ifelse(i1 == 1L, "", ", "), 
-arg[i1], 
-" = val[[", 
-i1, 
-"]][[', ", 
-if(parall == FALSE){
-if(base::length(val[[i1]]) > 1){
-paste0("i", i1)
-}else{
-"1" # a unique element in val[[i1]]
-}
-}else{
-paste0("i.list[[", i1, "]][i]")
-}, 
-", ']]"
-)
-arg.values <- paste0(
-arg.values, 
-"val[[", i1, "]][[", 
-if(parall == FALSE){
-if(base::length(val[[i1]]) > 1){
-paste0("i", i1)
-}else{
-"1" # a unique element in val[[i1]]
-}
-}else{
-paste0("i.list[[", i1, "]][i]")
-}, 
-"]]", 
-ifelse(i1 == base::length(arg), "", ", ")
-)
-error.values <- paste0(
-error.values, 
-ifelse(i1 == 1L, "", " | "), 
-"expect.error[[", i1, "]][[", 
-if(parall == FALSE){
-if(base::length(expect.error[[i1]]) > 1){
-paste0("i", i1)
-}else{
-"1" # a unique element in expect.error[[i1]]
-}
-}else{
-paste0("i.list[[", i1, "]][i]")
-}, 
-"]]"
-)
-}
-arg.values <- paste0(arg.values, ")")
-fun.test <- paste0(fun, "(", fun.args, ")")
-fun.test2 <- paste0("paste0('", fun, "(", fun.args2, ")')")
-# plot title for special plot functions
-if(plot.fun == TRUE){
-plot.kind <- "classic"
-if(fun %in% sp.plot.fun){
-plot.kind <- "special"
-if(any(arg %in% "title")){ # this is for the special functions
-tempo.match <- regmatches(x = fun.test, m = regexpr(text = fun.test, pattern = "title = .+[,)]"))
-tempo.match <- substring(tempo.match , 1, nchar(tempo.match) - 1)
-fun.test <- sub(x = fun.test, pattern = tempo.match, replacement = paste0(tempo.match, "\ntempo.title"))
-}else{
-fun.test <- sub(x = fun.test, pattern = ")$", replacement = ", title = tempo.title)")
-}
-}
-}
-# end plot title for special plot functions
-kind <- character()
-problem <- logical()
-expected.error <- logical()
-res <- character()
-count <- 0
-print.count.loop <- 0
-plot.count <- 0
-if(base::length(arg) == 1L){
-data <- data.frame()
-}else{ # base::length(arg) == 0L already tested above
-data <- data.frame(t(vector("character", base::length(arg))), stringsAsFactors = FALSE)[-1, ] # -1 to remove the single row created and to have an empty data frame with base::length(arg) columns
-}
-code <- paste(
-loop.string, '
-count <- count + 1
-print.count.loop <- print.count.loop + 1
-arg.values.print <- eval(parse(text = arg.values)) # recover the list of the i1 compartment
-for(j3 in 1:base::length(arg.values.print)){ # WARNING: do not use i1, i2 etc., here because already in loop.string
-tempo.capt <- capture.output(tempo.error <- fun_get_message(data =  paste0("paste(arg.values.print[[", j3, "]])"), kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))) # collapsing arg.values sometimes does not work (with function for instance)
-if( ! is.null(tempo.error)){
-arg.values.print[[j3]] <- paste0("SPECIAL VALUE OF CLASS ", base::class(arg.values.print[[j3]]), " AND TYPE ", base::typeof(arg.values.print[[j3]]))
-}
-}
-data <- rbind(data, as.character(sapply(arg.values.print, FUN = "paste", collapse = " ")), stringsAsFactors = FALSE) # each colum is a test
-tempo.capt <- capture.output(tempo.try.error <- fun_get_message(data = eval(parse(text = fun.test2)), kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE))) # data argument needs a character string but eval(parse(text = fun.test2)) provides it (eval parse replace the i1, i2, etc., by the correct values, meaning that only val is required in the env.name environment)
-tempo.capt <- capture.output(tempo.try.warning <- fun_get_message(data = eval(parse(text = fun.test2)), kind = "warning", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE), print.no = TRUE)) # data argument needs a character string but eval(parse(text = fun.test2)) provides it (eval parse replace the i1, i2, etc., by the correct values, meaning that only val is required in the env.name environment)
-if( ! is.null(expect.error)){
-expected.error <- c(expected.error, eval(parse(text = error.values)))
-}
-if( ! is.null(tempo.try.error)){
-kind <- c(kind, "ERROR")
-problem <- c(problem, TRUE)
-res <- c(res, tempo.try.error)
+if( ! is.null(tempo.try.error)){
+kind <- c(kind, "ERROR")
+problem <- c(problem, TRUE)
+res <- c(res, tempo.try.error)
 }else{
 if( ! is.null(tempo.try.warning)){
 kind <- c(kind, "WARNING")
@@ -2366,304 +2366,304 @@ cat(paste0(ifelse(parall == FALSE, "\nLOOP PROCESS ENDED | ", paste0("\nPROCESS
 }
 ', 
 end.loop.string
-)
-# end creation of the txt instruction that includes several loops
-if(parall == TRUE){
-# list of i numbers that will be split
-i.list <- vector("list", base::length(val)) # positions to split in parallel jobs
-for(i2 in 1:base::length(arg)){
-if(i2 == 1L){
-tempo.divisor <- total.comp.nb / base::length(val[[i2]])
-i.list[[i2]] <- rep(1:base::length(val[[i2]]), each = as.integer(tempo.divisor))
-tempo.multi <- base::length(val[[i2]])
-}else{
-tempo.divisor <- tempo.divisor / base::length(val[[i2]])
-i.list[[i2]] <- rep(rep(1:base::length(val[[i2]]), each = as.integer(tempo.divisor)), time = as.integer(tempo.multi))
-tempo.multi <- tempo.multi * base::length(val[[i2]])
-}
-}
-# end list of i numbers that will be split
-tempo.cat <- paste0("PARALLELIZATION INITIATED AT: ", ini.date)
-cat(paste0("\n", tempo.cat, "\n"))
-tempo.thread.nb = parallel::detectCores(all.tests = FALSE, logical = TRUE) # detect the number of threads
-if(tempo.thread.nb < thread.nb){
-thread.nb <- tempo.thread.nb
-}
-tempo.cat <- paste0("NUMBER OF THREADS USED: ", thread.nb)
-cat(paste0("\n    ", tempo.cat, "\n"))
-Clust <- parallel::makeCluster(thread.nb, outfile = paste0(res.path, "/fun_test_parall_log.txt")) # outfile to print or cat during parallelization (only possible in a file, outfile = "" do not work on windows)
-tempo.cat <- paste0("SPLIT OF TEST NUMBERS IN PARALLELISATION:")
-cat(paste0("\n    ", tempo.cat, "\n"))
-cluster.list <- parallel::clusterSplit(Clust, 1:total.comp.nb) # split according to the number of cluster
-str(cluster.list) # using print(str()) add a NULL below the result
-cat("\n")
-paral.output.list <- parallel::clusterApply( # paral.output.list is a list made of thread.nb compartments, each made of n / thread.nb (mat theo column number) compartment. Each compartment receive the corresponding results of fun_permut(), i.e., data (permuted mat1.perm), warning message, cor (final correlation) and count (number of permutations)
-cl = Clust,
-x = cluster.list,
-function.name = function.name, 
-instruction = instruction, 
-thread.nb = thread.nb, 
-print.count = print.count, 
-total.comp.nb = total.comp.nb, 
-sp.plot.fun = sp.plot.fun,
-i.list = i.list, 
-fun.tested = fun,
-arg.values = arg.values,
-fun.test = fun.test,
-fun.test2 = fun.test2,
-kind = kind,
-problem = problem,
-res = res,
-count = count,
-plot.count = plot.count,
-data = data,
-code = code,
-plot.fun = plot.fun, 
-res.path = res.path, 
-lib.path = lib.path, 
-cute.path = cute.path, 
-fun = function(
-x, 
-function.name, 
-instruction, 
-thread.nb, 
-print.count, 
-total.comp.nb, 
-sp.plot.fun, 
-i.list, 
-fun.tested, 
-arg.values, 
-fun.test, 
-fun.test2, 
-kind, 
-problem, 
-res, 
-count, 
-plot.count, 
-data, 
-code, 
-plot.fun, 
-res.path, 
-lib.path, 
-cute.path
-){
-# check again: very important because another R
-process.id <- Sys.getpid()
-cat(paste0("\nPROCESS ID ", process.id, " -> TESTS ", x[1], " TO ", x[base::length(x)], "\n"))
-source(cute.path, local = .GlobalEnv)
-fun_pack(req.package = "lubridate", lib.path = lib.path, load = TRUE) # load = TRUE to be sure that functions are present in the environment. And this prevent to use R.lib.path argument of fun_python_pack()
-# end check again: very important because another R
-# plot management
-if(plot.fun == TRUE){
-pdf(file = paste0(res.path, "/plots_from_fun_test_", x[1], ifelse(base::length(x) == 1L, ".pdf", paste0("-", x[base::length(x)], ".pdf"))))
-}else{
-pdf(file = NULL) # send plots into a NULL file, no pdf file created
-}
-window.nb <- dev.cur()
-invisible(dev.set(window.nb))
-# end plot management
-# new environment
-ini.date <- Sys.time()
-ini.time <- as.numeric(ini.date) # time of process begin, converted into 
-env.name <- paste0("env", ini.time)
-if(exists(env.name, where = -1)){ # verify if still ok when fun_test() is inside a function
-tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-assign(env.name, new.env())
-assign("val", val, envir = get(env.name, env = sys.nframe(), inherit = FALSE)) # var replaced by val
-}
-# end new environment
-print.count.loop <- 0
-suppressMessages(suppressWarnings(eval(parse(text = code))))
-colnames(data) <- arg
-if( ! is.null(expect.error)){
-data <- data.frame(data, kind = kind, problem = problem, expected.error = expected.error, message = res, stringsAsFactors = FALSE)
-}else{
-data <- data.frame(data, kind = kind, problem = problem, message = res, stringsAsFactors = FALSE)
-}
-row.names(data) <- paste0("test_", sprintf(paste0("%0", nchar(total.comp.nb), "d"), x))
-sys.info <- sessionInfo()
-sys.info$loadedOnly <- sys.info$loadedOnly[order(names(sys.info$loadedOnly))] # sort the packages
-invisible(dev.off(window.nb))
-rm(env.name) # optional, because should disappear at the end of the function execution
-# output
-output <- list(fun = fun, instruction = instruction, sys.info = sys.info) # data = data finally removed from the output list, because everything combined in a RData file at the end
-save(output, file = paste0(res.path, "/fun_test_", x[1], ifelse(base::length(x) == 1L, ".RData", paste0("-", x[base::length(x)], ".RData"))))
-if(plot.fun == TRUE & plot.count == 0L){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN PROCESS ", process.id, ": NO PDF PLOT BECAUSE ONLY ERRORS REPORTED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-file.remove(paste0(res.path, "/plots_from_fun_test_", x[1], ifelse(base::length(x) == 1L, ".pdf", paste0("-", x[base::length(x)], ".pdf"))))
-}
-table.out <- as.matrix(data)
-# table.out[table.out == ""] <- " " # does not work # because otherwise read.table() converts "" into NA
-table.out <- gsub(table.out, pattern = "\n", replacement = " ")
-write.table(table.out, file = paste0(res.path, "/table_from_fun_test_", x[1], ifelse(base::length(x) == 1L, ".txt", paste0("-", x[base::length(x)], ".txt"))), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n", na = "")
-}
-)
-parallel::stopCluster(Clust)
-# files assembly
-if(base::length(cluster.list) > 1){
-for(i2 in 1:base::length(cluster.list)){
-tempo.file <- paste0(res.path, "/table_from_fun_test_", min(cluster.list[[i2]], na.rm = TRUE), ifelse(base::length(cluster.list[[i2]]) == 1L, ".txt", paste0("-", max(cluster.list[[i2]], na.rm = TRUE), ".txt"))) # txt file
-tempo <- read.table(file = tempo.file, header = TRUE, stringsAsFactors = FALSE, sep = "\t", row.names = 1, comment.char = "", colClasses = "character") #  row.names = 1 (1st column) because now read.table() adds a NA in the header if the header starts by a tabulation, comment.char = "" because colors with #, colClasses = "character" otherwise convert "" (from NULL) into NA
-if(file.exists(paste0(res.path, "/plots_from_fun_test_", min(cluster.list[[i2]], na.rm = TRUE), ifelse(base::length(cluster.list[[i2]]) == 1L, ".pdf", paste0("-", max(cluster.list[[i2]], na.rm = TRUE), ".pdf"))))){
-tempo.pdf <- paste0(res.path, "/plots_from_fun_test_", min(cluster.list[[i2]], na.rm = TRUE), ifelse(base::length(cluster.list[[i2]]) == 1L, ".pdf", paste0("-", max(cluster.list[[i2]], na.rm = TRUE), ".pdf"))) # pdf file
-}else{
-tempo.pdf <- NULL
-}
-tempo.rdata <- paste0(res.path, "/fun_test_", min(cluster.list[[i2]], na.rm = TRUE), ifelse(base::length(cluster.list[[i2]]) == 1L, ".RData", paste0("-", max(cluster.list[[i2]], na.rm = TRUE), ".RData"))) # RData file
-if(i2 == 1L){
-final.file <- tempo
-final.pdf <- tempo.pdf
-# new env for RData combining
-env.name <- paste0("env", ini.time)
-if(exists(env.name, where = -1)){ # verify if still ok when fun_test() is inside a function
-tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-# end new env for RData combining
-}else{
-assign(env.name, new.env())
-load(tempo.rdata, envir = get(env.name))
-tempo.rdata1 <- tempo.rdata
-assign("final.output", get("output", envir = get(env.name)), envir = get(env.name))
-}
-}else{
-final.file <- rbind(final.file, tempo, stringsAsFactors = TRUE)
-final.pdf <- c(final.pdf, tempo.pdf)
-load(tempo.rdata, envir = get(env.name))
-if( ! identical(get("final.output", envir = get(env.name))[c("R.version", "locale", "platform")], get("output", envir = get(env.name))[c("R.version", "locale", "platform")])){
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIFFERENCE BETWEEN OUTPUTS WHILE THEY SHOULD BE IDENTICAL\nPLEASE CHECK\n", tempo.rdata1, "\n", tempo.rdata)
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-# add the differences in RData $sysinfo into final.output
-tempo.base1 <- sort(get("final.output", envir = get(env.name))$sys.info$basePkgs)
-tempo.base2 <- sort(get("output", envir = get(env.name))$sys.info$basePkgs)
-tempo.other1 <- names(get("final.output", envir = get(env.name))$sys.info$otherPkgs)
-tempo.other2 <- names(get("output", envir = get(env.name))$sys.info$otherPkgs)
-tempo.loaded1 <- names(get("final.output", envir = get(env.name))$sys.info$loadedOnly)
-tempo.loaded2 <- names(get("output", envir = get(env.name))$sys.info$loadedOnly)
-assign("final.output", {
-x <- get("final.output", envir = get(env.name))
-y <- get("output", envir = get(env.name))
-x$sys.info$basePkgs <- sort(unique(tempo.base1, tempo.base2))
-if( ! all(tempo.other2 %in% tempo.other1)){
-x$sys.info$otherPkgs <- c(x$sys.info$otherPkgs, y$sys.info$otherPkgs[ ! (tempo.other2 %in% tempo.other1)])
-x$sys.info$otherPkgs <- x$sys.info$otherPkgs[order(names(x$sys.info$otherPkgs))]
-}
-if( ! all(tempo.loaded2 %in% tempo.loaded1)){
-x$sys.info$loadedOnly <- c(x$sys.info$loadedOnly, y$sys.info$loadedOnly[ ! (tempo.loaded2 %in% tempo.loaded1)])
-x$sys.info$loadedOnly <- x$sys.info$loadedOnly[order(names(x$sys.info$loadedOnly))]
-}
-x
-}, envir = get(env.name))
-# add the differences in RData $sysinfo into final.output
-}
-}
-file.remove(c(tempo.file, tempo.rdata))
-}
-# combine pdf and save
-if( ! is.null(final.pdf)){
-pdftools::pdf_combine(
-input = final.pdf,
-output = paste0(res.path, "/plots_from_fun_test_1-", total.comp.nb, ".pdf")
-)
-file.remove(final.pdf)
-}
-# end combine pdf and save
-# save RData
-assign("output", c(get("final.output", envir = get(env.name)), data = list(final.file)), envir = get(env.name))
-save(output, file = paste0(res.path, "/fun_test__1-", total.comp.nb, ".RData"), envir = get(env.name))
-rm(env.name) # optional, because should disappear at the end of the function execution
-# end save RData
-# save txt
-write.table(final.file, file = paste0(res.path, "/table_from_fun_test_1-", total.comp.nb, ".txt"), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n", na = "")
-# end save txt
-if( ! is.null(expect.error)){
-final.file <- final.file[ ! final.file$problem == final.file$expected.error, ]
-if(nrow(final.file) == 0L){
-cat(paste0("NO DISCREPANCY BETWEEN EXPECTED AND OBSERVED ERRORS\n\n"))
-}else{
-cat(paste0("DISCREPANCIES BETWEEN EXPECTED AND OBSERVED ERRORS (SEE THE discrepancy_table_from_fun_test_1-", total.comp.nb, ".txt FILE)\n\n"))
-write.table(final.file, file = paste0(res.path, "/discrepancy_table_from_fun_test_1-", total.comp.nb, ".txt"), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n", na = "")
-}
-}
-}
-# end files assembly
-}else{
-# plot management
-if(plot.fun == TRUE){
-pdf(file = paste0(res.path, "/plots_from_fun_test_1", ifelse(total.comp.nb == 1L, ".pdf", paste0("-", total.comp.nb, ".pdf"))))
-}else{
-pdf(file = NULL) # send plots into a NULL file, no pdf file created
-}
-window.nb <- dev.cur()
-invisible(dev.set(window.nb))
-# end plot management
-# new environment
-env.name <- paste0("env", ini.time)
-if(exists(env.name, where = -1)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-assign(env.name, new.env())
-assign("val", val, envir = get(env.name, env = sys.nframe(), inherit = FALSE)) # var replaced by val
-}
-# end new environment
-suppressMessages(suppressWarnings(eval(parse(text = code))))
-colnames(data) <- arg
-expect.data <- data.frame()
-if( ! is.null(expect.error)){
-data <- data.frame(data, kind = kind, problem = problem, expected.error = expected.error, message = res, stringsAsFactors = FALSE)
-}else{
-data <- data.frame(data, kind = kind, problem = problem, message = res, stringsAsFactors = FALSE)
-}
-row.names(data) <- paste0("test_", sprintf(paste0("%0", nchar(total.comp.nb), "d"), 1:total.comp.nb))
-sys.info <- sessionInfo()
-sys.info$loadedOnly <- sys.info$loadedOnly[order(names(sys.info$loadedOnly))] # sort the packages
-invisible(dev.off(window.nb))
-rm(env.name) # optional, because should disappear at the end of the function execution
-# output
-output <- list(fun = fun, instruction = instruction, sys.info = sys.info, data = data)
-if(plot.fun == TRUE & plot.count == 0L){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NO PDF PLOT BECAUSE ONLY ERRORS REPORTED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-file.remove(paste0(res.path, "/plots_from_fun_test_1", ifelse(total.comp.nb == 1L, ".pdf", paste0("-", total.comp.nb, ".pdf"))))
-}
-if( ! is.null(expect.error)){
-expect.data <- output$data[ ! output$data$problem == output$data$expected.error, ]
-if(nrow(expect.data) == 0L){
-cat(paste0("NO DISCREPANCY BETWEEN EXPECTED AND OBSERVED ERRORS\n\n"))
-}else{
-cat(paste0("DISCREPANCIES BETWEEN EXPECTED AND OBSERVED ERRORS (SEE THE ", if(export == TRUE){paste0("discrepancy_table_from_fun_test_1", ifelse(total.comp.nb == 1L, "", paste0("-", total.comp.nb)), ".txt FILE")}else{"$data RESULT"}, ")\n\n"))
-if(export == TRUE){
-expect.data <- as.matrix(expect.data)
-expect.data <- gsub(expect.data, pattern = "\n", replacement = "  ")
-write.table(expect.data, file = paste0(res.path, "/discrepancy_table_from_fun_test_1", ifelse(total.comp.nb == 1L, ".txt", paste0("-", total.comp.nb, ".txt"))), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n", na = "")
-}
-}
-}
-if( ! is.null(warn)){
-base::options(warning.length = 8170)
-on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
-}
-on.exit(exp = base::options(warning.length = ini.warning.length), add = TRUE)
-if(export == TRUE){
-save(output, file = paste0(res.path, "/fun_test_1", ifelse(total.comp.nb == 1L, ".RData", paste0("-", total.comp.nb, ".RData"))))
-table.out <- as.matrix(output$data)
-table.out <- gsub(table.out, pattern = "\n", replacement = "  ")
-write.table(table.out, file = paste0(res.path, "/table_from_fun_test_1", ifelse(total.comp.nb == 1L, ".txt", paste0("-", total.comp.nb, ".txt"))), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n", na = "")
-}else{
-return(output)
-}
-}
-# after return() ?
-end.date <- Sys.time()
-end.time <- as.numeric(end.date)
-total.lapse <- round(lubridate::seconds_to_period(end.time - ini.time))
-cat(paste0("fun_test JOB END\n\nTIME: ", end.date, "\n\nTOTAL TIME LAPSE: ", total.lapse, "\n\n\n"))
+    )
+    # end creation of the txt instruction that includes several loops
+    if(parall == TRUE){
+        # list of i numbers that will be split
+        i.list <- vector("list", base::length(val)) # positions to split in parallel jobs
+        for(i2 in 1:base::length(arg)){
+            if(i2 == 1L){
+                tempo.divisor <- total.comp.nb / base::length(val[[i2]])
+                i.list[[i2]] <- rep(1:base::length(val[[i2]]), each = as.integer(tempo.divisor))
+                tempo.multi <- base::length(val[[i2]])
+            }else{
+                tempo.divisor <- tempo.divisor / base::length(val[[i2]])
+                i.list[[i2]] <- rep(rep(1:base::length(val[[i2]]), each = as.integer(tempo.divisor)), time = as.integer(tempo.multi))
+                tempo.multi <- tempo.multi * base::length(val[[i2]])
+            }
+        }
+        # end list of i numbers that will be split
+        tempo.cat <- paste0("PARALLELIZATION INITIATED AT: ", ini.date)
+        cat(paste0("\n", tempo.cat, "\n"))
+        tempo.thread.nb = parallel::detectCores(all.tests = FALSE, logical = TRUE) # detect the number of threads
+        if(tempo.thread.nb < thread.nb){
+            thread.nb <- tempo.thread.nb
+        }
+        tempo.cat <- paste0("NUMBER OF THREADS USED: ", thread.nb)
+        cat(paste0("\n    ", tempo.cat, "\n"))
+        Clust <- parallel::makeCluster(thread.nb, outfile = paste0(res.path, "/fun_test_parall_log.txt")) # outfile to print or cat during parallelization (only possible in a file, outfile = "" do not work on windows)
+        tempo.cat <- paste0("SPLIT OF TEST NUMBERS IN PARALLELISATION:")
+        cat(paste0("\n    ", tempo.cat, "\n"))
+        cluster.list <- parallel::clusterSplit(Clust, 1:total.comp.nb) # split according to the number of cluster
+        str(cluster.list) # using print(str()) add a NULL below the result
+        cat("\n")
+        paral.output.list <- parallel::clusterApply( # paral.output.list is a list made of thread.nb compartments, each made of n / thread.nb (mat theo column number) compartment. Each compartment receive the corresponding results of fun_permut(), i.e., data (permuted mat1.perm), warning message, cor (final correlation) and count (number of permutations)
+            cl = Clust,
+            x = cluster.list,
+            function.name = function.name, 
+            instruction = instruction, 
+            thread.nb = thread.nb, 
+            print.count = print.count, 
+            total.comp.nb = total.comp.nb, 
+            sp.plot.fun = sp.plot.fun,
+            i.list = i.list, 
+            fun.tested = fun,
+            arg.values = arg.values,
+            fun.test = fun.test,
+            fun.test2 = fun.test2,
+            kind = kind,
+            problem = problem,
+            res = res,
+            count = count,
+            plot.count = plot.count,
+            data = data,
+            code = code,
+            plot.fun = plot.fun, 
+            res.path = res.path, 
+            lib.path = lib.path, 
+            cute.path = cute.path, 
+            fun = function(
+                x, 
+                function.name, 
+                instruction, 
+                thread.nb, 
+                print.count, 
+                total.comp.nb, 
+                sp.plot.fun, 
+                i.list, 
+                fun.tested, 
+                arg.values, 
+                fun.test, 
+                fun.test2, 
+                kind, 
+                problem, 
+                res, 
+                count, 
+                plot.count, 
+                data, 
+                code, 
+                plot.fun, 
+                res.path, 
+                lib.path, 
+                cute.path
+            ){
+                # check again: very important because another R
+                process.id <- Sys.getpid()
+                cat(paste0("\nPROCESS ID ", process.id, " -> TESTS ", x[1], " TO ", x[base::length(x)], "\n"))
+                source(cute.path, local = .GlobalEnv)
+                fun_pack(req.package = "lubridate", lib.path = lib.path, load = TRUE) # load = TRUE to be sure that functions are present in the environment. And this prevent to use R.lib.path argument of fun_python_pack()
+                # end check again: very important because another R
+                # plot management
+                if(plot.fun == TRUE){
+                    pdf(file = paste0(res.path, "/plots_from_fun_test_", x[1], ifelse(base::length(x) == 1L, ".pdf", paste0("-", x[base::length(x)], ".pdf"))))
+                }else{
+                    pdf(file = NULL) # send plots into a NULL file, no pdf file created
+                }
+                window.nb <- dev.cur()
+                invisible(dev.set(window.nb))
+                # end plot management
+                # new environment
+                ini.date <- Sys.time()
+                ini.time <- as.numeric(ini.date) # time of process begin, converted into 
+                env.name <- paste0("env", ini.time)
+                if(exists(env.name, where = -1)){ # verify if still ok when fun_test() is inside a function
+                    tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+                }else{
+                    assign(env.name, new.env())
+                    assign("val", val, envir = get(env.name, env = sys.nframe(), inherit = FALSE)) # var replaced by val
+                }
+                # end new environment
+                print.count.loop <- 0
+                suppressMessages(suppressWarnings(eval(parse(text = code))))
+                colnames(data) <- arg
+                if( ! is.null(expect.error)){
+                    data <- data.frame(data, kind = kind, problem = problem, expected.error = expected.error, message = res, stringsAsFactors = FALSE)
+                }else{
+                    data <- data.frame(data, kind = kind, problem = problem, message = res, stringsAsFactors = FALSE)
+                }
+                row.names(data) <- paste0("test_", sprintf(paste0("%0", nchar(total.comp.nb), "d"), x))
+                sys.info <- sessionInfo()
+                sys.info$loadedOnly <- sys.info$loadedOnly[order(names(sys.info$loadedOnly))] # sort the packages
+                invisible(dev.off(window.nb))
+                rm(env.name) # optional, because should disappear at the end of the function execution
+                # output
+                output <- list(fun = fun, instruction = instruction, sys.info = sys.info) # data = data finally removed from the output list, because everything combined in a RData file at the end
+                save(output, file = paste0(res.path, "/fun_test_", x[1], ifelse(base::length(x) == 1L, ".RData", paste0("-", x[base::length(x)], ".RData"))))
+                if(plot.fun == TRUE & plot.count == 0L){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") IN PROCESS ", process.id, ": NO PDF PLOT BECAUSE ONLY ERRORS REPORTED")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    file.remove(paste0(res.path, "/plots_from_fun_test_", x[1], ifelse(base::length(x) == 1L, ".pdf", paste0("-", x[base::length(x)], ".pdf"))))
+                }
+                table.out <- as.matrix(data)
+                # table.out[table.out == ""] <- " " # does not work # because otherwise read.table() converts "" into NA
+                table.out <- gsub(table.out, pattern = "\n", replacement = " ")
+                write.table(table.out, file = paste0(res.path, "/table_from_fun_test_", x[1], ifelse(base::length(x) == 1L, ".txt", paste0("-", x[base::length(x)], ".txt"))), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n", na = "")
+            }
+        )
+        parallel::stopCluster(Clust)
+        # files assembly
+        if(base::length(cluster.list) > 1){
+            for(i2 in 1:base::length(cluster.list)){
+                tempo.file <- paste0(res.path, "/table_from_fun_test_", min(cluster.list[[i2]], na.rm = TRUE), ifelse(base::length(cluster.list[[i2]]) == 1L, ".txt", paste0("-", max(cluster.list[[i2]], na.rm = TRUE), ".txt"))) # txt file
+                tempo <- read.table(file = tempo.file, header = TRUE, stringsAsFactors = FALSE, sep = "\t", row.names = 1, comment.char = "", colClasses = "character") #  row.names = 1 (1st column) because now read.table() adds a NA in the header if the header starts by a tabulation, comment.char = "" because colors with #, colClasses = "character" otherwise convert "" (from NULL) into NA
+                if(file.exists(paste0(res.path, "/plots_from_fun_test_", min(cluster.list[[i2]], na.rm = TRUE), ifelse(base::length(cluster.list[[i2]]) == 1L, ".pdf", paste0("-", max(cluster.list[[i2]], na.rm = TRUE), ".pdf"))))){
+                    tempo.pdf <- paste0(res.path, "/plots_from_fun_test_", min(cluster.list[[i2]], na.rm = TRUE), ifelse(base::length(cluster.list[[i2]]) == 1L, ".pdf", paste0("-", max(cluster.list[[i2]], na.rm = TRUE), ".pdf"))) # pdf file
+                }else{
+                    tempo.pdf <- NULL
+                }
+                tempo.rdata <- paste0(res.path, "/fun_test_", min(cluster.list[[i2]], na.rm = TRUE), ifelse(base::length(cluster.list[[i2]]) == 1L, ".RData", paste0("-", max(cluster.list[[i2]], na.rm = TRUE), ".RData"))) # RData file
+                if(i2 == 1L){
+                    final.file <- tempo
+                    final.pdf <- tempo.pdf
+                    # new env for RData combining
+                    env.name <- paste0("env", ini.time)
+                    if(exists(env.name, where = -1)){ # verify if still ok when fun_test() is inside a function
+                        tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
+                        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+                        # end new env for RData combining
+                    }else{
+                        assign(env.name, new.env())
+                        load(tempo.rdata, envir = get(env.name))
+                        tempo.rdata1 <- tempo.rdata
+                        assign("final.output", get("output", envir = get(env.name)), envir = get(env.name))
+                    }
+                }else{
+                    final.file <- rbind(final.file, tempo, stringsAsFactors = TRUE)
+                    final.pdf <- c(final.pdf, tempo.pdf)
+                    load(tempo.rdata, envir = get(env.name))
+                    if( ! identical(get("final.output", envir = get(env.name))[c("R.version", "locale", "platform")], get("output", envir = get(env.name))[c("R.version", "locale", "platform")])){
+                        tempo.cat <- paste0("ERROR IN ", function.name, ": DIFFERENCE BETWEEN OUTPUTS WHILE THEY SHOULD BE IDENTICAL\nPLEASE CHECK\n", tempo.rdata1, "\n", tempo.rdata)
+                        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+                    }else{
+                        # add the differences in RData $sysinfo into final.output
+                        tempo.base1 <- sort(get("final.output", envir = get(env.name))$sys.info$basePkgs)
+                        tempo.base2 <- sort(get("output", envir = get(env.name))$sys.info$basePkgs)
+                        tempo.other1 <- names(get("final.output", envir = get(env.name))$sys.info$otherPkgs)
+                        tempo.other2 <- names(get("output", envir = get(env.name))$sys.info$otherPkgs)
+                        tempo.loaded1 <- names(get("final.output", envir = get(env.name))$sys.info$loadedOnly)
+                        tempo.loaded2 <- names(get("output", envir = get(env.name))$sys.info$loadedOnly)
+                        assign("final.output", {
+                            x <- get("final.output", envir = get(env.name))
+                            y <- get("output", envir = get(env.name))
+                            x$sys.info$basePkgs <- sort(unique(tempo.base1, tempo.base2))
+                            if( ! all(tempo.other2 %in% tempo.other1)){
+                                x$sys.info$otherPkgs <- c(x$sys.info$otherPkgs, y$sys.info$otherPkgs[ ! (tempo.other2 %in% tempo.other1)])
+                                x$sys.info$otherPkgs <- x$sys.info$otherPkgs[order(names(x$sys.info$otherPkgs))]
+                            }
+                            if( ! all(tempo.loaded2 %in% tempo.loaded1)){
+                                x$sys.info$loadedOnly <- c(x$sys.info$loadedOnly, y$sys.info$loadedOnly[ ! (tempo.loaded2 %in% tempo.loaded1)])
+                                x$sys.info$loadedOnly <- x$sys.info$loadedOnly[order(names(x$sys.info$loadedOnly))]
+                            }
+                            x
+                        }, envir = get(env.name))
+                        # add the differences in RData $sysinfo into final.output
+                    }
+                }
+                file.remove(c(tempo.file, tempo.rdata))
+            }
+            # combine pdf and save
+            if( ! is.null(final.pdf)){
+                pdftools::pdf_combine(
+                    input = final.pdf,
+                    output = paste0(res.path, "/plots_from_fun_test_1-", total.comp.nb, ".pdf")
+                )
+                file.remove(final.pdf)
+            }
+            # end combine pdf and save
+            # save RData
+            assign("output", c(get("final.output", envir = get(env.name)), data = list(final.file)), envir = get(env.name))
+            save(output, file = paste0(res.path, "/fun_test__1-", total.comp.nb, ".RData"), envir = get(env.name))
+            rm(env.name) # optional, because should disappear at the end of the function execution
+            # end save RData
+            # save txt
+            write.table(final.file, file = paste0(res.path, "/table_from_fun_test_1-", total.comp.nb, ".txt"), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n", na = "")
+            # end save txt
+            if( ! is.null(expect.error)){
+                final.file <- final.file[ ! final.file$problem == final.file$expected.error, ]
+                if(nrow(final.file) == 0L){
+                    cat(paste0("NO DISCREPANCY BETWEEN EXPECTED AND OBSERVED ERRORS\n\n"))
+                }else{
+                    cat(paste0("DISCREPANCIES BETWEEN EXPECTED AND OBSERVED ERRORS (SEE THE discrepancy_table_from_fun_test_1-", total.comp.nb, ".txt FILE)\n\n"))
+                    write.table(final.file, file = paste0(res.path, "/discrepancy_table_from_fun_test_1-", total.comp.nb, ".txt"), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n", na = "")
+                }
+            }
+        }
+        # end files assembly
+    }else{
+        # plot management
+        if(plot.fun == TRUE){
+            pdf(file = paste0(res.path, "/plots_from_fun_test_1", ifelse(total.comp.nb == 1L, ".pdf", paste0("-", total.comp.nb, ".pdf"))))
+        }else{
+            pdf(file = NULL) # send plots into a NULL file, no pdf file created
+        }
+        window.nb <- dev.cur()
+        invisible(dev.set(window.nb))
+        # end plot management
+        # new environment
+        env.name <- paste0("env", ini.time)
+        if(exists(env.name, where = -1)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            assign(env.name, new.env())
+            assign("val", val, envir = get(env.name, env = sys.nframe(), inherit = FALSE)) # var replaced by val
+        }
+        # end new environment
+        suppressMessages(suppressWarnings(eval(parse(text = code))))
+        colnames(data) <- arg
+        expect.data <- data.frame()
+        if( ! is.null(expect.error)){
+            data <- data.frame(data, kind = kind, problem = problem, expected.error = expected.error, message = res, stringsAsFactors = FALSE)
+        }else{
+            data <- data.frame(data, kind = kind, problem = problem, message = res, stringsAsFactors = FALSE)
+        }
+        row.names(data) <- paste0("test_", sprintf(paste0("%0", nchar(total.comp.nb), "d"), 1:total.comp.nb))
+        sys.info <- sessionInfo()
+        sys.info$loadedOnly <- sys.info$loadedOnly[order(names(sys.info$loadedOnly))] # sort the packages
+        invisible(dev.off(window.nb))
+        rm(env.name) # optional, because should disappear at the end of the function execution
+        # output
+        output <- list(fun = fun, instruction = instruction, sys.info = sys.info, data = data)
+        if(plot.fun == TRUE & plot.count == 0L){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") NO PDF PLOT BECAUSE ONLY ERRORS REPORTED")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            file.remove(paste0(res.path, "/plots_from_fun_test_1", ifelse(total.comp.nb == 1L, ".pdf", paste0("-", total.comp.nb, ".pdf"))))
+        }
+        if( ! is.null(expect.error)){
+            expect.data <- output$data[ ! output$data$problem == output$data$expected.error, ]
+            if(nrow(expect.data) == 0L){
+                cat(paste0("NO DISCREPANCY BETWEEN EXPECTED AND OBSERVED ERRORS\n\n"))
+            }else{
+                cat(paste0("DISCREPANCIES BETWEEN EXPECTED AND OBSERVED ERRORS (SEE THE ", if(export == TRUE){paste0("discrepancy_table_from_fun_test_1", ifelse(total.comp.nb == 1L, "", paste0("-", total.comp.nb)), ".txt FILE")}else{"$data RESULT"}, ")\n\n"))
+                if(export == TRUE){
+                    expect.data <- as.matrix(expect.data)
+                    expect.data <- gsub(expect.data, pattern = "\n", replacement = "  ")
+                    write.table(expect.data, file = paste0(res.path, "/discrepancy_table_from_fun_test_1", ifelse(total.comp.nb == 1L, ".txt", paste0("-", total.comp.nb, ".txt"))), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n", na = "")
+                }
+            }
+        }
+        if( ! is.null(warn)){
+            base::options(warning.length = 8170)
+            on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
+        }
+        on.exit(exp = base::options(warning.length = ini.warning.length), add = TRUE)
+        if(export == TRUE){
+            save(output, file = paste0(res.path, "/fun_test_1", ifelse(total.comp.nb == 1L, ".RData", paste0("-", total.comp.nb, ".RData"))))
+            table.out <- as.matrix(output$data)
+            table.out <- gsub(table.out, pattern = "\n", replacement = "  ")
+            write.table(table.out, file = paste0(res.path, "/table_from_fun_test_1", ifelse(total.comp.nb == 1L, ".txt", paste0("-", total.comp.nb, ".txt"))), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t", eol = "\n", na = "")
+        }else{
+            return(output)
+        }
+    }
+    # after return() ?
+    end.date <- Sys.time()
+    end.time <- as.numeric(end.date)
+    total.lapse <- round(lubridate::seconds_to_period(end.time - ini.time))
+    cat(paste0("fun_test JOB END\n\nTIME: ", end.date, "\n\nTOTAL TIME LAPSE: ", total.lapse, "\n\n\n"))
 }
 
 
@@ -2674,74 +2674,74 @@ cat(paste0("fun_test JOB END\n\nTIME: ", end.date, "\n\nTOTAL TIME LAPSE: ", tot
 
 
 fun_name_change <- function(data1, data2, added.string = "_modif"){
-# AIM
-# this function allow to check if a vector of character strings, like column names of a data frame, has elements present in another vector (vector of reserved words or column names of another data frame before merging)
-# ARGUMENTS
-# data1: vector of character strings to check and modify
-# data2: reference vector of character strings
-# added.string: string added at the end of the modified string in data1 if present in data2
-# RETURN
-# a list containing
-# $data: the modified data1 (in the same order as in the initial data1)
-# $ini: the initial elements before modification. NULL if no modification
-# $post: the modified elements in the same order as in ini. NULL if no modification
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# obs1 <- c("A", "B", "C", "D") ; obs2 <- c("A", "C") ; fun_name_change(obs1, obs2)
-# obs1 <- c("A", "B", "C", "C_modif1", "D") ; obs2 <- c("A", "A_modif1", "C") ; fun_name_change(obs1, obs2) # the function checks that the new names are neither in obs1 nor in obs2 (increment the number after the added string)
-# DEBUGGING
-# data1 = c("A", "B", "C", "D") ; data2 <- c("A", "C") ; added.string = "_modif" # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = data1, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = data2, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = added.string, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-ini <- NULL
-post <- NULL
-if(any(data1 %in% data2)){
-tempo.names <- data1[data1 %in% data2]
-ini <- NULL
-post <- NULL
-for(i2 in 1:length(tempo.names)){
-count <- 0
-tempo <- tempo.names[i2]
-while(any(tempo %in% data2) | any(tempo %in% data1)){
-count <- count + 1
-tempo <- paste0(tempo.names[i2], "_modif", count)
-}
-data1[data1 %in% tempo.names[i2]] <- paste0(tempo.names[i2], "_modif", count)
-if(count != 0){
-ini <- c(ini, tempo.names[i2])
-post <- c(post, paste0(tempo.names[i2], "_modif", count))
-}
-}
-data <- data1
-}else{
-data <- data1
-}
-output <- list(data = data, ini = ini, post = post)
-return(output)
+    # AIM
+    # this function allow to check if a vector of character strings, like column names of a data frame, has elements present in another vector (vector of reserved words or column names of another data frame before merging)
+    # ARGUMENTS
+    # data1: vector of character strings to check and modify
+    # data2: reference vector of character strings
+    # added.string: string added at the end of the modified string in data1 if present in data2
+    # RETURN
+    # a list containing
+    # $data: the modified data1 (in the same order as in the initial data1)
+    # $ini: the initial elements before modification. NULL if no modification
+    # $post: the modified elements in the same order as in ini. NULL if no modification
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # obs1 <- c("A", "B", "C", "D") ; obs2 <- c("A", "C") ; fun_name_change(obs1, obs2)
+    # obs1 <- c("A", "B", "C", "C_modif1", "D") ; obs2 <- c("A", "A_modif1", "C") ; fun_name_change(obs1, obs2) # the function checks that the new names are neither in obs1 nor in obs2 (increment the number after the added string)
+    # DEBUGGING
+    # data1 = c("A", "B", "C", "D") ; data2 <- c("A", "C") ; added.string = "_modif" # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = data1, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = data2, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = added.string, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    ini <- NULL
+    post <- NULL
+    if(any(data1 %in% data2)){
+        tempo.names <- data1[data1 %in% data2]
+        ini <- NULL
+        post <- NULL
+        for(i2 in 1:length(tempo.names)){
+            count <- 0
+            tempo <- tempo.names[i2]
+            while(any(tempo %in% data2) | any(tempo %in% data1)){
+                count <- count + 1
+                tempo <- paste0(tempo.names[i2], "_modif", count)
+            }
+            data1[data1 %in% tempo.names[i2]] <- paste0(tempo.names[i2], "_modif", count)
+            if(count != 0){
+                ini <- c(ini, tempo.names[i2])
+                post <- c(post, paste0(tempo.names[i2], "_modif", count))
+            }
+        }
+        data <- data1
+    }else{
+        data <- data1
+    }
+    output <- list(data = data, ini = ini, post = post)
+    return(output)
 }
 
 
@@ -2749,123 +2749,123 @@ return(output)
 
 
 fun_df_remod <- function(
-data, 
-quanti.col.name = "quanti", 
-quali.col.name = "quali"
+    data, 
+    quanti.col.name = "quanti", 
+    quali.col.name = "quali"
 ){
-# AIM
-# if the data frame is made of n numeric columns, a new data frame is created, with the 1st column gathering all the numeric values, and the 2nd column being the name of the columns of the initial data frame. If row names were present in the initial data frame, then a new ini_rowname column is added with the names of the rows
-
- 
-# If the data frame is made of one numeric column and one character or factor column, a new data frame is created, with the new columns corresponding to the split numeric values (according to the character column). NA are added a the end of each column to have the same number of rows. BEWARE: in such data frame, rows are not individuals. This means that in the example below, values 10 and 20 are associated on the same row but that means nothing in term of association
-
- 
-
-# ARGUMENTS
-# data: data frame to convert
-# quanti.col.name: optional name for the quanti column of the new data frame
-# quali.col.name: optional name for the quali column of the new data frame
-# RETURN
-# the modified data frame
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# obs <- data.frame(col1 = (1:4)*10, col2 = c("A", "B", "A", "A"), stringsAsFactors = TRUE) ; obs ; fun_df_remod(obs)
-# obs <- data.frame(col1 = (1:4)*10, col2 = 5:8, stringsAsFactors = TRUE) ; obs ; fun_df_remod(obs, quanti.col.name = "quanti", quali.col.name = "quali")
-# obs <- data.frame(col1 = (1:4)*10, col2 = 5:8, stringsAsFactors = TRUE) ; rownames(obs) <- paste0("row", 1:4) ; obs ; fun_df_remod(obs, quanti.col.name = "quanti", quali.col.name = "quali")
-# DEBUGGING
-# data = data.frame(a = 1:3, b = 4:6, stringsAsFactors = TRUE) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
-# data = data.frame(a = 1:3, b = 4:6, c = 11:13, stringsAsFactors = TRUE) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
-# data = data.frame(a = 1:3, b = letters[1:3], stringsAsFactors = TRUE) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
-# data = data.frame(a = 1:3, b = letters[1:3], stringsAsFactors = TRUE) ; quanti.col.name = "TEST" ; quali.col.name = "quali" # for function debugging
-# data = data.frame(b = letters[1:3], a = 1:3, stringsAsFactors = TRUE) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
-# data = data.frame(b = c("e", "e", "h"), a = 1:3, stringsAsFactors = TRUE) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-# argument checking without fun_check()
-if( ! any(class(data) %in% "data.frame")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data ARGUMENT MUST BE A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end argument checking without fun_check()
-# argument checking with fun_check()
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = quanti.col.name, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = quali.col.name, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end argument checking with fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-tempo.factor <- unlist(lapply(data, class))
-for(i in 1:length(tempo.factor)){ # convert factor columns as character
-if(all(tempo.factor[i] == "factor")){
-data[, i] <- as.character(data[, i])
-}
-}
-tempo.factor <- unlist(lapply(data, mode))
-if(length(data) == 2L){
-if( ! ((base::mode(data[, 1]) == "character" & base::mode(data[, 2]) == "numeric") | base::mode(data[, 2]) == "character" & base::mode(data[, 1]) == "numeric" | base::mode(data[, 2]) == "numeric" & base::mode(data[, 1]) == "numeric") ){
-tempo.cat <- paste0("ERROR IN ", function.name, ": IF data ARGUMENT IS A DATA FRAME MADE OF 2 COLUMNS, EITHER A COLUMN MUST BE NUMERIC AND THE OTHER CHARACTER, OR THE TWO COLUMNS MUST BE NUMERIC")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if((base::mode(data[, 1]) == "character" | base::mode(data[, 2]) == "character") & (quanti.col.name != "quanti" | quali.col.name != "quali")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": IMPROPER quanti.col.name OR quali.col.name RESETTINGS. THESE ARGUMENTS ARE RESERVED FOR DATA FRAMES MADE OF n NUMERIC COLUMNS ONLY")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}else{
-if( ! all(tempo.factor %in% "numeric")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": IF data ARGUMENT IS A DATA FRAME MADE OF ONE COLUMN, OR MORE THAN 2 COLUMNS, THESE COLUMNS MUST BE NUMERIC")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if(( ! any(tempo.factor %in% "character")) & is.null(names(data))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": NUMERIC DATA FRAME in the data ARGUMENT MUST HAVE COLUMN NAMES")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(all(tempo.factor %in% "numeric")){ # transfo 1
-quanti <- NULL
-for(i in 1:length(data)){
-quanti <-c(quanti, data[, i])
-}
-quali <- rep(names(data), each = nrow(data))
-output.data <- data.frame(quanti, quali, stringsAsFactors = TRUE, check.names = FALSE)
-names(output.data) <- c(quanti.col.name, quali.col.name)
-# add the ini_rowname column
-ini.rownames <- rownames(data)
-tempo.data <- data
-rownames(tempo.data) <- NULL
-null.rownames <- (tempo.data)
-if( ! identical(ini.rownames, null.rownames)){
-ini_rowname <- rep(ini.rownames, times = ncol(data))
-output.data <- cbind(output.data, ini_rowname, stringsAsFactors = TRUE)
-}
-}else{ # transfo 2
-if(class(data[, 1]) == "character"){
-data <- cbind(data[2], data[1], stringsAsFactors = TRUE)
-}
-nc.max <- max(table(data[, 2])) # effectif maximum des classes
-nb.na <- nc.max - table(data[,2]) # nombre de NA à ajouter pour réaliser la data frame
-tempo<-split(data[, 1], data[, 2])
-for(i in 1:length(tempo)){tempo[[i]] <- append(tempo[[i]], rep(NA, nb.na[i]))} # des NA doivent être ajoutés lorsque les effectifs sont différents entre les classes. C'est uniquement pour que chaque colonne ait le même nombre de lignes
-output.data<-data.frame(tempo, stringsAsFactors = TRUE, check.names = FALSE)
-}
-return(output.data)
+    # AIM
+    # if the data frame is made of n numeric columns, a new data frame is created, with the 1st column gathering all the numeric values, and the 2nd column being the name of the columns of the initial data frame. If row names were present in the initial data frame, then a new ini_rowname column is added with the names of the rows
+    
+    
+    # If the data frame is made of one numeric column and one character or factor column, a new data frame is created, with the new columns corresponding to the split numeric values (according to the character column). NA are added a the end of each column to have the same number of rows. BEWARE: in such data frame, rows are not individuals. This means that in the example below, values 10 and 20 are associated on the same row but that means nothing in term of association
+    
+    
+    
+    # ARGUMENTS
+    # data: data frame to convert
+    # quanti.col.name: optional name for the quanti column of the new data frame
+    # quali.col.name: optional name for the quali column of the new data frame
+    # RETURN
+    # the modified data frame
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # obs <- data.frame(col1 = (1:4)*10, col2 = c("A", "B", "A", "A"), stringsAsFactors = TRUE) ; obs ; fun_df_remod(obs)
+    # obs <- data.frame(col1 = (1:4)*10, col2 = 5:8, stringsAsFactors = TRUE) ; obs ; fun_df_remod(obs, quanti.col.name = "quanti", quali.col.name = "quali")
+    # obs <- data.frame(col1 = (1:4)*10, col2 = 5:8, stringsAsFactors = TRUE) ; rownames(obs) <- paste0("row", 1:4) ; obs ; fun_df_remod(obs, quanti.col.name = "quanti", quali.col.name = "quali")
+    # DEBUGGING
+    # data = data.frame(a = 1:3, b = 4:6, stringsAsFactors = TRUE) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
+    # data = data.frame(a = 1:3, b = 4:6, c = 11:13, stringsAsFactors = TRUE) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
+    # data = data.frame(a = 1:3, b = letters[1:3], stringsAsFactors = TRUE) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
+    # data = data.frame(a = 1:3, b = letters[1:3], stringsAsFactors = TRUE) ; quanti.col.name = "TEST" ; quali.col.name = "quali" # for function debugging
+    # data = data.frame(b = letters[1:3], a = 1:3, stringsAsFactors = TRUE) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
+    # data = data.frame(b = c("e", "e", "h"), a = 1:3, stringsAsFactors = TRUE) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    # argument checking without fun_check()
+    if( ! any(class(data) %in% "data.frame")){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": THE data ARGUMENT MUST BE A DATA FRAME")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end argument checking without fun_check()
+    # argument checking with fun_check()
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = quanti.col.name, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = quali.col.name, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end argument checking with fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    tempo.factor <- unlist(lapply(data, class))
+    for(i in 1:length(tempo.factor)){ # convert factor columns as character
+        if(all(tempo.factor[i] == "factor")){
+            data[, i] <- as.character(data[, i])
+        }
+    }
+    tempo.factor <- unlist(lapply(data, mode))
+    if(length(data) == 2L){
+        if( ! ((base::mode(data[, 1]) == "character" & base::mode(data[, 2]) == "numeric") | base::mode(data[, 2]) == "character" & base::mode(data[, 1]) == "numeric" | base::mode(data[, 2]) == "numeric" & base::mode(data[, 1]) == "numeric") ){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": IF data ARGUMENT IS A DATA FRAME MADE OF 2 COLUMNS, EITHER A COLUMN MUST BE NUMERIC AND THE OTHER CHARACTER, OR THE TWO COLUMNS MUST BE NUMERIC")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if((base::mode(data[, 1]) == "character" | base::mode(data[, 2]) == "character") & (quanti.col.name != "quanti" | quali.col.name != "quali")){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": IMPROPER quanti.col.name OR quali.col.name RESETTINGS. THESE ARGUMENTS ARE RESERVED FOR DATA FRAMES MADE OF n NUMERIC COLUMNS ONLY")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }else{
+        if( ! all(tempo.factor %in% "numeric")){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": IF data ARGUMENT IS A DATA FRAME MADE OF ONE COLUMN, OR MORE THAN 2 COLUMNS, THESE COLUMNS MUST BE NUMERIC")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if(( ! any(tempo.factor %in% "character")) & is.null(names(data))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": NUMERIC DATA FRAME in the data ARGUMENT MUST HAVE COLUMN NAMES")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(all(tempo.factor %in% "numeric")){ # transfo 1
+        quanti <- NULL
+        for(i in 1:length(data)){
+            quanti <-c(quanti, data[, i])
+        }
+        quali <- rep(names(data), each = nrow(data))
+        output.data <- data.frame(quanti, quali, stringsAsFactors = TRUE, check.names = FALSE)
+        names(output.data) <- c(quanti.col.name, quali.col.name)
+        # add the ini_rowname column
+        ini.rownames <- rownames(data)
+        tempo.data <- data
+        rownames(tempo.data) <- NULL
+        null.rownames <- (tempo.data)
+        if( ! identical(ini.rownames, null.rownames)){
+            ini_rowname <- rep(ini.rownames, times = ncol(data))
+            output.data <- cbind(output.data, ini_rowname, stringsAsFactors = TRUE)
+        }
+    }else{ # transfo 2
+        if(class(data[, 1]) == "character"){
+            data <- cbind(data[2], data[1], stringsAsFactors = TRUE)
+        }
+        nc.max <- max(table(data[, 2])) # effectif maximum des classes
+        nb.na <- nc.max - table(data[,2]) # nombre de NA à ajouter pour réaliser la data frame
+        tempo<-split(data[, 1], data[, 2])
+        for(i in 1:length(tempo)){tempo[[i]] <- append(tempo[[i]], rep(NA, nb.na[i]))} # des NA doivent être ajoutés lorsque les effectifs sont différents entre les classes. C'est uniquement pour que chaque colonne ait le même nombre de lignes
+        output.data<-data.frame(tempo, stringsAsFactors = TRUE, check.names = FALSE)
+    }
+    return(output.data)
 }
 
 
@@ -2875,85 +2875,85 @@ return(output.data)
 
 
 fun_round <- function(data, dec.nb = 2, after.lead.zero = TRUE){
-# AIM
-# round a vector of values, if decimal, with the desired number of decimal digits after the decimal leading zeros
-# WARNINGS
-# Work well with numbers as character strings, but not always with numerical numbers because of the floating point
-# Numeric values are really truncated from a part of their decimal digits, whatever options(digits) settings
-# See ?.Machine or https://stackoverflow.com/questions/5173692/how-to-return-number-of-decimal-places-in-r, with the interexting formula: abs(x - round(x)) > .Machine$double.eps^0.5
-# ARGUMENTS
-# data: a vector of numbers (numeric or character mode)
-# dec.nb: number of required decimal digits
-# after.lead.zero: logical. If FALSE, rounding is performed for all the decimal numbers, whatever the leading zeros (e.g., 0.123 -> 0.12 and 0.00128 -> 0.00). If TRUE, dec.nb are taken after the leading zeros (e.g., 0.123 -> 0.12 and 0.00128 -> 0.0013)
-# RETURN
-# the modified vector
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# ini.options <- options()$digits ; options(digits = 8) ; cat(fun_round(data = c(NA, 10, 100.001, 333.0001254, 12312.1235), dec.nb = 2, after.lead.zero = FALSE), "\n\n") ; options(digits = ini.options)
-# ini.options <- options()$digits ; options(digits = 8) ; cat(fun_round(data = c(NA, 10, 100.001, 333.0001254, 12312.1235), dec.nb = 2, after.lead.zero = TRUE), "\n\n") ; options(digits = ini.options)
-# ini.options <- options()$digits ; options(digits = 8) ; cat(fun_round(data = c(NA, "10", "100.001", "333.0001254", "12312.1235"), dec.nb = 2, after.lead.zero = FALSE), "\n\n") ; options(digits = ini.options)
-# ini.options <- options()$digits ; options(digits = 8) ; cat(fun_round(data = c(NA, "10", "100.001", "333.0001254", "12312.1235"), dec.nb = 2, after.lead.zero = TRUE), "\n\n") ; options(digits = ini.options)
-# DEBUGGING
-# data = data = c(10, 100.001, 333.0001254, 12312.1235) ; dec.nb = 2 ; after.lead.zero = FALSE # # for function debugging
-# data = data = c("10", "100.001", "333.0001254", "12312.1235") ; dec.nb = 2 ; after.lead.zero = TRUE # # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-# argument checking without fun_check()
-if( ! (all(typeof(data) == "character") | all(typeof(data) == "double") | all(typeof(data) == "integer"))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data ARGUMENT MUST BE A VECTOR OF NUMBERS (IN NUMERIC OR CHARACTER MODE)")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end argument checking without fun_check()
-# argument checking with fun_check()
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = data, class = "vector", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = dec.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = after.lead.zero, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end argument checking with fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-tempo <- grepl(x = data, pattern = "\\.") # detection of decimal numbers
-ini.mode <- base::mode(data)
-data <- as.character(data) # to really truncate decimal digits
-for(i in 1:length(data)){ # scan all the numbers of the vector
-if(tempo[i] == TRUE){ # means decimal number
-if(after.lead.zero == TRUE){
-zero.pos <- unlist(gregexpr(text=data[i], pattern = 0)) # recover all the position of the zeros in the number. -1 if no zeros (do not record the leading and trailing zeros)
-}else{
-zero.pos <- -1 # -1 as if no zero
-}
-dot.pos <- unlist(gregexpr(text=data[i], pattern = "\\.")) # recover all the position of the zeros in the number
-digit.pos <- unlist(gregexpr(text=data[i], pattern = "[[:digit:]]")) # recover all the position of the digits in the number
-dec.pos <- digit.pos[digit.pos > dot.pos]
-count <- 0
-while((dot.pos + count + 1) %in% zero.pos & (dot.pos + count + 1) <= max(dec.pos) & (count + dec.nb) < length(dec.pos)){ # count the number of leading zeros in the decimal part
-count <- count + 1
-}
-data[i] <- formatC(as.numeric(data[i]), digits = (count + dec.nb), format = "f")
-}
-}
-if(ini.mode != "character"){
-data <- as.numeric(data)
-}
-return(data)
+    # AIM
+    # round a vector of values, if decimal, with the desired number of decimal digits after the decimal leading zeros
+    # WARNINGS
+    # Work well with numbers as character strings, but not always with numerical numbers because of the floating point
+    # Numeric values are really truncated from a part of their decimal digits, whatever options(digits) settings
+    # See ?.Machine or https://stackoverflow.com/questions/5173692/how-to-return-number-of-decimal-places-in-r, with the interexting formula: abs(x - round(x)) > .Machine$double.eps^0.5
+    # ARGUMENTS
+    # data: a vector of numbers (numeric or character mode)
+    # dec.nb: number of required decimal digits
+    # after.lead.zero: logical. If FALSE, rounding is performed for all the decimal numbers, whatever the leading zeros (e.g., 0.123 -> 0.12 and 0.00128 -> 0.00). If TRUE, dec.nb are taken after the leading zeros (e.g., 0.123 -> 0.12 and 0.00128 -> 0.0013)
+    # RETURN
+    # the modified vector
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # ini.options <- options()$digits ; options(digits = 8) ; cat(fun_round(data = c(NA, 10, 100.001, 333.0001254, 12312.1235), dec.nb = 2, after.lead.zero = FALSE), "\n\n") ; options(digits = ini.options)
+    # ini.options <- options()$digits ; options(digits = 8) ; cat(fun_round(data = c(NA, 10, 100.001, 333.0001254, 12312.1235), dec.nb = 2, after.lead.zero = TRUE), "\n\n") ; options(digits = ini.options)
+    # ini.options <- options()$digits ; options(digits = 8) ; cat(fun_round(data = c(NA, "10", "100.001", "333.0001254", "12312.1235"), dec.nb = 2, after.lead.zero = FALSE), "\n\n") ; options(digits = ini.options)
+    # ini.options <- options()$digits ; options(digits = 8) ; cat(fun_round(data = c(NA, "10", "100.001", "333.0001254", "12312.1235"), dec.nb = 2, after.lead.zero = TRUE), "\n\n") ; options(digits = ini.options)
+    # DEBUGGING
+    # data = data = c(10, 100.001, 333.0001254, 12312.1235) ; dec.nb = 2 ; after.lead.zero = FALSE # # for function debugging
+    # data = data = c("10", "100.001", "333.0001254", "12312.1235") ; dec.nb = 2 ; after.lead.zero = TRUE # # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    # argument checking without fun_check()
+    if( ! (all(typeof(data) == "character") | all(typeof(data) == "double") | all(typeof(data) == "integer"))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": data ARGUMENT MUST BE A VECTOR OF NUMBERS (IN NUMERIC OR CHARACTER MODE)")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end argument checking without fun_check()
+    # argument checking with fun_check()
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = data, class = "vector", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = dec.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = after.lead.zero, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end argument checking with fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    tempo <- grepl(x = data, pattern = "\\.") # detection of decimal numbers
+    ini.mode <- base::mode(data)
+    data <- as.character(data) # to really truncate decimal digits
+    for(i in 1:length(data)){ # scan all the numbers of the vector
+        if(tempo[i] == TRUE){ # means decimal number
+            if(after.lead.zero == TRUE){
+                zero.pos <- unlist(gregexpr(text=data[i], pattern = 0)) # recover all the position of the zeros in the number. -1 if no zeros (do not record the leading and trailing zeros)
+            }else{
+                zero.pos <- -1 # -1 as if no zero
+            }
+            dot.pos <- unlist(gregexpr(text=data[i], pattern = "\\.")) # recover all the position of the zeros in the number
+            digit.pos <- unlist(gregexpr(text=data[i], pattern = "[[:digit:]]")) # recover all the position of the digits in the number
+            dec.pos <- digit.pos[digit.pos > dot.pos]
+            count <- 0
+            while((dot.pos + count + 1) %in% zero.pos & (dot.pos + count + 1) <= max(dec.pos) & (count + dec.nb) < length(dec.pos)){ # count the number of leading zeros in the decimal part
+                count <- count + 1
+            }
+            data[i] <- formatC(as.numeric(data[i]), digits = (count + dec.nb), format = "f")
+        }
+    }
+    if(ini.mode != "character"){
+        data <- as.numeric(data)
+    }
+    return(data)
 }
 
 
@@ -2961,46 +2961,46 @@ return(data)
 
 
 fun_mat_rotate <- function(data){
-# AIM
-# 90° clockwise matrix rotation
-# applied twice, the function provide the mirror matrix, according to vertical and horizontal symmetry
-# ARGUMENTS
-# data: matrix (matrix class)
-# RETURN
-# the modified matrix
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# obs <- matrix(1:10, ncol = 1) ; obs ; fun_mat_rotate(obs)
-# obs <- matrix(LETTERS[1:10], ncol = 5) ; obs ; fun_mat_rotate(obs)
-# DEBUGGING
-# data = matrix(1:10, ncol = 1)
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = data, class = "matrix", fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-for (i in 1:ncol(data)){data[,i] <- rev(data[,i])}
-data <- t(data)
-return(data)
+    # AIM
+    # 90° clockwise matrix rotation
+    # applied twice, the function provide the mirror matrix, according to vertical and horizontal symmetry
+    # ARGUMENTS
+    # data: matrix (matrix class)
+    # RETURN
+    # the modified matrix
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # obs <- matrix(1:10, ncol = 1) ; obs ; fun_mat_rotate(obs)
+    # obs <- matrix(LETTERS[1:10], ncol = 5) ; obs ; fun_mat_rotate(obs)
+    # DEBUGGING
+    # data = matrix(1:10, ncol = 1)
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = data, class = "matrix", fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    for (i in 1:ncol(data)){data[,i] <- rev(data[,i])}
+    data <- t(data)
+    return(data)
 }
 
 
@@ -3008,136 +3008,136 @@ return(data)
 
 
 fun_mat_num2color <- function(
-mat1, 
-mat.hsv.h = TRUE, 
-notch = 1, 
-s = 1, 
-v = 1, 
-forced.color = NULL
+    mat1, 
+    mat.hsv.h = TRUE, 
+    notch = 1, 
+    s = 1, 
+    v = 1, 
+    forced.color = NULL
 ){
-# AIM
-# convert a matrix made of numbers into a hexadecimal matrix for rgb colorization
-# ARGUMENTS:
-# mat1: matrix 1 of non negative numerical values that has to be colored (matrix class). NA allowed
-# mat.hsv.h: logical. Is mat1 the h of hsv colors ? (if TRUE, mat1 must be between zero and 1). If FALSE, mat1 must be made of positive integer values without 0
-# notch: single value between 0 and 1 to shift the successive colors on the hsv circle by + notch
-# s: s argument of hsv(). Must be between 0 and 1
-# v: v argument of hsv(). Must be between 0 and 1
-# forced.color: Must be NULL or hexadecimal color code or name given by colors(). The first minimal values of mat1 will be these colors. All the color of mat1 can be forced using this argument
-# RETURN
-# a list containing:
-# $mat1.name: name of mat1
-# $colored.mat: colors of mat1 in hexa
-# $problem: logical. Is any colors of forced.color overlap the colors designed by the function. NULL if forced.color = NULL
-# $text.problem: text when overlapping colors. NULL if forced.color = NULL or problem == FALSE
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# mat1 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; dimnames(mat1) <- list(LETTERS[1:4], letters[1:2]) ; fun_mat_num2color(mat1, mat.hsv.h = FALSE, notch = 1, s = 1, v = 1, forced.color = NULL)
-# DEBUGGING
-# mat1 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; dimnames(mat1) <- list(LETTERS[1:4], letters[1:2]); mat.hsv.h = FALSE ; notch = 1 ; s = 1 ; v = 1 ; forced.color = c(hsv(1,1,1), hsv(0,0,0)) # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-# argument checking with fun_check()
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = mat1, mode = "numeric", class = "matrix", na.contain = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = mat.hsv.h, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = notch, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = s, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = v, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end argument checking with fun_check()
-# argument checking without fun_check()
-if(mat.hsv.h == TRUE & fun_check(data = mat1, mode = "numeric", prop = TRUE)$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": mat1 ARGUMENT MUST BE A MATRIX OF PROPORTIONS SINCE THE mat.hsv.h ARGUMENT IS SET TO TRUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! is.null(forced.color)){
-tempo <- fun_check(data = forced.color, class = "character")
-if(any(tempo$problem == TRUE)){
-paste0("\n\n================\n\n", paste(tempo$text[tempo$problem], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! all(forced.color %in% colors() | grepl(pattern = "^#", forced.color))){ # check that all strings of forced.color start by #
-tempo.cat <- paste0("ERROR IN ", function.name, ": forced.color ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors()")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end argument checking without fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-problem <- NULL
-text.problem <- NULL
-mat1.name <- deparse(substitute(mat1))
-# change the scale of the plotted matrix
-if(mat.hsv.h == TRUE){
-if(any(min(mat1, na.rm = TRUE) < 0 | max(mat1, na.rm = TRUE) > 1, na.rm = TRUE)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": mat1 MUST BE MADE OF VALUES BETWEEN 0 AND 1 BECAUSE mat.hsv.h ARGUMENT SET TO TRUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}else{
-if(any(mat1 - floor(mat1) > 0, na.rm = TRUE) | any(mat1 == 0L, na.rm = TRUE)){ # no need of isTRUE(all.equal()) because we do not require approx here but strictly 0, thus == is ok
-tempo.cat <- paste0("ERROR IN ", function.name, ": mat1 MUST BE MADE OF INTEGER VALUES WITHOUT 0 BECAUSE mat.hsv.h ARGUMENT SET TO FALSE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-mat1 <- mat1 / max(mat1, na.rm = TRUE)
-}
-}
-if(notch != 1){
-different.color <- unique(as.vector(mat1))
-different.color <- different.color[ ! is.na(different.color)]
-tempo.different.color <- different.color + c(0, cumsum(rep(notch, length(different.color) - 1)))
-tempo.different.color <- tempo.different.color - floor(tempo.different.color)
-if(any(duplicated(tempo.different.color) == TRUE)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": DUPLICATED VALUES AFTER USING notch (", paste(tempo.different.color[duplicated(tempo.different.color)], collapse = " "), "). TRY ANOTHER notch VALUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(length(different.color) != length(tempo.different.color)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": LENGTH OF different.color (", paste(different.color, collapse = " "), ") DIFFERENT FROM LENGTH OF tempo.different.color (", paste(tempo.different.color, collapse = " "), ")")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-for(i in 1:length(different.color)){
-mat1[mat1 == different.color[i]] <- tempo.different.color[i] # no need of isTRUE(all.equal()) because different.color comes from mat1
-}
-}
-}
-if( ! is.null(forced.color)){
-hexa.values.to.change <- hsv(unique(sort(mat1))[1:length(forced.color)], s, v)
-}
-mat1[ ! is.na(mat1)] <- hsv(mat1[ ! is.na(mat1)], s, v)
-if( ! is.null(forced.color)){
-if(any(forced.color %in% mat1, na.rm = TRUE)){
-problem <- TRUE
-text.problem <- paste0("THE FOLLOWING COLORS WHERE INTRODUCED USING forced.color BUT WHERE ALREADY PRESENT IN THE COLORED MATRIX :", paste(forced.color[forced.color %in% mat1], collapse = " "))
-}else{
-problem <- FALSE
-}
-for(i in 1:length(hexa.values.to.change)){
-if( ! any(mat1 == hexa.values.to.change[i], na.rm = TRUE)){# no need of isTRUE(all.equal()) because character
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE ", hexa.values.to.change[i], " VALUE FROM hexa.values.to.change IS NOT REPRESENTED IN mat1 : ", paste(unique(as.vector(mat1)), collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-mat1[which(mat1 == hexa.values.to.change[i])] <- forced.color[i] # no need of isTRUE(all.equal()) because character
-}
-}
-}
-output <- list(mat1.name = mat1.name, colored.mat = mat1, problem = problem, text.problem = text.problem)
-return(output)
+    # AIM
+    # convert a matrix made of numbers into a hexadecimal matrix for rgb colorization
+    # ARGUMENTS:
+    # mat1: matrix 1 of non negative numerical values that has to be colored (matrix class). NA allowed
+    # mat.hsv.h: logical. Is mat1 the h of hsv colors ? (if TRUE, mat1 must be between zero and 1). If FALSE, mat1 must be made of positive integer values without 0
+    # notch: single value between 0 and 1 to shift the successive colors on the hsv circle by + notch
+    # s: s argument of hsv(). Must be between 0 and 1
+    # v: v argument of hsv(). Must be between 0 and 1
+    # forced.color: Must be NULL or hexadecimal color code or name given by colors(). The first minimal values of mat1 will be these colors. All the color of mat1 can be forced using this argument
+    # RETURN
+    # a list containing:
+    # $mat1.name: name of mat1
+    # $colored.mat: colors of mat1 in hexa
+    # $problem: logical. Is any colors of forced.color overlap the colors designed by the function. NULL if forced.color = NULL
+    # $text.problem: text when overlapping colors. NULL if forced.color = NULL or problem == FALSE
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # mat1 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; dimnames(mat1) <- list(LETTERS[1:4], letters[1:2]) ; fun_mat_num2color(mat1, mat.hsv.h = FALSE, notch = 1, s = 1, v = 1, forced.color = NULL)
+    # DEBUGGING
+    # mat1 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; dimnames(mat1) <- list(LETTERS[1:4], letters[1:2]); mat.hsv.h = FALSE ; notch = 1 ; s = 1 ; v = 1 ; forced.color = c(hsv(1,1,1), hsv(0,0,0)) # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    # argument checking with fun_check()
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = mat1, mode = "numeric", class = "matrix", na.contain = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = mat.hsv.h, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = notch, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = s, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = v, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end argument checking with fun_check()
+    # argument checking without fun_check()
+    if(mat.hsv.h == TRUE & fun_check(data = mat1, mode = "numeric", prop = TRUE)$problem == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": mat1 ARGUMENT MUST BE A MATRIX OF PROPORTIONS SINCE THE mat.hsv.h ARGUMENT IS SET TO TRUE")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! is.null(forced.color)){
+        tempo <- fun_check(data = forced.color, class = "character")
+        if(any(tempo$problem == TRUE)){
+            paste0("\n\n================\n\n", paste(tempo$text[tempo$problem], collapse = "\n"))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if( ! all(forced.color %in% colors() | grepl(pattern = "^#", forced.color))){ # check that all strings of forced.color start by #
+            tempo.cat <- paste0("ERROR IN ", function.name, ": forced.color ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors()")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # end argument checking without fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    problem <- NULL
+    text.problem <- NULL
+    mat1.name <- deparse(substitute(mat1))
+    # change the scale of the plotted matrix
+    if(mat.hsv.h == TRUE){
+        if(any(min(mat1, na.rm = TRUE) < 0 | max(mat1, na.rm = TRUE) > 1, na.rm = TRUE)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": mat1 MUST BE MADE OF VALUES BETWEEN 0 AND 1 BECAUSE mat.hsv.h ARGUMENT SET TO TRUE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }else{
+        if(any(mat1 - floor(mat1) > 0, na.rm = TRUE) | any(mat1 == 0L, na.rm = TRUE)){ # no need of isTRUE(all.equal()) because we do not require approx here but strictly 0, thus == is ok
+            tempo.cat <- paste0("ERROR IN ", function.name, ": mat1 MUST BE MADE OF INTEGER VALUES WITHOUT 0 BECAUSE mat.hsv.h ARGUMENT SET TO FALSE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            mat1 <- mat1 / max(mat1, na.rm = TRUE)
+        }
+    }
+    if(notch != 1){
+        different.color <- unique(as.vector(mat1))
+        different.color <- different.color[ ! is.na(different.color)]
+        tempo.different.color <- different.color + c(0, cumsum(rep(notch, length(different.color) - 1)))
+        tempo.different.color <- tempo.different.color - floor(tempo.different.color)
+        if(any(duplicated(tempo.different.color) == TRUE)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": DUPLICATED VALUES AFTER USING notch (", paste(tempo.different.color[duplicated(tempo.different.color)], collapse = " "), "). TRY ANOTHER notch VALUE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else if(length(different.color) != length(tempo.different.color)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": LENGTH OF different.color (", paste(different.color, collapse = " "), ") DIFFERENT FROM LENGTH OF tempo.different.color (", paste(tempo.different.color, collapse = " "), ")")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            for(i in 1:length(different.color)){
+                mat1[mat1 == different.color[i]] <- tempo.different.color[i] # no need of isTRUE(all.equal()) because different.color comes from mat1
+            }
+        }
+    }
+    if( ! is.null(forced.color)){
+        hexa.values.to.change <- hsv(unique(sort(mat1))[1:length(forced.color)], s, v)
+    }
+    mat1[ ! is.na(mat1)] <- hsv(mat1[ ! is.na(mat1)], s, v)
+    if( ! is.null(forced.color)){
+        if(any(forced.color %in% mat1, na.rm = TRUE)){
+            problem <- TRUE
+            text.problem <- paste0("THE FOLLOWING COLORS WHERE INTRODUCED USING forced.color BUT WHERE ALREADY PRESENT IN THE COLORED MATRIX :", paste(forced.color[forced.color %in% mat1], collapse = " "))
+        }else{
+            problem <- FALSE
+        }
+        for(i in 1:length(hexa.values.to.change)){
+            if( ! any(mat1 == hexa.values.to.change[i], na.rm = TRUE)){# no need of isTRUE(all.equal()) because character
+                tempo.cat <- paste0("ERROR IN ", function.name, ": THE ", hexa.values.to.change[i], " VALUE FROM hexa.values.to.change IS NOT REPRESENTED IN mat1 : ", paste(unique(as.vector(mat1)), collapse = " "))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }else{
+                mat1[which(mat1 == hexa.values.to.change[i])] <- forced.color[i] # no need of isTRUE(all.equal()) because character
+            }
+        }
+    }
+    output <- list(mat1.name = mat1.name, colored.mat = mat1, problem = problem, text.problem = text.problem)
+    return(output)
 }
 
 
@@ -3145,104 +3145,104 @@ return(output)
 
 
 fun_mat_op <- function(mat.list, kind.of.operation = "+"){
-# AIM
-# assemble several matrices of same dimensions by performing by case operation. For instance add the value of all the case 1 (row1 & column1) of the matrices and put it in the case 1 of a new matrix M, add the value of all the case 2 (row2 & column1) of the matrices and put it in the case 2 of a new matrix M, etc.
- 
-# c: case
-# i: row number
-# j: column number
-# k: matrix number
-# z: number of matrices
-# ARGUMENTS:
-# mat.list: list of matrices
-# kind.of.operation: either "+" (by case addition), "-" (by case subtraction) or "*" (by case multiplication)
-# RETURN
-# the assembled matrix, with row and/or column names only if all the matrices have identical row/column names
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# fun_comp_2d()
-# EXAMPLES
-# mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; fun_mat_op(mat.list = list(mat1, mat2), kind.of.operation = "+")
-# mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; fun_mat_op(mat.list = list(mat1, mat2), kind.of.operation = "*")
-# mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2, dimnames = list(LETTERS[1:4], c(NA, NA))) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; fun_mat_op(mat.list = list(mat1, mat2), kind.of.operation = "-")
-# mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2, dimnames = list(c("A1", "A2", "A3", "A4"), letters[1:2])) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; mat3 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; fun_mat_op(mat.list = list(mat1, mat2, mat3), kind.of.operation = "+")
-# DEBUGGING
-# mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; mat.list = list(mat1, mat2) ; kind.of.operation = "+" # for function debugging
-# mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2, dimnames = list(LETTERS[1:4], c(NA, NA))) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; mat.list = list(mat1, mat2) ; kind.of.operation = "*" # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_comp_2d() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-# argument checking with fun_check()
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = mat.list, class = "list", fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = kind.of.operation, options = c("+", "-", "*"), length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end argument checking with fun_check()
-# argument checking without fun_check()
-if(length(mat.list) < 2){
-tempo.cat <- paste0("ERROR IN ", function.name, ": mat.list ARGUMENT MUST BE A LIST CONTAINING AT LEAST 2 MATRICES")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-for(i1 in 1:length(mat.list)){
-tempo <- fun_check(data = mat.list[[i1]], class = "matrix", mode = "numeric", na.contain = TRUE)
-if(tempo$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ELEMENT ", i1, " OF mat.list ARGUMENT MUST BE A NUMERIC MATRIX")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-ident.row.names <- TRUE
-ident.col.names <- TRUE
-for(i1 in 2:length(mat.list)){
-tempo <- fun_comp_2d(data1 = mat.list[[1]], data2 = mat.list[[i1]])
-if(tempo$same.dim == FALSE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": MATRIX ", i1, " OF mat.list ARGUMENT MUST HAVE THE SAME DIMENSION (", paste(dim(mat.list[[i1]]), collapse = " "), ") THAN THE MATRIX 1 IN mat.list (", paste(dim(mat.list[[1]]), collapse = " "), ")")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! is.null(tempo$same.row.name)){
-if(tempo$same.row.name != TRUE){ # != TRUE to deal with NA
-ident.row.names <- FALSE
-}
-}
-if( ! is.null(tempo$same.col.name)){
-if(tempo$same.col.name != TRUE){ # != TRUE to deal with NA
-ident.col.names <- FALSE
-}
-}
-}
-# end argument checking without fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-output <- mat.list[[1]]
-for(i1 in 2:length(mat.list)){
-output <- get(kind.of.operation)(output, mat.list[[i1]]) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-}
-dimnames(output) <- NULL
-if(ident.row.names == TRUE){
-rownames(output) <- rownames(mat.list[[1]])
-}
-if(ident.col.names == TRUE){
-colnames(output) <- colnames(mat.list[[1]])
-}
-return(output)
+    # AIM
+    # assemble several matrices of same dimensions by performing by case operation. For instance add the value of all the case 1 (row1 & column1) of the matrices and put it in the case 1 of a new matrix M, add the value of all the case 2 (row2 & column1) of the matrices and put it in the case 2 of a new matrix M, etc.
+    
+    # c: case
+    # i: row number
+    # j: column number
+    # k: matrix number
+    # z: number of matrices
+    # ARGUMENTS:
+    # mat.list: list of matrices
+    # kind.of.operation: either "+" (by case addition), "-" (by case subtraction) or "*" (by case multiplication)
+    # RETURN
+    # the assembled matrix, with row and/or column names only if all the matrices have identical row/column names
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # fun_comp_2d()
+    # EXAMPLES
+    # mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; fun_mat_op(mat.list = list(mat1, mat2), kind.of.operation = "+")
+    # mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; fun_mat_op(mat.list = list(mat1, mat2), kind.of.operation = "*")
+    # mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2, dimnames = list(LETTERS[1:4], c(NA, NA))) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; fun_mat_op(mat.list = list(mat1, mat2), kind.of.operation = "-")
+    # mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2, dimnames = list(c("A1", "A2", "A3", "A4"), letters[1:2])) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; mat3 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; fun_mat_op(mat.list = list(mat1, mat2, mat3), kind.of.operation = "+")
+    # DEBUGGING
+    # mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; mat.list = list(mat1, mat2) ; kind.of.operation = "+" # for function debugging
+    # mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2, dimnames = list(LETTERS[1:4], c(NA, NA))) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; mat.list = list(mat1, mat2) ; kind.of.operation = "*" # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_comp_2d() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    # argument checking with fun_check()
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = mat.list, class = "list", fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = kind.of.operation, options = c("+", "-", "*"), length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end argument checking with fun_check()
+    # argument checking without fun_check()
+    if(length(mat.list) < 2){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": mat.list ARGUMENT MUST BE A LIST CONTAINING AT LEAST 2 MATRICES")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    for(i1 in 1:length(mat.list)){
+        tempo <- fun_check(data = mat.list[[i1]], class = "matrix", mode = "numeric", na.contain = TRUE)
+        if(tempo$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": ELEMENT ", i1, " OF mat.list ARGUMENT MUST BE A NUMERIC MATRIX")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    ident.row.names <- TRUE
+    ident.col.names <- TRUE
+    for(i1 in 2:length(mat.list)){
+        tempo <- fun_comp_2d(data1 = mat.list[[1]], data2 = mat.list[[i1]])
+        if(tempo$same.dim == FALSE){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": MATRIX ", i1, " OF mat.list ARGUMENT MUST HAVE THE SAME DIMENSION (", paste(dim(mat.list[[i1]]), collapse = " "), ") THAN THE MATRIX 1 IN mat.list (", paste(dim(mat.list[[1]]), collapse = " "), ")")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if( ! is.null(tempo$same.row.name)){
+            if(tempo$same.row.name != TRUE){ # != TRUE to deal with NA
+                ident.row.names <- FALSE
+            }
+        }
+        if( ! is.null(tempo$same.col.name)){
+            if(tempo$same.col.name != TRUE){ # != TRUE to deal with NA
+                ident.col.names <- FALSE
+            }
+        }
+    }
+    # end argument checking without fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    output <- mat.list[[1]]
+    for(i1 in 2:length(mat.list)){
+        output <- get(kind.of.operation)(output, mat.list[[i1]]) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
+    }
+    dimnames(output) <- NULL
+    if(ident.row.names == TRUE){
+        rownames(output) <- rownames(mat.list[[1]])
+    }
+    if(ident.col.names == TRUE){
+        colnames(output) <- colnames(mat.list[[1]])
+    }
+    return(output)
 }
 
 
@@ -3250,74 +3250,74 @@ return(output)
 
 
 fun_mat_inv <- function(mat){
-# AIM
-# return the inverse of a square matrix when solve() cannot
-# ARGUMENTS:
-# mat: a square numeric matrix without NULL, NA, Inf or single case (dimension 1, 1) of 0
-# RETURN
-# the inversed matrix
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# mat1 = matrix(c(1,1,1,2,1,5,9,8,9), ncol = 3) ; fun_mat_inv(mat = mat1) # use solve()
-# mat1 = matrix(c(0,0,0,0,0,0,0,0,0), ncol = 3) ; fun_mat_inv(mat = mat1) # use the trick
-# mat1 = matrix(c(1,1,1,2,Inf,5,9,8,9), ncol = 3) ; fun_mat_inv(mat = mat1)
-# mat1 = matrix(c(1,1,1,2,NA,5,9,8,9), ncol = 3) ; fun_mat_inv(mat = mat1)
-# mat1 = matrix(c(1,2), ncol = 1) ; fun_mat_inv(mat = mat1)
-# mat1 = matrix(0, ncol = 1) ; fun_mat_inv(mat = mat1)
-# mat1 = matrix(2, ncol = 1) ; fun_mat_inv(mat = mat1)
-# DEBUGGING
-# mat = matrix(c(1,1,1,2,1,5,9,8,9), ncol = 3) # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-# argument checking with fun_check()
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = mat, class = "matrix", mode = "numeric", fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end argument checking with fun_check()
-# argument checking without fun_check()
-if(ncol(mat) != nrow(mat)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT MUST BE A SQUARE MATRIX")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(mat %in% c(Inf, -Inf, NA))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT MUST BE A MATRIX WITHOUT Inf, -Inf OR NA")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(all(mat == 0L) & ncol(mat) == 1L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT CANNOT BE A SQUARE MATRIX MADE OF A SINGLE CASE OF 0")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end argument checking without fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-if(any(grepl(x = try(solve(mat), silent = TRUE)[], pattern = "[Ee]rror"))){
-tempo <- svd(mat)
-val.critique <- which(tempo$d < 10^-8)
-Diag.mod <- diag(1 / tempo$d)
-for(i in val.critique){
-Diag.mod[i, i] <- 0
-}
-return(tempo$v %*% Diag.mod %*% t(tempo$u))
-}else{
-return(solve(mat))
-}
+    # AIM
+    # return the inverse of a square matrix when solve() cannot
+    # ARGUMENTS:
+    # mat: a square numeric matrix without NULL, NA, Inf or single case (dimension 1, 1) of 0
+    # RETURN
+    # the inversed matrix
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # mat1 = matrix(c(1,1,1,2,1,5,9,8,9), ncol = 3) ; fun_mat_inv(mat = mat1) # use solve()
+    # mat1 = matrix(c(0,0,0,0,0,0,0,0,0), ncol = 3) ; fun_mat_inv(mat = mat1) # use the trick
+    # mat1 = matrix(c(1,1,1,2,Inf,5,9,8,9), ncol = 3) ; fun_mat_inv(mat = mat1)
+    # mat1 = matrix(c(1,1,1,2,NA,5,9,8,9), ncol = 3) ; fun_mat_inv(mat = mat1)
+    # mat1 = matrix(c(1,2), ncol = 1) ; fun_mat_inv(mat = mat1)
+    # mat1 = matrix(0, ncol = 1) ; fun_mat_inv(mat = mat1)
+    # mat1 = matrix(2, ncol = 1) ; fun_mat_inv(mat = mat1)
+    # DEBUGGING
+    # mat = matrix(c(1,1,1,2,1,5,9,8,9), ncol = 3) # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    # argument checking with fun_check()
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = mat, class = "matrix", mode = "numeric", fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end argument checking with fun_check()
+    # argument checking without fun_check()
+    if(ncol(mat) != nrow(mat)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT MUST BE A SQUARE MATRIX")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(any(mat %in% c(Inf, -Inf, NA))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT MUST BE A MATRIX WITHOUT Inf, -Inf OR NA")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(all(mat == 0L) & ncol(mat) == 1L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT CANNOT BE A SQUARE MATRIX MADE OF A SINGLE CASE OF 0")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end argument checking without fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    if(any(grepl(x = try(solve(mat), silent = TRUE)[], pattern = "[Ee]rror"))){
+        tempo <- svd(mat)
+        val.critique <- which(tempo$d < 10^-8)
+        Diag.mod <- diag(1 / tempo$d)
+        for(i in val.critique){
+            Diag.mod[i, i] <- 0
+        }
+        return(tempo$v %*% Diag.mod %*% t(tempo$u))
+    }else{
+        return(solve(mat))
+    }
 }
 
 
@@ -3325,155 +3325,155 @@ return(solve(mat))
 
 
 fun_mat_fill <- function(mat, empty.cell.string = 0, warn.print = FALSE){
-# AIM
-# detect the empty half part of a symmetric square matrix (either topleft, topright, bottomleft or bottomright)
-# fill this empty half part using the other symmetric half part of the matrix
-# WARNINGS
-# a plot verification using fun_gg_heatmap() is recommanded
-# ARGUMENTS:
-# mat: a numeric or character square matrix with the half part (according to the grand diagonal) filled with NA (any kind of matrix), "0" (character matrix) or 0 (numeric matrix) exclusively (not a mix of 0 and NA in the empty part)
-# empty.cell.string: a numeric, character or NA (no quotes) indicating what empty cells are filled with
-# warn.print: logical. Print warnings at the end of the execution? No print if no warning messages
-# RETURN
-# a list containing:
-# $mat: the filled matrix
-# $warn: the warning messages. Use cat() for proper display. NULL if no warning
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# mat1 = matrix(c(1,NA,NA,NA, 0,2,NA,NA, NA,3,4,NA, 5,6,7,8), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = NA, warn.print = TRUE) # bottomleft example
-# mat1 = matrix(c(1,1,1,2, 0,2,3,0, NA,3,0,0, 5,0,0,0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = NA, warn.print = TRUE) # error example
-# mat1 = matrix(c(1,1,1,2, 0,2,3,0, NA,3,0,0, 5,0,0,0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = 0, warn.print = TRUE) # bottomright example
-# mat1 = matrix(c(1,1,1,2, "a",2,3,NA, "a","a",0,0, "a","a","a",0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = "a", warn.print = TRUE) # topright example
-# mat1 = matrix(c(0,0,0,2, 0,0,3,0, 0,3,0,NA, 5,0,0,0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = 0, warn.print = TRUE) # topleft example
-# mat1 = matrix(c(0,0,0,2, 0,0,3,0, 0,3,0,0, 5,0,0,0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = 0, warn.print = TRUE) # error example
-# DEBUGGING
-# mat = matrix(c(1,NA,NA,NA, 0,2,NA,NA, NA,3,4,NA, 5,6,7,8), ncol = 4) ; empty.cell.string = NA ; warn.print = TRUE # for function debugging
-# mat = matrix(c(0,0,0,2, 0,0,3,0, 0,3,0,NA, 5,0,0,0), ncol = 4) ; empty.cell.string = 0 ; warn.print = TRUE # for function debugging # topleft example
-# mat = matrix(c(0,0,0,2, 0,0,3,0, 0,3,0,NA, 5,0,0,0), ncol = 4) ; empty.cell.string = NA ; warn.print = TRUE # for function debugging # topleft example
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-# argument checking with fun_check()
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = mat, class = "matrix", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = empty.cell.string, class = "vector", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end argument checking with fun_check()
-# argument checking without fun_check()
-if(ncol(mat) != nrow(mat)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT MUST BE A SQUARE MATRIX")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! (base::mode(mat) %in% c("numeric", "character"))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT MUST BE A NUMERIC OR CHARACTER MATRIX")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(nrow(mat) == 1L & ncol(mat) == 1L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT CANNOT BE A SQUARE MATRIX MADE OF A SINGLE CASE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(ifelse(is.na(empty.cell.string), ! any(is.na(mat)), ! any(mat == empty.cell.string, na.rm = TRUE))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT MATRIX MUST HAVE CELLS WITH THE EMPTY STRING SPECIFIED IN empty.cell.string ARGUMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end argument checking without fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-list.diag <- vector("list", length = nrow(mat) - 1) 
-for(i1 in 1:(nrow(mat) - 1)){
-list.diag[[i1]] <- numeric(length = nrow(mat) - i1) # list made of zero
-}
-sector <- c("topleft", "topright", "bottomright", "bottomleft")
-diag.scan <-c( # same order as sector. Recover each diag from center to corner
-"mat[as.matrix(as.data.frame(list(1:(nrow(mat) - i2), (ncol(mat) -i2):1), stringsAsFactors = TRUE))]", # topleft part
-"mat[as.matrix(as.data.frame(list(1:(nrow(mat) - i2), (1:ncol(mat))[-(1:i2)]), stringsAsFactors = TRUE))]", # topright part
-"mat[as.matrix(as.data.frame(list((1 + i2):nrow(mat), ncol(mat):(1 + i2)), stringsAsFactors = TRUE))]", # bottomright part
-"mat[as.matrix(as.data.frame(list((1 + i2):nrow(mat), 1:(ncol(mat) -i2)), stringsAsFactors = TRUE))]" # bottomleft part
-)
-# empty part detection
-empty.sector <- NULL
-full.sector <- NULL
-ini.warning.length <- options()$warning.length
-options(warning.length = 8170)
-warn <- NULL
-warn.count <- 0
-for(i1 in 1:length(sector)){
-tempo.list.diag <- list.diag
-for(i2 in 1:(nrow(mat) - 1)){
-tempo.list.diag[[i2]] <- eval(parse(text = diag.scan[i1]))
-if(ifelse(is.na(empty.cell.string), ! all(is.na(tempo.list.diag[[i2]])), ! (all(tempo.list.diag[[i2]] == empty.cell.string, na.rm = TRUE) & ! (is.na(all(tempo.list.diag[[i2]] == empty.cell.string, na.rm = FALSE)))))){ # I had to add this ! (is.na(all(tempo.list.diag[[i2]] == empty.cell.string, na.rm = FALSE))) because all(tempo.list.diag[[i2]] == empty.cell.string, na.rm = FALSE) gives NA and not FALSE if one NA in tempo.list.diag[[i2]] -> not good for if()
-full.sector <- c(full.sector, sector[i1])
-break
-}
-}
-if(i2 == nrow(mat) - 1){
-if(all(unlist(lapply(tempo.list.diag, FUN = function(x){if(is.na(empty.cell.string)){is.na(x)}else{x == empty.cell.string}})), na.rm = TRUE)){
-empty.sector <- c(empty.sector, sector[i1])
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") EMPTY SECTOR DETECTED ON THE ", toupper(sector[i1]), " CORNER, FULL OF ", empty.cell.string)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE ", toupper(sector[i1]), " SECTOR, DETECTED AS EMPTY, IS NOT? DIFFERENT VALUES IN THIS SECTOR:\n", paste(names(table(unlist(tempo.list.diag), useNA = "ifany")), collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-}
-# end empty part detection
-if(length(empty.sector) == 0L){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") ACCORDING TO empty.cell.string ARGUMENT (", empty.cell.string, "), mat ARGUMENT MATRIX HAS ZERO EMPTY HALF PART")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else{
-if(length(empty.sector) > 1){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ACCORDING TO empty.cell.string ARGUMENT (", empty.cell.string, "), mat ARGUMENT MATRIX HAS MORE THAN ONE EMPTY HALF PART (ACCORDING TO THE GRAND DIAGONAL): ", paste(empty.sector, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(any(full.sector %in% empty.sector, na.rm = TRUE)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE FUNCTION HAS DETECTED EMPTY AND NON EMPTY HALF PART IN THE SAME SECTOR: ", paste(full.sector[full.sector %in% empty.sector], collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(length(empty.sector) + length(full.sector)!= 4){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE FUNCTION HAS DETECTED MORE OR LESS SECTORS THAN 4:\nHALF SECTORS:", paste(empty.sector, collapse = " "), "\nFULL SECTORS:", paste(full.sector, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") ", toupper(empty.sector), " SECTOR HAS BEEN COMPLETED TO BECOME SYMMETRICAL")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# matrix filling
-for(i2 in 1:(nrow(mat) - 1)){
-if(empty.sector == "topleft"){
-eval(parse(text = paste0(diag.scan[1], " <- ", diag.scan[3])))
-}else if(empty.sector == "topright"){
-eval(parse(text = paste0(diag.scan[2], " <- ", diag.scan[4])))
-}else if(empty.sector == "bottomright"){
-eval(parse(text = paste0(diag.scan[3], " <- ", diag.scan[1])))
-}else if(empty.sector == "bottomleft"){
-eval(parse(text = paste0(diag.scan[4], " <- ", diag.scan[2])))
-}
-}
-# end matrix filling
-}
-if(warn.print == TRUE & ! is.null(warn)){
-on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
-}
-on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
-return(list(mat = mat, warn = warn))
+    # AIM
+    # detect the empty half part of a symmetric square matrix (either topleft, topright, bottomleft or bottomright)
+    # fill this empty half part using the other symmetric half part of the matrix
+    # WARNINGS
+    # a plot verification using fun_gg_heatmap() is recommanded
+    # ARGUMENTS:
+    # mat: a numeric or character square matrix with the half part (according to the grand diagonal) filled with NA (any kind of matrix), "0" (character matrix) or 0 (numeric matrix) exclusively (not a mix of 0 and NA in the empty part)
+    # empty.cell.string: a numeric, character or NA (no quotes) indicating what empty cells are filled with
+    # warn.print: logical. Print warnings at the end of the execution? No print if no warning messages
+    # RETURN
+    # a list containing:
+    # $mat: the filled matrix
+    # $warn: the warning messages. Use cat() for proper display. NULL if no warning
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # mat1 = matrix(c(1,NA,NA,NA, 0,2,NA,NA, NA,3,4,NA, 5,6,7,8), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = NA, warn.print = TRUE) # bottomleft example
+    # mat1 = matrix(c(1,1,1,2, 0,2,3,0, NA,3,0,0, 5,0,0,0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = NA, warn.print = TRUE) # error example
+    # mat1 = matrix(c(1,1,1,2, 0,2,3,0, NA,3,0,0, 5,0,0,0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = 0, warn.print = TRUE) # bottomright example
+    # mat1 = matrix(c(1,1,1,2, "a",2,3,NA, "a","a",0,0, "a","a","a",0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = "a", warn.print = TRUE) # topright example
+    # mat1 = matrix(c(0,0,0,2, 0,0,3,0, 0,3,0,NA, 5,0,0,0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = 0, warn.print = TRUE) # topleft example
+    # mat1 = matrix(c(0,0,0,2, 0,0,3,0, 0,3,0,0, 5,0,0,0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = 0, warn.print = TRUE) # error example
+    # DEBUGGING
+    # mat = matrix(c(1,NA,NA,NA, 0,2,NA,NA, NA,3,4,NA, 5,6,7,8), ncol = 4) ; empty.cell.string = NA ; warn.print = TRUE # for function debugging
+    # mat = matrix(c(0,0,0,2, 0,0,3,0, 0,3,0,NA, 5,0,0,0), ncol = 4) ; empty.cell.string = 0 ; warn.print = TRUE # for function debugging # topleft example
+    # mat = matrix(c(0,0,0,2, 0,0,3,0, 0,3,0,NA, 5,0,0,0), ncol = 4) ; empty.cell.string = NA ; warn.print = TRUE # for function debugging # topleft example
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    # argument checking with fun_check()
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = mat, class = "matrix", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = empty.cell.string, class = "vector", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end argument checking with fun_check()
+    # argument checking without fun_check()
+    if(ncol(mat) != nrow(mat)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT MUST BE A SQUARE MATRIX")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! (base::mode(mat) %in% c("numeric", "character"))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT MUST BE A NUMERIC OR CHARACTER MATRIX")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(nrow(mat) == 1L & ncol(mat) == 1L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT CANNOT BE A SQUARE MATRIX MADE OF A SINGLE CASE")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(ifelse(is.na(empty.cell.string), ! any(is.na(mat)), ! any(mat == empty.cell.string, na.rm = TRUE))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": mat ARGUMENT MATRIX MUST HAVE CELLS WITH THE EMPTY STRING SPECIFIED IN empty.cell.string ARGUMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end argument checking without fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    list.diag <- vector("list", length = nrow(mat) - 1) 
+    for(i1 in 1:(nrow(mat) - 1)){
+        list.diag[[i1]] <- numeric(length = nrow(mat) - i1) # list made of zero
+    }
+    sector <- c("topleft", "topright", "bottomright", "bottomleft")
+    diag.scan <-c( # same order as sector. Recover each diag from center to corner
+        "mat[as.matrix(as.data.frame(list(1:(nrow(mat) - i2), (ncol(mat) -i2):1), stringsAsFactors = TRUE))]", # topleft part
+        "mat[as.matrix(as.data.frame(list(1:(nrow(mat) - i2), (1:ncol(mat))[-(1:i2)]), stringsAsFactors = TRUE))]", # topright part
+        "mat[as.matrix(as.data.frame(list((1 + i2):nrow(mat), ncol(mat):(1 + i2)), stringsAsFactors = TRUE))]", # bottomright part
+        "mat[as.matrix(as.data.frame(list((1 + i2):nrow(mat), 1:(ncol(mat) -i2)), stringsAsFactors = TRUE))]" # bottomleft part
+    )
+    # empty part detection
+    empty.sector <- NULL
+    full.sector <- NULL
+    ini.warning.length <- options()$warning.length
+    options(warning.length = 8170)
+    warn <- NULL
+    warn.count <- 0
+    for(i1 in 1:length(sector)){
+        tempo.list.diag <- list.diag
+        for(i2 in 1:(nrow(mat) - 1)){
+            tempo.list.diag[[i2]] <- eval(parse(text = diag.scan[i1]))
+            if(ifelse(is.na(empty.cell.string), ! all(is.na(tempo.list.diag[[i2]])), ! (all(tempo.list.diag[[i2]] == empty.cell.string, na.rm = TRUE) & ! (is.na(all(tempo.list.diag[[i2]] == empty.cell.string, na.rm = FALSE)))))){ # I had to add this ! (is.na(all(tempo.list.diag[[i2]] == empty.cell.string, na.rm = FALSE))) because all(tempo.list.diag[[i2]] == empty.cell.string, na.rm = FALSE) gives NA and not FALSE if one NA in tempo.list.diag[[i2]] -> not good for if()
+                full.sector <- c(full.sector, sector[i1])
+                break
+            }
+        }
+        if(i2 == nrow(mat) - 1){
+            if(all(unlist(lapply(tempo.list.diag, FUN = function(x){if(is.na(empty.cell.string)){is.na(x)}else{x == empty.cell.string}})), na.rm = TRUE)){
+                empty.sector <- c(empty.sector, sector[i1])
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") EMPTY SECTOR DETECTED ON THE ", toupper(sector[i1]), " CORNER, FULL OF ", empty.cell.string)
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }else{
+                tempo.cat <- paste0("ERROR IN ", function.name, ": THE ", toupper(sector[i1]), " SECTOR, DETECTED AS EMPTY, IS NOT? DIFFERENT VALUES IN THIS SECTOR:\n", paste(names(table(unlist(tempo.list.diag), useNA = "ifany")), collapse = " "))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+        }
+    }
+    # end empty part detection
+    if(length(empty.sector) == 0L){
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") ACCORDING TO empty.cell.string ARGUMENT (", empty.cell.string, "), mat ARGUMENT MATRIX HAS ZERO EMPTY HALF PART")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }else{
+        if(length(empty.sector) > 1){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": ACCORDING TO empty.cell.string ARGUMENT (", empty.cell.string, "), mat ARGUMENT MATRIX HAS MORE THAN ONE EMPTY HALF PART (ACCORDING TO THE GRAND DIAGONAL): ", paste(empty.sector, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else if(any(full.sector %in% empty.sector, na.rm = TRUE)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": THE FUNCTION HAS DETECTED EMPTY AND NON EMPTY HALF PART IN THE SAME SECTOR: ", paste(full.sector[full.sector %in% empty.sector], collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else if(length(empty.sector) + length(full.sector)!= 4){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": THE FUNCTION HAS DETECTED MORE OR LESS SECTORS THAN 4:\nHALF SECTORS:", paste(empty.sector, collapse = " "), "\nFULL SECTORS:", paste(full.sector, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") ", toupper(empty.sector), " SECTOR HAS BEEN COMPLETED TO BECOME SYMMETRICAL")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+        # matrix filling
+        for(i2 in 1:(nrow(mat) - 1)){
+            if(empty.sector == "topleft"){
+                eval(parse(text = paste0(diag.scan[1], " <- ", diag.scan[3])))
+            }else if(empty.sector == "topright"){
+                eval(parse(text = paste0(diag.scan[2], " <- ", diag.scan[4])))
+            }else if(empty.sector == "bottomright"){
+                eval(parse(text = paste0(diag.scan[3], " <- ", diag.scan[1])))
+            }else if(empty.sector == "bottomleft"){
+                eval(parse(text = paste0(diag.scan[4], " <- ", diag.scan[2])))
+            }
+        }
+        # end matrix filling
+    }
+    if(warn.print == TRUE & ! is.null(warn)){
+        on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
+    }
+    on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
+    return(list(mat = mat, warn = warn))
 }
 
 
@@ -3481,393 +3481,393 @@ return(list(mat = mat, warn = warn))
 
 
 fun_permut <- function(
-data1, 
-data2 = NULL, 
-n = NULL, 
-seed = NULL, 
-print.count = 10, 
-text.print = "", 
-cor.method = "spearman", 
-cor.limit = 0.2, 
-warn.print = FALSE, 
-lib.path = NULL
+    data1, 
+    data2 = NULL, 
+    n = NULL, 
+    seed = NULL, 
+    print.count = 10, 
+    text.print = "", 
+    cor.method = "spearman", 
+    cor.limit = 0.2, 
+    warn.print = FALSE, 
+    lib.path = NULL
 ){
-# AIM
-# reorder the elements of the data1 vector by flipping 2 randomly selected  consecutive positions either:
-# 1) n times (when n is precised) or
-# 2) until the correlation between data1 and data2 decreases down to the cor.limit (0.2 by default). See cor.limit below to deal with negative correlations
-# Example of consecutive position flipping: ABCD -> BACD -> BADC, etc.
-# designed for discrete values, but worls also for continuous values
-# WARNINGS
-# see # https://www.r-bloggers.com/strategies-to-speedup-r-code/ for code speedup
-# the random switch of non consecutive positions (ABCD -> DBCA for instance) does not work very well as the correlation is quickly obtained but the initial vector structure is mainly kept (no much order). Ths code would be: pos <- ini.pos[1:2] ; pos <- sample.int(n = n , size = 2, replace = FALSE) ; tempo.pos[pos] <- tempo.pos[rev(pos)]
-# ARGUMENTS
-# data1: a vector of at least 2 elements. Must be numeric if data2 is specified
-# data2: a numeric vector of same length as data1
-# n: number of times "flipping 2 randomly selected consecutive positions". Ignored if data2 is specified
-# seed: integer number used by set.seed(). Write NULL if random result is required, an integer otherwise. BEWARE: if not NULL, fun_permut() will systematically return the same result when the other parameters keep the same settings
-# print.count: interger value. Print a working progress message every print.count during loops. BEWARE: can increase substentially the time to complete the process using a small value, like 10 for instance. Use Inf is no loop message desired
-# text.print: optional message to add to the working progress message every print.count loop
-# cor.method: correlation method. Either "pearson", "kendall" or "spearman". Ignored if data2 is not specified
-# cor.limit: a correlation limit (between 0 and 1). Ignored if data2 is not specified. Compute the correlation between data1 and data2, permute the data1 values, and stop the permutation process when the correlation between data1 and data2 decreases down below the cor limit value (0.2 by default). If cor(data1, data2) is negative, then -cor.limit is used and the process stops until the correlation between data1 and data2 increases up over cor.limit (-0.2 by default). BEWARE: write a positive cor.limit even if cor(data1, data2) is known to be negative. The function will automatically uses -cor.limit. If the initial correlation is already below cor.limit (positive correlation) or over -cor.limit (negative correlation), then the data1 value positions are completely randomized (correlation between data1 and data2 is expected to be 0)
-# warn.print: logical. Print warnings at the end of the execution? No print if no warning messages
-# lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
-# RETURN
-# a list containing:
-# $data: the modified vector
-# $warn: potential warning messages (in case of negative correlation when data2 is specified). NULL if non warning message
-# $cor: a spearman correlation between the initial positions (1:length(data1) and the final positions if data2 is not specified and the final correlation between data1 and data2 otherwise, according to cor.method
-# $count: the number of loops used
-# REQUIRED PACKAGES
-# lubridate
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# fun_pack()
-# fun_round()
-# EXAMPLES
-# example (1) showing that for loop, used in fun_permut(), is faster than while loop
-# ini.time <- as.numeric(Sys.time()) ; count <- 0 ; for(i0 in 1:1e9){count <- count + 1} ; tempo.time <- as.numeric(Sys.time()) ; tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time)) ; tempo.lapse
-# example (2) showing that for loop, used in fun_permut(), is faster than while loop
-# ini.time <- as.numeric(Sys.time()) ; count <- 0 ; while(count < 1e9){count <- count + 1} ; tempo.time <- as.numeric(Sys.time()) ; tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time)) ; tempo.lapse
-# fun_permut(data1 = LETTERS[1:5], data2 = NULL, n = 100, seed = 1, print.count = 10, text.print = "CPU NB 4")
-# fun_permut(data1 = 101:110, data2 = 21:30, seed = 1, print.count = 1e4, text.print = "", cor.method = "spearman", cor.limit = 0.2)
-# a way to use the cor.limit argument just considering data1
-# obs1 <- 101:110 ; fun_permut(data1 = obs1, data2 = obs1, seed = 1, print.count = 10, cor.method = "spearman", cor.limit = 0.2)
-# fun_permut(data1 = 1:1e3, data2 = 1e3:1, seed = 1, print.count = 1e6, text.print = "", cor.method = "spearman", cor.limit = 0.7)
-# fun_permut(data1 = 1:1e2, data2 = 1e2:1, seed = 1, print.count = 1e3, cor.limit = 0.5)
-# fun_permut(data1 = c(0,0,0,0,0), n = 5, data2 = NULL, seed = 1, print.count = 1e3, cor.limit = 0.5)
-# DEBUGGING
-# data1 = LETTERS[1:5] ; data2 = NULL ; n = 1e6 ; seed = NULL ; print.count = 1e3 ; text.print = "" ; cor.method = "spearman" ; cor.limit = 0.2 ; warn.print = TRUE ; lib.path = NULL
-# data1 = LETTERS[1:5] ; data2 = NULL ; n = 10 ; seed = 22 ; print.count = 10 ; text.print = "" ; cor.method = "spearman" ; cor.limit = 0.2 ; warn.print = TRUE ; lib.path = NULL
-# data1 = 101:110 ; data2 = 21:30 ; n = 10 ; seed = 22 ; print.count = 10 ; text.print = "" ; cor.method = "spearman" ; cor.limit = 0.2 ; warn.print = TRUE ; lib.path = NULL
-# data1 = 1:1e3 ; data2 = 1e3:1 ; n = 20 ; seed = 22 ; print.count = 1e6 ; text.print = "" ; cor.method = "spearman" ; cor.limit = 0.5 ; warn.print = TRUE ; lib.path = NULL
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_pack", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_round", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = data1, class = "vector", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & length(data1) < 2){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data1 ARGUMENT MUST BE A VECTOR OF MINIMUM LENGTH 2. HERE IT IS: ", length(data1))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-if( ! is.null(data2)){
-tempo <- fun_check(data = data1, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
-if(tempo$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data1 MUST BE A NUMERIC VECTOR IF data2 ARGUMENT IS SPECIFIED")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo <- fun_check(data = data2, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
-if(length(data1) != length(data2)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data1 AND data2 MUST BE VECTOR OF SAME LENGTH. HERE IT IS ", length(data1)," AND ", length(data2))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else if(is.null(n)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": n ARGUMENT CANNOT BE NULL IF data2 ARGUMENT IS NULL")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-if( ! is.null(n)){
-tempo <- fun_check(data = n, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(seed)){
-tempo <- fun_check(data = seed, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = TRUE, fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = print.count, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = text.print, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = cor.method, options = c("pearson", "kendall", "spearman"), length =1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = cor.limit, class = "vector", mode = "numeric", prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(lib.path)){
-tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# package checking
-fun_pack(req.package = "lubridate", lib.path = lib.path)
-# end package checking
-# main code
-# code that protects set.seed() in the global environment
-# see also Protocol 100-rev0 Parallelization in R.docx
-if(exists(".Random.seed", envir = .GlobalEnv)){ # if .Random.seed does not exists, it means that no random operation has been performed yet in any R environment
-tempo.random.seed <- .Random.seed
-on.exit(assign(".Random.seed", tempo.random.seed, env = .GlobalEnv))
-}else{
-on.exit(set.seed(NULL)) # inactivate seeding -> return to complete randomness
-}
-set.seed(seed)
-# end code that protects set.seed() in the global environment
-ini.date <- Sys.time() # time of process begin, converted into seconds
-ini.time <- as.numeric(ini.date) # time of process begin, converted into seconds
-ini.pos <- 1:length(data1) # positions of data1 before permutation loops
-tempo.pos <- ini.pos # positions of data1 that will be modified during loops
-# pos.selec.seq <- ini.pos[-length(data1)] # selection of 1 position in initial position, without the last because always up permutation (pos -> pos+1 & pos+1 -> pos)
-pos.selec.seq.max <- length(ini.pos) - 1 # max position (used by sample.int() function). See  below for - 1
-ini.warning.length <- options()$warning.length
-options(warning.length = 8170)
-warn <- NULL
-warn.count <- 0
-count <- 0
-round <- 0
-BREAK <- FALSE
-tempo.cor <- 0
-if(is.null(data2)){
-if(length(table(data1)) == 1L){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NO PERMUTATION PERFORMED BECAUSE data1 ARGUMENT SEEMS TO BE MADE OF IDENTICAL ELEMENTS: ", names(table(data1)))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn))) #
-}else{
-if(print.count > n){
-print.count <- n
-}
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FOR LOOP OF ", n, " LOOPS INITIATED | LOOP COUNT: ", format(count, big.mark=",")))
-print.count.loop <- logical(length = print.count)
-print.count.loop[length(print.count.loop)] <- TRUE # not this to avoid long vector, but not forget to reset during printing: print.count.loop[(1:trunc(n / print.count) * print.count)] <- TRUE # counter to speedup
-count.loop <- 0
-pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # selection of random positions. BEWARE: n = pos.selec.seq.max because already - 1 (see above) but is connected to tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
-tempo.date.loop <- Sys.time()
-tempo.time.loop <- as.numeric(tempo.date.loop)
-for(i3 in 1:n){
-count.loop <- count.loop + 1
-pos2 <- pos[count.loop] # selection of 1 position
-tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
-if(print.count.loop[count.loop]){
-count.loop <- 0
-pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # BEWARE: never forget to resample here
-tempo.time <- as.numeric(Sys.time())
-tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - tempo.time.loop))
-final.loop <- (tempo.time - tempo.time.loop) / i3 * n # expected duration in seconds
-final.exp <- as.POSIXct(final.loop, origin = tempo.date.loop)
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FOR LOOP ", i3, " / ", n, " | TIME SPENT: ", tempo.lapse, " | EXPECTED END: ", final.exp))
-}
-}
-count <- count + n # out of the loop to speedup
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FOR LOOP ENDED | LOOP COUNT: ", format(count, big.mark=",")))
-cat("\n\n")
-}
-}else{
-if(length(table(data1)) == 1L){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NO PERMUTATION PERFORMED BECAUSE data1 ARGUMENT SEEMS TO BE MADE OF IDENTICAL ELEMENTS: ", names(table(data1)))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn))) #
-tempo.cor <- 1
-}else if(length(table(data2)) == 1L){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NO PERMUTATION PERFORMED BECAUSE data2 ARGUMENT SEEMS TO BE MADE OF IDENTICAL ELEMENTS: ", names(table(data2)))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn))) #
-tempo.cor <- 1
-}else{
-cor.ini <- cor(x = data1, y = data2, use = "pairwise.complete.obs", method = cor.method)
-tempo.cor <- cor.ini # correlation that will be modified during loops
-neg.cor <- FALSE
-if(tempo.cor < 0){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") INITIAL ", toupper(cor.method), " CORRELATION BETWEEN data1 AND data2 HAS BEEN DETECTED AS NEGATIVE: ", tempo.cor, ". THE LOOP STEPS WILL BE PERFORMED USING POSITIVE CORRELATIONS BUT THE FINAL CORRELATION WILL BE NEGATIVE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn))) #
-neg.cor <- TRUE
-tempo.cor <- abs(tempo.cor)
-cor.ini <- abs(cor.ini)
-}
-if(tempo.cor < cor.limit){ # randomize directly all the position to be close to correlation zero
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") INITIAL ABSOLUTE VALUE OF THE ", toupper(cor.method), " CORRELATION ", fun_round(tempo.cor), " BETWEEN data1 AND data2 HAS BEEN DETECTED AS BELOW THE CORRELATION LIMIT PARAMETER ", cor.limit, "\nTHE data1 SEQUENCE HAS BEEN COMPLETELY RANDOMIZED TO CORRESPOND TO CORRELATION ZERO")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn))) #
-for(i4 in 1:5){ # done 5 times to be sure of the complete randomness
-tempo.pos <- sample(x = tempo.pos, size = length(tempo.pos), replace = FALSE)
-}
-count <- count + 5 # out of the loop to speedup
-}else{
-# smallest correlation decrease
-count <- count + 1 # 1 and not 0 because already 1 performed just below
-pos <- sample.int(n = pos.selec.seq.max , size = 1, replace = TRUE) # selection of 1 position # pos.selec.seq.max  because selection of 1 position in initial position, without the last because always up permutation (pos -> pos+1 & pos+1 -> pos)
-tempo.pos[c(pos + 1, pos)] <- tempo.pos[c(pos, pos + 1)]
-tempo.cor <- abs(cor(x = data1[tempo.pos], y = data2, use = "pairwise.complete.obs", method = cor.method))
-smallest.cor.dec <- cor.ini - tempo.cor
-# end smallest correlation decrease
-# going out of tempo.cor == cor.ini
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "CORRELATION DECREASE AFTER A SINGLE PERMUTATION: ", fun_round(smallest.cor.dec, 4)))
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FIRST WHILE LOOP STEP -> GOING OUT FROM EQUALITY | LOOP COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4)))
-print.count.loop <- logical(length = print.count)
-print.count.loop[length(print.count.loop)] <- TRUE # counter to speedup
-count.loop <- 0 # 
-pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # selection of random positions. BEWARE: n = pos.selec.seq.max because already - 1 (see above) but is connected to tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
-tempo.date.loop <- Sys.time()
-tempo.time.loop <- as.numeric(tempo.date.loop)
-while(tempo.cor == cor.ini){ # to be out of equality between tempo.cor and cor.ini at the beginning (only valid for very long vector)
-count <- count + 1
-count.loop <- count.loop + 1
-pos2 <- pos[count.loop]
-tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
-tempo.cor <- abs(cor(x = data1[tempo.pos], y = data2, use = "pairwise.complete.obs", method = cor.method))
-if(print.count.loop[count.loop]){
-count.loop <- 0
-pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # BEWARE: never forget to resample here
-tempo.time <- as.numeric(Sys.time())
-tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - tempo.time.loop))
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FIRST WHILE LOOP STEP", format(count.loop, big.mark=","), " / ? | COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4), " | TIME SPENT: ", tempo.lapse))
-}
-}
-tempo.time <- as.numeric(Sys.time())
-tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time))
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FIRST WHILE LOOP STEP END | LOOP COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4), " | TOTAL SPENT TIME: ", tempo.lapse))
-if(tempo.cor < cor.limit){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE FIRST FOR & WHILE LOOP STEPS HAVE BEEN TOO FAR AND SUBSEQUENT LOOP STEPS WILL NOT RUN")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# end going out of tempo.cor == cor.ini
-# estimation of the average correlation decrease per loop on x loops and for loop execution
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "WHILE/FOR LOOPS INITIATION | LOOP COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4)))
-count.est <- 1e5
-first.round <- TRUE
-GOBACK <- FALSE
-while(tempo.cor > cor.limit){
-round <- round + 1
-# estimation step
-if(first.round == TRUE){
-first.round <- FALSE
-cor.dec.per.loop <- numeric(length = 5)
-loop.nb.est <- Inf
-cor.est.ini <- tempo.cor
-cor.est <- numeric(length = 5)
-for(i6 in 1:5){ # connected to cor.dec.per.loop
-tempo.pos.est <- tempo.pos
-pos <- sample.int(n = pos.selec.seq.max , size = count.est, replace = TRUE) # selection of n position
-for(i7 in 1:count.est){
-pos2 <- pos[i7] # selection of 1 position
-tempo.pos.est[c(pos2 + 1, pos2)] <- tempo.pos.est[c(pos2, pos2 + 1)]
-}
-tempo.cor.est <- abs(cor(x = data1[tempo.pos.est], y = data2, use = "pairwise.complete.obs", method = cor.method))
-cor.est[i6] <- tempo.cor.est
-tempo.cor.dec.per.loop <- (cor.est.ini - tempo.cor.est) / count.est # correlation decrease per loop
-if(is.na(tempo.cor.dec.per.loop) | ! is.finite(tempo.cor.dec.per.loop)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 2\ncor.est.ini: ", cor.est.ini, "\ntempo.cor.est: ", tempo.cor.est)
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-cor.dec.per.loop[i6] <- tempo.cor.dec.per.loop
-}
-cor.est <- cor.est[which.max(cor.dec.per.loop)] # max to avoid to go to far with for loop (tempo.cor below tempo.limit)
-cor.dec.per.loop <- max(cor.dec.per.loop, na.rm = TRUE) # max to avoid to go to far with for loop (tempo.cor below tempo.limit)
-loop.nb.est <- round((tempo.cor - cor.limit) / cor.dec.per.loop)
-}else{
-if(GOBACK == TRUE){
-loop.nb.est <- round(loop.nb.est / 2)
-}else{
-cor.dec.per.loop <- (cor.ini - tempo.cor) / count
-loop.nb.est <- round((tempo.cor - cor.limit) / cor.dec.per.loop)
-}
-}
-# end estimation step
-# loop step
-if(is.na(loop.nb.est) | ! is.finite(loop.nb.est)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 1\nloop.nb.est: ", loop.nb.est, "\ncor.ini: ", cor.ini, "\ntempo.cor: ", tempo.cor, "\ncor.limit: ", cor.limit, "\ncor.dec.per.loop: ", cor.dec.per.loop)
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(loop.nb.est > 1e4){ # below -> leave the while loop
-tempo.pos.secu <- tempo.pos
-count.secu <- count
-tempo.cor.secu <- tempo.cor
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "INITIAL SETTINGS BEFORE ROUND: ", round, " | LOOP COUNT: ", format(count, big.mark=","), " | GO BACK: ", GOBACK, " | LOOP NUMBER ESTIMATION: ", format(loop.nb.est, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4)))
-print.count.loop <- logical(length = print.count)
-print.count.loop[length(print.count.loop)] <- TRUE # not this to avoid long vector, but not forget to reset during printing: print.count.loop[(1:trunc(n / print.count) * print.count)] <- TRUE # counter to speedup
-count.loop <- 0
-pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # selection of random positions. BEWARE: n = pos.selec.seq.max because already - 1 (see above) but is connected to tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
-tempo.date.loop <- Sys.time()
-tempo.time.loop <- as.numeric(tempo.date.loop)
-for(i6 in 1:loop.nb.est){
-count.loop <- count.loop + 1
-pos2 <- pos[count.loop] # selection of 1 position
-tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
-if(print.count.loop[count.loop]){
-count.loop <- 0
-pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # BEWARE: never forget to resample here
-tempo.time <- as.numeric(Sys.time())
-tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - tempo.time.loop))
-final.loop <- (tempo.time - tempo.time.loop) / i6 * loop.nb.est # expected duration in seconds # intra nb.compar loop lapse: time lapse / cycles done * cycles remaining
-final.exp <- as.POSIXct(final.loop, origin = tempo.date.loop)
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FOR LOOP | ROUND ", round, " | LOOP: ", format(i6, big.mark=","), " / ", format(loop.nb.est, big.mark=","), " | TIME SPENT: ", tempo.lapse, " | EXPECTED END: ", final.exp))
-}
-}
-count <- count + loop.nb.est # out of the loop to speedup
-tempo.cor <- abs(cor(x = data1[tempo.pos], y = data2, use = "pairwise.complete.obs", method = cor.method))
-if(tempo.cor > tempo.cor.secu | ((tempo.cor - cor.limit) < 0 & abs(tempo.cor - cor.limit) > smallest.cor.dec * round(log10(max(ini.pos, na.rm = TRUE))))){
-GOBACK <- TRUE
-tempo.pos <- tempo.pos.secu
-count <- count.secu
-tempo.cor <- tempo.cor.secu
-}else{
-GOBACK <- FALSE
-}
-}else{
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FINAL WHILE LOOP | LOOP COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4)))
-print.count.loop <- logical(length = print.count)
-print.count.loop[length(print.count.loop)] <- TRUE # counter to speedup
-count.loop <- 0 # 
-pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # selection of random positions. BEWARE: n = pos.selec.seq.max because already - 1 (see above) but is connected to tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
-tempo.cor.loop <- tempo.cor
-tempo.date.loop <- Sys.time()
-tempo.time.loop <- as.numeric(tempo.date.loop)
-while(tempo.cor > cor.limit){
-count <- count + 1
-count.loop <- count.loop + 1
-pos2 <- pos[count.loop]
-tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
-tempo.cor <- abs(cor(x = data1[tempo.pos], y = data2, use = "pairwise.complete.obs", method = cor.method))
-if(print.count.loop[count.loop]){
-count.loop <- 0
-pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # BEWARE: never forget to resample here
-tempo.time <- as.numeric(Sys.time())
-tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - tempo.time.loop))
-final.loop <- (tempo.time - tempo.time.loop) / (tempo.cor.loop - tempo.cor) * (tempo.cor - cor.limit) # expected duration in seconds # tempo.cor.loop - tempo.cor always positive and tempo.cor decreases progressively starting from tempo.cor.loop
-final.exp <- as.POSIXct(final.loop, origin = tempo.date.loop)
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "WHILE LOOP | LOOP NB: ", format(count.loop, big.mark=","), " | COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4), " | TIME SPENT: ", tempo.lapse, " | EXPECTED END: ", final.exp))
-}
-}
-}
-}
-tempo.time <- as.numeric(Sys.time())
-tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time))
-cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "WHILE/FOR LOOPS END | LOOP COUNT: ", format(count, big.mark=","), " | NB OF ROUNDS: ", round, " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4), " | TOTAL SPENT TIME: ", tempo.lapse))
-}
-tempo.cor <- ifelse(neg.cor == TRUE, -tempo.cor, tempo.cor)
-}
-}
-cat("\n\n")
-if(warn.print == TRUE & ! is.null(warn)){
-on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE), add = TRUE)
-}
-on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
-output <- list(data = data1[tempo.pos], warn = warn, cor = if(is.null(data2)){cor(ini.pos, tempo.pos, method = "spearman")}else{tempo.cor}, count = count)
-return(output)
+    # AIM
+    # reorder the elements of the data1 vector by flipping 2 randomly selected  consecutive positions either:
+    # 1) n times (when n is precised) or
+    # 2) until the correlation between data1 and data2 decreases down to the cor.limit (0.2 by default). See cor.limit below to deal with negative correlations
+    # Example of consecutive position flipping: ABCD -> BACD -> BADC, etc.
+    # designed for discrete values, but worls also for continuous values
+    # WARNINGS
+    # see # https://www.r-bloggers.com/strategies-to-speedup-r-code/ for code speedup
+    # the random switch of non consecutive positions (ABCD -> DBCA for instance) does not work very well as the correlation is quickly obtained but the initial vector structure is mainly kept (no much order). Ths code would be: pos <- ini.pos[1:2] ; pos <- sample.int(n = n , size = 2, replace = FALSE) ; tempo.pos[pos] <- tempo.pos[rev(pos)]
+    # ARGUMENTS
+    # data1: a vector of at least 2 elements. Must be numeric if data2 is specified
+    # data2: a numeric vector of same length as data1
+    # n: number of times "flipping 2 randomly selected consecutive positions". Ignored if data2 is specified
+    # seed: integer number used by set.seed(). Write NULL if random result is required, an integer otherwise. BEWARE: if not NULL, fun_permut() will systematically return the same result when the other parameters keep the same settings
+    # print.count: interger value. Print a working progress message every print.count during loops. BEWARE: can increase substentially the time to complete the process using a small value, like 10 for instance. Use Inf is no loop message desired
+    # text.print: optional message to add to the working progress message every print.count loop
+    # cor.method: correlation method. Either "pearson", "kendall" or "spearman". Ignored if data2 is not specified
+    # cor.limit: a correlation limit (between 0 and 1). Ignored if data2 is not specified. Compute the correlation between data1 and data2, permute the data1 values, and stop the permutation process when the correlation between data1 and data2 decreases down below the cor limit value (0.2 by default). If cor(data1, data2) is negative, then -cor.limit is used and the process stops until the correlation between data1 and data2 increases up over cor.limit (-0.2 by default). BEWARE: write a positive cor.limit even if cor(data1, data2) is known to be negative. The function will automatically uses -cor.limit. If the initial correlation is already below cor.limit (positive correlation) or over -cor.limit (negative correlation), then the data1 value positions are completely randomized (correlation between data1 and data2 is expected to be 0)
+    # warn.print: logical. Print warnings at the end of the execution? No print if no warning messages
+    # lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
+    # RETURN
+    # a list containing:
+    # $data: the modified vector
+    # $warn: potential warning messages (in case of negative correlation when data2 is specified). NULL if non warning message
+    # $cor: a spearman correlation between the initial positions (1:length(data1) and the final positions if data2 is not specified and the final correlation between data1 and data2 otherwise, according to cor.method
+    # $count: the number of loops used
+    # REQUIRED PACKAGES
+    # lubridate
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # fun_pack()
+    # fun_round()
+    # EXAMPLES
+    # example (1) showing that for loop, used in fun_permut(), is faster than while loop
+    # ini.time <- as.numeric(Sys.time()) ; count <- 0 ; for(i0 in 1:1e9){count <- count + 1} ; tempo.time <- as.numeric(Sys.time()) ; tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time)) ; tempo.lapse
+    # example (2) showing that for loop, used in fun_permut(), is faster than while loop
+    # ini.time <- as.numeric(Sys.time()) ; count <- 0 ; while(count < 1e9){count <- count + 1} ; tempo.time <- as.numeric(Sys.time()) ; tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time)) ; tempo.lapse
+    # fun_permut(data1 = LETTERS[1:5], data2 = NULL, n = 100, seed = 1, print.count = 10, text.print = "CPU NB 4")
+    # fun_permut(data1 = 101:110, data2 = 21:30, seed = 1, print.count = 1e4, text.print = "", cor.method = "spearman", cor.limit = 0.2)
+    # a way to use the cor.limit argument just considering data1
+    # obs1 <- 101:110 ; fun_permut(data1 = obs1, data2 = obs1, seed = 1, print.count = 10, cor.method = "spearman", cor.limit = 0.2)
+    # fun_permut(data1 = 1:1e3, data2 = 1e3:1, seed = 1, print.count = 1e6, text.print = "", cor.method = "spearman", cor.limit = 0.7)
+    # fun_permut(data1 = 1:1e2, data2 = 1e2:1, seed = 1, print.count = 1e3, cor.limit = 0.5)
+    # fun_permut(data1 = c(0,0,0,0,0), n = 5, data2 = NULL, seed = 1, print.count = 1e3, cor.limit = 0.5)
+    # DEBUGGING
+    # data1 = LETTERS[1:5] ; data2 = NULL ; n = 1e6 ; seed = NULL ; print.count = 1e3 ; text.print = "" ; cor.method = "spearman" ; cor.limit = 0.2 ; warn.print = TRUE ; lib.path = NULL
+    # data1 = LETTERS[1:5] ; data2 = NULL ; n = 10 ; seed = 22 ; print.count = 10 ; text.print = "" ; cor.method = "spearman" ; cor.limit = 0.2 ; warn.print = TRUE ; lib.path = NULL
+    # data1 = 101:110 ; data2 = 21:30 ; n = 10 ; seed = 22 ; print.count = 10 ; text.print = "" ; cor.method = "spearman" ; cor.limit = 0.2 ; warn.print = TRUE ; lib.path = NULL
+    # data1 = 1:1e3 ; data2 = 1e3:1 ; n = 20 ; seed = 22 ; print.count = 1e6 ; text.print = "" ; cor.method = "spearman" ; cor.limit = 0.5 ; warn.print = TRUE ; lib.path = NULL
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(length(utils::find("fun_pack", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(length(utils::find("fun_round", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = data1, class = "vector", fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & length(data1) < 2){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": data1 ARGUMENT MUST BE A VECTOR OF MINIMUM LENGTH 2. HERE IT IS: ", length(data1))
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    if( ! is.null(data2)){
+        tempo <- fun_check(data = data1, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
+        if(tempo$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": data1 MUST BE A NUMERIC VECTOR IF data2 ARGUMENT IS SPECIFIED")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+        tempo <- fun_check(data = data2, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
+        if(length(data1) != length(data2)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": data1 AND data2 MUST BE VECTOR OF SAME LENGTH. HERE IT IS ", length(data1)," AND ", length(data2))
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else if(is.null(n)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": n ARGUMENT CANNOT BE NULL IF data2 ARGUMENT IS NULL")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    if( ! is.null(n)){
+        tempo <- fun_check(data = n, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(seed)){
+        tempo <- fun_check(data = seed, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = TRUE, fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = print.count, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = text.print, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = cor.method, options = c("pearson", "kendall", "spearman"), length =1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = cor.limit, class = "vector", mode = "numeric", prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(lib.path)){
+        tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
+                tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # package checking
+    fun_pack(req.package = "lubridate", lib.path = lib.path)
+    # end package checking
+    # main code
+    # code that protects set.seed() in the global environment
+    # see also Protocol 100-rev0 Parallelization in R.docx
+    if(exists(".Random.seed", envir = .GlobalEnv)){ # if .Random.seed does not exists, it means that no random operation has been performed yet in any R environment
+        tempo.random.seed <- .Random.seed
+        on.exit(assign(".Random.seed", tempo.random.seed, env = .GlobalEnv))
+    }else{
+        on.exit(set.seed(NULL)) # inactivate seeding -> return to complete randomness
+    }
+    set.seed(seed)
+    # end code that protects set.seed() in the global environment
+    ini.date <- Sys.time() # time of process begin, converted into seconds
+    ini.time <- as.numeric(ini.date) # time of process begin, converted into seconds
+    ini.pos <- 1:length(data1) # positions of data1 before permutation loops
+    tempo.pos <- ini.pos # positions of data1 that will be modified during loops
+    # pos.selec.seq <- ini.pos[-length(data1)] # selection of 1 position in initial position, without the last because always up permutation (pos -> pos+1 & pos+1 -> pos)
+    pos.selec.seq.max <- length(ini.pos) - 1 # max position (used by sample.int() function). See  below for - 1
+    ini.warning.length <- options()$warning.length
+    options(warning.length = 8170)
+    warn <- NULL
+    warn.count <- 0
+    count <- 0
+    round <- 0
+    BREAK <- FALSE
+    tempo.cor <- 0
+    if(is.null(data2)){
+        if(length(table(data1)) == 1L){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") NO PERMUTATION PERFORMED BECAUSE data1 ARGUMENT SEEMS TO BE MADE OF IDENTICAL ELEMENTS: ", names(table(data1)))
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn))) #
+        }else{
+            if(print.count > n){
+                print.count <- n
+            }
+            cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FOR LOOP OF ", n, " LOOPS INITIATED | LOOP COUNT: ", format(count, big.mark=",")))
+            print.count.loop <- logical(length = print.count)
+            print.count.loop[length(print.count.loop)] <- TRUE # not this to avoid long vector, but not forget to reset during printing: print.count.loop[(1:trunc(n / print.count) * print.count)] <- TRUE # counter to speedup
+            count.loop <- 0
+            pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # selection of random positions. BEWARE: n = pos.selec.seq.max because already - 1 (see above) but is connected to tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
+            tempo.date.loop <- Sys.time()
+            tempo.time.loop <- as.numeric(tempo.date.loop)
+            for(i3 in 1:n){
+                count.loop <- count.loop + 1
+                pos2 <- pos[count.loop] # selection of 1 position
+                tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
+                if(print.count.loop[count.loop]){
+                    count.loop <- 0
+                    pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # BEWARE: never forget to resample here
+                    tempo.time <- as.numeric(Sys.time())
+                    tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - tempo.time.loop))
+                    final.loop <- (tempo.time - tempo.time.loop) / i3 * n # expected duration in seconds
+                    final.exp <- as.POSIXct(final.loop, origin = tempo.date.loop)
+                    cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FOR LOOP ", i3, " / ", n, " | TIME SPENT: ", tempo.lapse, " | EXPECTED END: ", final.exp))
+                }
+            }
+            count <- count + n # out of the loop to speedup
+            cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FOR LOOP ENDED | LOOP COUNT: ", format(count, big.mark=",")))
+            cat("\n\n")
+        }
+    }else{
+        if(length(table(data1)) == 1L){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") NO PERMUTATION PERFORMED BECAUSE data1 ARGUMENT SEEMS TO BE MADE OF IDENTICAL ELEMENTS: ", names(table(data1)))
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn))) #
+            tempo.cor <- 1
+        }else if(length(table(data2)) == 1L){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") NO PERMUTATION PERFORMED BECAUSE data2 ARGUMENT SEEMS TO BE MADE OF IDENTICAL ELEMENTS: ", names(table(data2)))
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn))) #
+            tempo.cor <- 1
+        }else{
+            cor.ini <- cor(x = data1, y = data2, use = "pairwise.complete.obs", method = cor.method)
+            tempo.cor <- cor.ini # correlation that will be modified during loops
+            neg.cor <- FALSE
+            if(tempo.cor < 0){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") INITIAL ", toupper(cor.method), " CORRELATION BETWEEN data1 AND data2 HAS BEEN DETECTED AS NEGATIVE: ", tempo.cor, ". THE LOOP STEPS WILL BE PERFORMED USING POSITIVE CORRELATIONS BUT THE FINAL CORRELATION WILL BE NEGATIVE")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn))) #
+                neg.cor <- TRUE
+                tempo.cor <- abs(tempo.cor)
+                cor.ini <- abs(cor.ini)
+            }
+            if(tempo.cor < cor.limit){ # randomize directly all the position to be close to correlation zero
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") INITIAL ABSOLUTE VALUE OF THE ", toupper(cor.method), " CORRELATION ", fun_round(tempo.cor), " BETWEEN data1 AND data2 HAS BEEN DETECTED AS BELOW THE CORRELATION LIMIT PARAMETER ", cor.limit, "\nTHE data1 SEQUENCE HAS BEEN COMPLETELY RANDOMIZED TO CORRESPOND TO CORRELATION ZERO")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn))) #
+                for(i4 in 1:5){ # done 5 times to be sure of the complete randomness
+                    tempo.pos <- sample(x = tempo.pos, size = length(tempo.pos), replace = FALSE)
+                }
+                count <- count + 5 # out of the loop to speedup
+            }else{
+                # smallest correlation decrease
+                count <- count + 1 # 1 and not 0 because already 1 performed just below
+                pos <- sample.int(n = pos.selec.seq.max , size = 1, replace = TRUE) # selection of 1 position # pos.selec.seq.max  because selection of 1 position in initial position, without the last because always up permutation (pos -> pos+1 & pos+1 -> pos)
+                tempo.pos[c(pos + 1, pos)] <- tempo.pos[c(pos, pos + 1)]
+                tempo.cor <- abs(cor(x = data1[tempo.pos], y = data2, use = "pairwise.complete.obs", method = cor.method))
+                smallest.cor.dec <- cor.ini - tempo.cor
+                # end smallest correlation decrease
+                # going out of tempo.cor == cor.ini
+                cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "CORRELATION DECREASE AFTER A SINGLE PERMUTATION: ", fun_round(smallest.cor.dec, 4)))
+                cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FIRST WHILE LOOP STEP -> GOING OUT FROM EQUALITY | LOOP COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4)))
+                print.count.loop <- logical(length = print.count)
+                print.count.loop[length(print.count.loop)] <- TRUE # counter to speedup
+                count.loop <- 0 # 
+                pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # selection of random positions. BEWARE: n = pos.selec.seq.max because already - 1 (see above) but is connected to tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
+                tempo.date.loop <- Sys.time()
+                tempo.time.loop <- as.numeric(tempo.date.loop)
+                while(tempo.cor == cor.ini){ # to be out of equality between tempo.cor and cor.ini at the beginning (only valid for very long vector)
+                    count <- count + 1
+                    count.loop <- count.loop + 1
+                    pos2 <- pos[count.loop]
+                    tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
+                    tempo.cor <- abs(cor(x = data1[tempo.pos], y = data2, use = "pairwise.complete.obs", method = cor.method))
+                    if(print.count.loop[count.loop]){
+                        count.loop <- 0
+                        pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # BEWARE: never forget to resample here
+                        tempo.time <- as.numeric(Sys.time())
+                        tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - tempo.time.loop))
+                        cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FIRST WHILE LOOP STEP", format(count.loop, big.mark=","), " / ? | COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4), " | TIME SPENT: ", tempo.lapse))
+                    }
+                }
+                tempo.time <- as.numeric(Sys.time())
+                tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time))
+                cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FIRST WHILE LOOP STEP END | LOOP COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4), " | TOTAL SPENT TIME: ", tempo.lapse))
+                if(tempo.cor < cor.limit){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") THE FIRST FOR & WHILE LOOP STEPS HAVE BEEN TOO FAR AND SUBSEQUENT LOOP STEPS WILL NOT RUN")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+                # end going out of tempo.cor == cor.ini
+                # estimation of the average correlation decrease per loop on x loops and for loop execution
+                cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "WHILE/FOR LOOPS INITIATION | LOOP COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4)))
+                count.est <- 1e5
+                first.round <- TRUE
+                GOBACK <- FALSE
+                while(tempo.cor > cor.limit){
+                    round <- round + 1
+                    # estimation step
+                    if(first.round == TRUE){
+                        first.round <- FALSE
+                        cor.dec.per.loop <- numeric(length = 5)
+                        loop.nb.est <- Inf
+                        cor.est.ini <- tempo.cor
+                        cor.est <- numeric(length = 5)
+                        for(i6 in 1:5){ # connected to cor.dec.per.loop
+                            tempo.pos.est <- tempo.pos
+                            pos <- sample.int(n = pos.selec.seq.max , size = count.est, replace = TRUE) # selection of n position
+                            for(i7 in 1:count.est){
+                                pos2 <- pos[i7] # selection of 1 position
+                                tempo.pos.est[c(pos2 + 1, pos2)] <- tempo.pos.est[c(pos2, pos2 + 1)]
+                            }
+                            tempo.cor.est <- abs(cor(x = data1[tempo.pos.est], y = data2, use = "pairwise.complete.obs", method = cor.method))
+                            cor.est[i6] <- tempo.cor.est
+                            tempo.cor.dec.per.loop <- (cor.est.ini - tempo.cor.est) / count.est # correlation decrease per loop
+                            if(is.na(tempo.cor.dec.per.loop) | ! is.finite(tempo.cor.dec.per.loop)){
+                                tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 2\ncor.est.ini: ", cor.est.ini, "\ntempo.cor.est: ", tempo.cor.est)
+                                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+                            }
+                            cor.dec.per.loop[i6] <- tempo.cor.dec.per.loop
+                        }
+                        cor.est <- cor.est[which.max(cor.dec.per.loop)] # max to avoid to go to far with for loop (tempo.cor below tempo.limit)
+                        cor.dec.per.loop <- max(cor.dec.per.loop, na.rm = TRUE) # max to avoid to go to far with for loop (tempo.cor below tempo.limit)
+                        loop.nb.est <- round((tempo.cor - cor.limit) / cor.dec.per.loop)
+                    }else{
+                        if(GOBACK == TRUE){
+                            loop.nb.est <- round(loop.nb.est / 2)
+                        }else{
+                            cor.dec.per.loop <- (cor.ini - tempo.cor) / count
+                            loop.nb.est <- round((tempo.cor - cor.limit) / cor.dec.per.loop)
+                        }
+                    }
+                    # end estimation step
+                    # loop step
+                    if(is.na(loop.nb.est) | ! is.finite(loop.nb.est)){
+                        tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 1\nloop.nb.est: ", loop.nb.est, "\ncor.ini: ", cor.ini, "\ntempo.cor: ", tempo.cor, "\ncor.limit: ", cor.limit, "\ncor.dec.per.loop: ", cor.dec.per.loop)
+                        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+                    }else if(loop.nb.est > 1e4){ # below -> leave the while loop
+                        tempo.pos.secu <- tempo.pos
+                        count.secu <- count
+                        tempo.cor.secu <- tempo.cor
+                        cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "INITIAL SETTINGS BEFORE ROUND: ", round, " | LOOP COUNT: ", format(count, big.mark=","), " | GO BACK: ", GOBACK, " | LOOP NUMBER ESTIMATION: ", format(loop.nb.est, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4)))
+                        print.count.loop <- logical(length = print.count)
+                        print.count.loop[length(print.count.loop)] <- TRUE # not this to avoid long vector, but not forget to reset during printing: print.count.loop[(1:trunc(n / print.count) * print.count)] <- TRUE # counter to speedup
+                        count.loop <- 0
+                        pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # selection of random positions. BEWARE: n = pos.selec.seq.max because already - 1 (see above) but is connected to tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
+                        tempo.date.loop <- Sys.time()
+                        tempo.time.loop <- as.numeric(tempo.date.loop)
+                        for(i6 in 1:loop.nb.est){
+                            count.loop <- count.loop + 1
+                            pos2 <- pos[count.loop] # selection of 1 position
+                            tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
+                            if(print.count.loop[count.loop]){
+                                count.loop <- 0
+                                pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # BEWARE: never forget to resample here
+                                tempo.time <- as.numeric(Sys.time())
+                                tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - tempo.time.loop))
+                                final.loop <- (tempo.time - tempo.time.loop) / i6 * loop.nb.est # expected duration in seconds # intra nb.compar loop lapse: time lapse / cycles done * cycles remaining
+                                final.exp <- as.POSIXct(final.loop, origin = tempo.date.loop)
+                                cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FOR LOOP | ROUND ", round, " | LOOP: ", format(i6, big.mark=","), " / ", format(loop.nb.est, big.mark=","), " | TIME SPENT: ", tempo.lapse, " | EXPECTED END: ", final.exp))
+                            }
+                        }
+                        count <- count + loop.nb.est # out of the loop to speedup
+                        tempo.cor <- abs(cor(x = data1[tempo.pos], y = data2, use = "pairwise.complete.obs", method = cor.method))
+                        if(tempo.cor > tempo.cor.secu | ((tempo.cor - cor.limit) < 0 & abs(tempo.cor - cor.limit) > smallest.cor.dec * round(log10(max(ini.pos, na.rm = TRUE))))){
+                            GOBACK <- TRUE
+                            tempo.pos <- tempo.pos.secu
+                            count <- count.secu
+                            tempo.cor <- tempo.cor.secu
+                        }else{
+                            GOBACK <- FALSE
+                        }
+                    }else{
+                        cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "FINAL WHILE LOOP | LOOP COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4)))
+                        print.count.loop <- logical(length = print.count)
+                        print.count.loop[length(print.count.loop)] <- TRUE # counter to speedup
+                        count.loop <- 0 # 
+                        pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # selection of random positions. BEWARE: n = pos.selec.seq.max because already - 1 (see above) but is connected to tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
+                        tempo.cor.loop <- tempo.cor
+                        tempo.date.loop <- Sys.time()
+                        tempo.time.loop <- as.numeric(tempo.date.loop)
+                        while(tempo.cor > cor.limit){
+                            count <- count + 1
+                            count.loop <- count.loop + 1
+                            pos2 <- pos[count.loop]
+                            tempo.pos[c(pos2 + 1, pos2)] <- tempo.pos[c(pos2, pos2 + 1)]
+                            tempo.cor <- abs(cor(x = data1[tempo.pos], y = data2, use = "pairwise.complete.obs", method = cor.method))
+                            if(print.count.loop[count.loop]){
+                                count.loop <- 0
+                                pos <- sample.int(n = pos.selec.seq.max , size = print.count, replace = TRUE) # BEWARE: never forget to resample here
+                                tempo.time <- as.numeric(Sys.time())
+                                tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - tempo.time.loop))
+                                final.loop <- (tempo.time - tempo.time.loop) / (tempo.cor.loop - tempo.cor) * (tempo.cor - cor.limit) # expected duration in seconds # tempo.cor.loop - tempo.cor always positive and tempo.cor decreases progressively starting from tempo.cor.loop
+                                final.exp <- as.POSIXct(final.loop, origin = tempo.date.loop)
+                                cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "WHILE LOOP | LOOP NB: ", format(count.loop, big.mark=","), " | COUNT: ", format(count, big.mark=","), " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4), " | TIME SPENT: ", tempo.lapse, " | EXPECTED END: ", final.exp))
+                            }
+                        }
+                    }
+                }
+                tempo.time <- as.numeric(Sys.time())
+                tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time))
+                cat(paste0("\n", ifelse(text.print == "", "", paste0(text.print, " | ")), "WHILE/FOR LOOPS END | LOOP COUNT: ", format(count, big.mark=","), " | NB OF ROUNDS: ", round, " | CORRELATION LIMIT: ", fun_round(cor.limit, 4), " | ABS TEMPO CORRELATION: ", fun_round(tempo.cor, 4), " | TOTAL SPENT TIME: ", tempo.lapse))
+            }
+            tempo.cor <- ifelse(neg.cor == TRUE, -tempo.cor, tempo.cor)
+        }
+    }
+    cat("\n\n")
+    if(warn.print == TRUE & ! is.null(warn)){
+        on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE), add = TRUE)
+    }
+    on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
+    output <- list(data = data1[tempo.pos], warn = warn, cor = if(is.null(data2)){cor(ini.pos, tempo.pos, method = "spearman")}else{tempo.cor}, count = count)
+    return(output)
 }
 
 
@@ -3875,598 +3875,598 @@ return(output)
 
 
 fun_slide <- function(
-data, 
-window.size, 
-step, 
-from = NULL, 
-to = NULL, 
-fun, 
-args = NULL, 
-boundary = "left", 
-parall = FALSE, 
-thread.nb = NULL, 
-print.count = 100, 
-res.path = NULL, 
-lib.path = NULL, 
-verbose = TRUE, 
-cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
+    data, 
+    window.size, 
+    step, 
+    from = NULL, 
+    to = NULL, 
+    fun, 
+    args = NULL, 
+    boundary = "left", 
+    parall = FALSE, 
+    thread.nb = NULL, 
+    print.count = 100, 
+    res.path = NULL, 
+    lib.path = NULL, 
+    verbose = TRUE, 
+    cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
 ){
-# AIM
-# return a computation made on a vector using a sliding window
-# WARNINGS
-# The function uses two strategies, depending on the amout of memory required which depends on the data, window.size and step arguments. The first one uses lapply(), is generally fast but requires lots of memory. The second one uses a parallelized loop. The choice between the two strategies is automatic if parall argument is FALSE, and is forced toward parallelization if parall argument is TRUE
-# The parall argument forces the parallelization, which is convenient when the data argument is big, because the lapply() function is sometimes slower than the parallelization
-# Always use the env argument when fun_slide() is used inside functions
-# ARGUMENTS
-# data: vector, matrix, table or array of numeric values (mode must be numeric). Inf not allowed. NA will be removed before computation
-# window.size: single numeric value indicating the width of the window sliding across data (in the same unit as data value)
-# step: single numeric value indicating the step between each window (in the same unit as data value). Cannot be larger than window.size
-# from: value of the left boundary of the first sliding window. If NULL, min(data) is used. The first window will strictly have from or min(data) as left boundary
-# to: value of the right boundary of the last sliding window. If NULL, max(data) is used. Warning: (1) the final last window will not necessary have to|max(data) as right boundary. In fact the last window will be the one that contains to|max(data) for the first time, i.e., min[from|min(data) + window.size + n * step >= to|max(data)]; (2) In fact, the >= in min[from|min(data) + window.size + n * step >= to|max(data)] depends on the boundary argument (>= for "right" and > for "left"); (3) to have the rule (1) but for the center of the last window, use to argument as to = to|max(data) + window.size / 2
-# fun: function or character string (without brackets) indicating the name of the function to apply in each window. Example: fun = "mean", or fun = mean
-# args: character string of additional arguments of fun (separated by a comma between the quotes). Example args = "na.rm = TRUE" for fun = mean. Ignored if NULL
-# boundary: either "left" or "right". Indicates if the sliding window includes values equal to left boundary and exclude values equal to right boundary ("left") or the opposite ("right")
-# parall: logical. Force parallelization ?
-# thread.nb: numeric value indicating the number of threads to use if ever parallelization is required. If NULL, all the available threads will be used. Ignored if parall is FALSE
-# print.count: interger value. Print a working progress message every print.count during loops. BEWARE: can increase substentially the time to complete the process using a small value, like 10 for instance. Use Inf is no loop message desired
-# res.path: character string indicating the absolute pathway where the parallelization log file will be created if parallelization is used. If NULL, will be created in the R current directory
-# lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
-# verbose: logical. Display messages?
-# cute.path: character string indicating the absolute path of the cute.R file. Will be remove when cute will be a package. Ignored if parall is FALSE
-# RETURN
-# a data frame containing
-#$left : the left boundary of each window (in the unit of the data argument)
-#$right : the right boundary of each window (in the unit of data argument)
-#$center : the center of each window (in the unit of data argument)
-#$value : the computed value by the fun argument in each window)
-# REQUIRED PACKAGES
-# lubridate
-# parallel if parall arguemtn is TRUE (included in the R installation packages but not automatically loaded)
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# fun_get_message
-# fun_pack()
-# EXAMPLES
-# fun_slide(data = c(1:10, 100:110, 500), window.size = 5, step = 2, fun = length, boundary = "left")
-# fun_slide(data = c(1:10, 100:110, 500), window.size = 5, step = 2, fun = length, boundary = "right") # effect of boundary argument
-# fun_slide(data = c(1:10, 100:110, 500), window.size = 5, step = 2, fun = length, boundary = "left", parall = TRUE) # effect of parall argument
-# DEBUGGING
-# data = c(1:10, 100:110, 500) ; window.size = 5 ; step = 2 ; from = NULL ; to = NULL ; fun = length ; args = NULL ; boundary = "left" ; parall = FALSE ; thread.nb = NULL ; print.count = 100 ; res.path = NULL ; lib.path = NULL ; verbose = TRUE ; env = NULL ; cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
-# data = lag.pos; window.size = window.size; step = step; fun = length; from = min(a$pos); to = max(a$pos)
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
-arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
-# end function name
-# required function checking
-req.function <- c(
-"fun_check", 
-"fun_get_message", 
-"fun_pack"
-)
-tempo <- NULL
-for(i1 in req.function){
-if(length(find(i1, mode = "function")) == 0L){
-tempo <- c(tempo, i1)
-}
-}
-if( ! is.null(tempo)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# reserved words
-# end reserved words
-# arg with no default values
-mandat.args <- c(
-"data", 
-"window.size", 
-"step", 
-"fun"
-)
-tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
-if(any(tempo)){ # normally no NA for missing() output
-tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end arg with no default values
-# argument primary checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = data, mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = window.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = step, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(from)){
-tempo <- fun_check(data = from, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(to)){
-tempo <- fun_check(data = to, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-}
-tempo1 <- fun_check(data = fun, class = "vector", mode = "character", length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = fun, class = "function", length = 1, fun.name = function.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": fun ARGUMENT MUST BE A FUNCTION OR A CHARACTER STRING OF THE NAME OF A FUNCTION")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-if( ! is.null(args)){
-tempo <- fun_check(data = args, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = boundary, options = c("left", "right"), length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = parall, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(parall == TRUE){
-if( ! is.null(thread.nb)){
-tempo <- fun_check(data = thread.nb, typeof = "integer", double.as.integer.allowed = TRUE, neg.values = FALSE, length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & thread.nb < 1){
-tempo.cat <- paste0("ERROR IN ", function.name, ": thread.nb PARAMETER MUST EQUAL OR GREATER THAN 1: ", thread.nb)
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}
-tempo <- fun_check(data = print.count, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-if( ! is.null(res.path)){
-tempo <- fun_check(data = res.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(lib.path)){
-tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = verbose, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = cute.path, class = "vector", typeof = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end using fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument primary checking
-# second round of checking and data preparation
-# new environment
-env.name <- paste0("env", as.numeric(Sys.time()))
-if(exists(env.name, where = -1)){ # verify if still ok when fun_info() is inside a function
-tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-assign(env.name, new.env())
-assign("data", data, envir = get(env.name, env = sys.nframe(), inherit = FALSE)) # data assigned in a new envir for test
-}
-# end new environment
-# management of NA arguments
-tempo.arg <- names(arg.user.setting) # values provided by the user
-tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
-if(any(tempo.log) == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS", "THIS ARGUMENT"), " CANNOT JUST BE NA:", paste0(tempo.arg[tempo.log], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NA arguments
-# management of NULL arguments
-tempo.arg <-c(
-"data", 
-"window.size", 
-"step", 
-# "from", # because can be NULL
-# "to", # because can be NULL
-"fun", 
-# "args", # because can be NULL
-"boundary", 
-"parall", 
-# "thread.nb", # because can be NULL
-"print.count", 
-# "res.path", # because can be NULL
-# "lib.path", # because can be NULL
-"verbose", 
-"cute.path"
-)
-tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
-if(any(tempo.log) == TRUE){# normally no NA with is.null()
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NULL arguments
-# code that protects set.seed() in the global environment
-# end code that protects set.seed() in the global environment
-# warning initiation
-# end warning initiation
-# other checkings
-if(length(data) == 0){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data ARGUMENT CANNOT BE LENGTH 0")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-if(any( ! is.finite(data))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data ARGUMENT CANNOT CONTAIN Inf VALUES")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-if(step > window.size){
-tempo.cat <- paste0("ERROR IN ", function.name, ": step ARGUMENT MUST BE LOWER THAN window.size ARGUMENT\nstep: ", paste(step, collapse = " "), "\nwindow.size: ", paste(window.size, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-if( ! is.null(res.path)){
-if( ! all(dir.exists(res.path))){ # separation to avoid the problem of tempo$problem == FALSE and res.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE res.path ARGUMENT DOES NOT EXISTS:\n", paste(res.path, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-}else{
-res.path <- getwd() # working directory
-}
-if( ! is.null(lib.path)){
-if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
-}
-}
-if(grepl(x = cute.path, pattern = "^http")){
-tempo.error1 <- any(grepl(x = fun_get_message(data = "source(cute.path)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE)), pattern = "^[Ee]rror"))
-tempo.error2 <- FALSE
-}else{
-tempo.error1 <- FALSE
-tempo.error2 <- ! file.exists(cute.path)
-}
-if(tempo.error1 | tempo.error2){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(grepl(x = cute.path, pattern = "^http"), "URL", "FILE"), " PATH INDICATED IN THE cute.path PARAMETER DOES NOT EXISTS:\n", cute.path)
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-# end other checkings
-# reserved word checking
-# end reserved word checking
-# end second round of checking and data preparation
-# package checking
-fun_pack(req.package = c("lubridate"), lib.path = lib.path)
-fun_pack(req.package = c("parallel"), lib.path = lib.path)
-# end package checking
-# main code
-if(verbose == TRUE){
-cat("\nfun_slide JOB IGNITION\n")
-}
-ini.date <- Sys.time()
-ini.time <- as.numeric(ini.date) # time of process begin, converted into seconds
-fun <- match.fun(fun) # make fun <- get(fun) is fun is a function name written as character string of length 1
-if(boundary == "left"){
-left <- ">="
-right <- "<"
-right.last.wind <- ">"
-}else if(boundary == "right"){
-left <- ">"
-right <- "<="
-right.last.wind <- ">="
-}else{
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 1")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-data <- as.vector(data)
-data <- sort(data, na.last = NA) # NA removed
-wind <- data.frame(left = seq(from = if(is.null(from)){min(data, na.rm = TRUE)}else{from}, to = if(is.null(to)){max(data, na.rm = TRUE)}else{to}, by = step), stringsAsFactors = TRUE)
-wind <- data.frame(wind, right = wind$left + window.size, stringsAsFactors = TRUE)
-wind <- data.frame(wind, center = (wind$left + wind$right) / 2, stringsAsFactors = TRUE)
-if(all(wind$right < if(is.null(to)){max(data, na.rm = TRUE)}else{to})){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 2")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# The 3 next lines is for the rule of to argument with center (see to argument description)
-# if(any(wind$center > max(data, na.rm = TRUE))){
-# wind <- wind[ ! wind$center > max(data, na.rm = TRUE),]
-# }
-if(sum(get(right.last.wind)(wind$right, if(is.null(to)){max(data, na.rm = TRUE)}else{to}), na.rm = TRUE) > 1){  # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-tempo.log <- get(right.last.wind)(wind$right, if(is.null(to)){max(data, na.rm = TRUE)}else{to}) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-tempo.log[min(which(tempo.log), na.rm = TRUE)] <- FALSE # convert the first left boundary that goes above max(data, na.rm = TRUE) to FALSE to keep it (the next ones will be removed)
-wind <- wind[ ! tempo.log,]
+    # AIM
+    # return a computation made on a vector using a sliding window
+    # WARNINGS
+    # The function uses two strategies, depending on the amout of memory required which depends on the data, window.size and step arguments. The first one uses lapply(), is generally fast but requires lots of memory. The second one uses a parallelized loop. The choice between the two strategies is automatic if parall argument is FALSE, and is forced toward parallelization if parall argument is TRUE
+    # The parall argument forces the parallelization, which is convenient when the data argument is big, because the lapply() function is sometimes slower than the parallelization
+    # Always use the env argument when fun_slide() is used inside functions
+    # ARGUMENTS
+    # data: vector, matrix, table or array of numeric values (mode must be numeric). Inf not allowed. NA will be removed before computation
+    # window.size: single numeric value indicating the width of the window sliding across data (in the same unit as data value)
+    # step: single numeric value indicating the step between each window (in the same unit as data value). Cannot be larger than window.size
+    # from: value of the left boundary of the first sliding window. If NULL, min(data) is used. The first window will strictly have from or min(data) as left boundary
+    # to: value of the right boundary of the last sliding window. If NULL, max(data) is used. Warning: (1) the final last window will not necessary have to|max(data) as right boundary. In fact the last window will be the one that contains to|max(data) for the first time, i.e., min[from|min(data) + window.size + n * step >= to|max(data)]; (2) In fact, the >= in min[from|min(data) + window.size + n * step >= to|max(data)] depends on the boundary argument (>= for "right" and > for "left"); (3) to have the rule (1) but for the center of the last window, use to argument as to = to|max(data) + window.size / 2
+    # fun: function or character string (without brackets) indicating the name of the function to apply in each window. Example: fun = "mean", or fun = mean
+    # args: character string of additional arguments of fun (separated by a comma between the quotes). Example args = "na.rm = TRUE" for fun = mean. Ignored if NULL
+    # boundary: either "left" or "right". Indicates if the sliding window includes values equal to left boundary and exclude values equal to right boundary ("left") or the opposite ("right")
+    # parall: logical. Force parallelization ?
+    # thread.nb: numeric value indicating the number of threads to use if ever parallelization is required. If NULL, all the available threads will be used. Ignored if parall is FALSE
+    # print.count: interger value. Print a working progress message every print.count during loops. BEWARE: can increase substentially the time to complete the process using a small value, like 10 for instance. Use Inf is no loop message desired
+    # res.path: character string indicating the absolute pathway where the parallelization log file will be created if parallelization is used. If NULL, will be created in the R current directory
+    # lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
+    # verbose: logical. Display messages?
+    # cute.path: character string indicating the absolute path of the cute.R file. Will be remove when cute will be a package. Ignored if parall is FALSE
+    # RETURN
+    # a data frame containing
+    #$left : the left boundary of each window (in the unit of the data argument)
+    #$right : the right boundary of each window (in the unit of data argument)
+    #$center : the center of each window (in the unit of data argument)
+    #$value : the computed value by the fun argument in each window)
+    # REQUIRED PACKAGES
+    # lubridate
+    # parallel if parall arguemtn is TRUE (included in the R installation packages but not automatically loaded)
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # fun_get_message
+    # fun_pack()
+    # EXAMPLES
+    # fun_slide(data = c(1:10, 100:110, 500), window.size = 5, step = 2, fun = length, boundary = "left")
+    # fun_slide(data = c(1:10, 100:110, 500), window.size = 5, step = 2, fun = length, boundary = "right") # effect of boundary argument
+    # fun_slide(data = c(1:10, 100:110, 500), window.size = 5, step = 2, fun = length, boundary = "left", parall = TRUE) # effect of parall argument
+    # DEBUGGING
+    # data = c(1:10, 100:110, 500) ; window.size = 5 ; step = 2 ; from = NULL ; to = NULL ; fun = length ; args = NULL ; boundary = "left" ; parall = FALSE ; thread.nb = NULL ; print.count = 100 ; res.path = NULL ; lib.path = NULL ; verbose = TRUE ; env = NULL ; cute.path = "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
+    # data = lag.pos; window.size = window.size; step = step; fun = length; from = min(a$pos); to = max(a$pos)
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
+    arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
+    # end function name
+    # required function checking
+    req.function <- c(
+        "fun_check", 
+        "fun_get_message", 
+        "fun_pack"
+    )
+    tempo <- NULL
+    for(i1 in req.function){
+        if(length(find(i1, mode = "function")) == 0L){
+            tempo <- c(tempo, i1)
+        }
+    }
+    if( ! is.null(tempo)){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # reserved words
+    # end reserved words
+    # arg with no default values
+    mandat.args <- c(
+        "data", 
+        "window.size", 
+        "step", 
+        "fun"
+    )
+    tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
+    if(any(tempo)){ # normally no NA for missing() output
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end arg with no default values
+    # argument primary checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = data, mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = window.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = step, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(from)){
+        tempo <- fun_check(data = from, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(to)){
+        tempo <- fun_check(data = to, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    }
+    tempo1 <- fun_check(data = fun, class = "vector", mode = "character", length = 1, fun.name = function.name)
+    tempo2 <- fun_check(data = fun, class = "function", length = 1, fun.name = function.name)
+    if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": fun ARGUMENT MUST BE A FUNCTION OR A CHARACTER STRING OF THE NAME OF A FUNCTION")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    if( ! is.null(args)){
+        tempo <- fun_check(data = args, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = boundary, options = c("left", "right"), length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = parall, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if(parall == TRUE){
+        if( ! is.null(thread.nb)){
+            tempo <- fun_check(data = thread.nb, typeof = "integer", double.as.integer.allowed = TRUE, neg.values = FALSE, length = 1, fun.name = function.name) ; eval(ee)
+            if(tempo$problem == FALSE & thread.nb < 1){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": thread.nb PARAMETER MUST EQUAL OR GREATER THAN 1: ", thread.nb)
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }
+    tempo <- fun_check(data = print.count, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    if( ! is.null(res.path)){
+        tempo <- fun_check(data = res.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(lib.path)){
+        tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = verbose, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = cute.path, class = "vector", typeof = "character", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end using fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument primary checking
+    # second round of checking and data preparation
+    # new environment
+    env.name <- paste0("env", as.numeric(Sys.time()))
+    if(exists(env.name, where = -1)){ # verify if still ok when fun_info() is inside a function
+        tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else{
+        assign(env.name, new.env())
+        assign("data", data, envir = get(env.name, env = sys.nframe(), inherit = FALSE)) # data assigned in a new envir for test
+    }
+    # end new environment
+    # management of NA arguments
+    tempo.arg <- names(arg.user.setting) # values provided by the user
+    tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
+    if(any(tempo.log) == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS", "THIS ARGUMENT"), " CANNOT JUST BE NA:", paste0(tempo.arg[tempo.log], collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NA arguments
+    # management of NULL arguments
+    tempo.arg <-c(
+        "data", 
+        "window.size", 
+        "step", 
+        # "from", # because can be NULL
+        # "to", # because can be NULL
+        "fun", 
+        # "args", # because can be NULL
+        "boundary", 
+        "parall", 
+        # "thread.nb", # because can be NULL
+        "print.count", 
+        # "res.path", # because can be NULL
+        # "lib.path", # because can be NULL
+        "verbose", 
+        "cute.path"
+    )
+    tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
+    if(any(tempo.log) == TRUE){# normally no NA with is.null()
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NULL arguments
+    # code that protects set.seed() in the global environment
+    # end code that protects set.seed() in the global environment
+    # warning initiation
+    # end warning initiation
+    # other checkings
+    if(length(data) == 0){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": data ARGUMENT CANNOT BE LENGTH 0")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+    }
+    if(any( ! is.finite(data))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": data ARGUMENT CANNOT CONTAIN Inf VALUES")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+    }
+    if(step > window.size){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": step ARGUMENT MUST BE LOWER THAN window.size ARGUMENT\nstep: ", paste(step, collapse = " "), "\nwindow.size: ", paste(window.size, collapse = " "))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+    }
+    if( ! is.null(res.path)){
+        if( ! all(dir.exists(res.path))){ # separation to avoid the problem of tempo$problem == FALSE and res.path == NA
+            tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE res.path ARGUMENT DOES NOT EXISTS:\n", paste(res.path, collapse = "\n"))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+        }
+    }else{
+        res.path <- getwd() # working directory
+    }
+    if( ! is.null(lib.path)){
+        if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
+            tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
+        }
+    }
+    if(grepl(x = cute.path, pattern = "^http")){
+        tempo.error1 <- any(grepl(x = fun_get_message(data = "source(cute.path)", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE)), pattern = "^[Ee]rror"))
+        tempo.error2 <- FALSE
+    }else{
+        tempo.error1 <- FALSE
+        tempo.error2 <- ! file.exists(cute.path)
+    }
+    if(tempo.error1 | tempo.error2){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(grepl(x = cute.path, pattern = "^http"), "URL", "FILE"), " PATH INDICATED IN THE cute.path PARAMETER DOES NOT EXISTS:\n", cute.path)
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    # end other checkings
+    # reserved word checking
+    # end reserved word checking
+    # end second round of checking and data preparation
+    # package checking
+    fun_pack(req.package = c("lubridate"), lib.path = lib.path)
+    fun_pack(req.package = c("parallel"), lib.path = lib.path)
+    # end package checking
+    # main code
+    if(verbose == TRUE){
+        cat("\nfun_slide JOB IGNITION\n")
+    }
+    ini.date <- Sys.time()
+    ini.time <- as.numeric(ini.date) # time of process begin, converted into seconds
+    fun <- match.fun(fun) # make fun <- get(fun) is fun is a function name written as character string of length 1
+    if(boundary == "left"){
+        left <- ">="
+        right <- "<"
+        right.last.wind <- ">"
+    }else if(boundary == "right"){
+        left <- ">"
+        right <- "<="
+        right.last.wind <- ">="
+    }else{
+        tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 1")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    data <- as.vector(data)
+    data <- sort(data, na.last = NA) # NA removed
+    wind <- data.frame(left = seq(from = if(is.null(from)){min(data, na.rm = TRUE)}else{from}, to = if(is.null(to)){max(data, na.rm = TRUE)}else{to}, by = step), stringsAsFactors = TRUE)
+    wind <- data.frame(wind, right = wind$left + window.size, stringsAsFactors = TRUE)
+    wind <- data.frame(wind, center = (wind$left + wind$right) / 2, stringsAsFactors = TRUE)
+    if(all(wind$right < if(is.null(to)){max(data, na.rm = TRUE)}else{to})){
+        tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 2")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # The 3 next lines is for the rule of to argument with center (see to argument description)
+    # if(any(wind$center > max(data, na.rm = TRUE))){
+    # wind <- wind[ ! wind$center > max(data, na.rm = TRUE),]
+    # }
+    if(sum(get(right.last.wind)(wind$right, if(is.null(to)){max(data, na.rm = TRUE)}else{to}), na.rm = TRUE) > 1){  # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
+        tempo.log <- get(right.last.wind)(wind$right, if(is.null(to)){max(data, na.rm = TRUE)}else{to}) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
+        tempo.log[min(which(tempo.log), na.rm = TRUE)] <- FALSE # convert the first left boundary that goes above max(data, na.rm = TRUE) to FALSE to keep it (the next ones will be removed)
+        wind <- wind[ ! tempo.log,]
+    }
+    
+    # test if lapply can be used
+    if(parall == FALSE){
+        # new environment
+        env.name <- paste0("env", ini.time)
+        if(exists(env.name, where = -1)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            assign(env.name, new.env())
+            assign("wind", wind, envir = get(env.name, env = sys.nframe(), inherit = FALSE))
+            assign("data", data, envir = get(env.name, env = sys.nframe(), inherit = FALSE))
+        }
+        # end new environment
+        tempo.message <- fun_get_message(data="lapply(X = wind$left, Y = data, FUN = function(X, Y){res <- get(left)(Y, X) ; return(res)})", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE), print.no = FALSE) # no env = sys.nframe(), inherit = FALSE in get(left) because look for function in the classical scope
+        rm(env.name) # optional, because should disappear at the end of the function execution
+    }else{
+        tempo.message <- "ERROR" # with this, force the parallelization by default
+    }
+    # end test if lapply can be used
+    if( ! any(grepl(x = tempo.message, pattern = "ERROR.*"))){
+        left.log <- lapply(X = wind$left, Y = data, FUN = function(X, Y){
+            res <- get(left)(Y, X) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
+            return(res)
+        })
+        right.log <- lapply(X = wind$right, Y = data, FUN = function(X, Y){
+            res <- get(right)(Y, X) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
+            return(res)
+        })
+        log <- mapply(FUN = "&", left.log, right.log, SIMPLIFY = FALSE)
+        output <- eval(parse(text = paste0("sapply(lapply(log, FUN = function(X){(data[X])}), FUN = fun", if( ! is.null(args)){paste0(", ", args)}, ")"))) # take the values of the data vector according to log (list of logical, each compartment of length(data)) and apply fun with args of fun
+        if(length(output) != nrow(wind)){
+            tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 3")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            output <- data.frame(wind, value = output, stringsAsFactors = TRUE)
+        }
+    }else{
+        if(verbose == TRUE){
+            tempo.cat <- paste0("PARALLELIZATION INITIATED AT: ", ini.date)
+            cat(paste0("\n", tempo.cat, "\n"))
+        }
+        tempo.thread.nb = parallel::detectCores(all.tests = FALSE, logical = TRUE) # detect the number of threads
+        if( ! is.null(thread.nb)){
+            if(tempo.thread.nb < thread.nb){
+                thread.nb <- tempo.thread.nb
+                if(verbose == TRUE){
+                    tempo.cat <- paste0("ONLY: ", tempo.thread.nb, " THREADS AVAILABLE")
+                    cat(paste0("\n", tempo.cat, "\n"))
+                }
+            }
+        }else{
+            thread.nb <- tempo.thread.nb
+        }
+        if(verbose == TRUE){
+            tempo.cat <- paste0("NUMBER OF THREADS USED: ", thread.nb)
+            cat(paste0("\n    ", tempo.cat, "\n"))
+        }
+        Clust <- parallel::makeCluster(thread.nb, outfile = paste0(res.path, "/fun_slide_parall_log.txt")) # outfile to print or cat during parallelization (only possible in a file, outfile = "" do not work on windows)
+        cluster.list <- parallel::clusterSplit(Clust, 1:nrow(wind)) # split according to the number of cluster
+        if(verbose == TRUE){
+            tempo.cat <- paste0("SPLIT OF TEST NUMBERS IN PARALLELISATION:")
+            cat(paste0("\n    ", tempo.cat, "\n"))
+            str(cluster.list) # using print(str()) add a NULL below the result
+            cat("\n")
+        }
+        paral.output.list <- parallel::clusterApply( #
+            cl = Clust,
+            x = cluster.list,
+            function.name = function.name, 
+            data = data, 
+            FUN = fun, # because fun argument of clusterApply
+            args = args, 
+            thread.nb = thread.nb, 
+            print.count = print.count, 
+            wind = wind, 
+            left = left, 
+            right = right, 
+            res.path = res.path, 
+            lib.path = lib.path, 
+            verbose = verbose, 
+            env = env, 
+            cute.path = cute.path, 
+            fun = function(
+                x, 
+                function.name, 
+                data, 
+                FUN, 
+                args, 
+                thread.nb, 
+                print.count, 
+                wind, 
+                left, 
+                right, 
+                res.path, 
+                lib.path, 
+                verbose, 
+                env, 
+                cute.path
+            ){
+                # check again: very important because another R
+                process.id <- Sys.getpid()
+                cat(paste0("\nPROCESS ID ", process.id, " -> TESTS ", x[1], " TO ", x[length(x)], "\n"))
+                source(cute.path, local = .GlobalEnv)
+                fun_pack(req.package = "lubridate", lib.path = lib.path, load = TRUE) # load = TRUE to be sure that functions are present in the environment. And this prevent to use R.lib.path argument of fun_python_pack()
+                # end check again: very important because another R
+                ini.date <- Sys.time()
+                ini.time <- as.numeric(ini.date) # time of process begin, converted into 
+                output <- NULL
+                print.count.loop <- 0
+                for(i4 in 1:length(x)){
+                    print.count.loop <- print.count.loop + 1
+                    log <- get(left)(data, wind$left[x[i4]]) & get(right)(data, wind$right[x[i4]]) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
+                    output <- c(output, eval(parse(text = paste0("FUN(data[log]", if( ! is.null(args)){paste0(", ", args)}, ")"))))
+                    if(verbose == TRUE){
+                        if(print.count.loop == print.count){
+                            print.count.loop <- 0
+                            tempo.time <- as.numeric(Sys.time())
+                            tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time))
+                            final.loop <- (tempo.time - ini.time) / i4 * length(x) # expected duration in seconds # intra nb.compar loop lapse: time lapse / cycles done * cycles remaining
+                            final.exp <- as.POSIXct(final.loop, origin = ini.date)
+                            cat(paste0("\nIN PROCESS ", process.id, " | LOOP ", format(i4, big.mark=","), " / ", format(length(x), big.mark=","), " | TIME SPENT: ", tempo.lapse, " | EXPECTED END: ", final.exp))
+                        }
+                        if(i4 == length(x)){
+                            tempo.time <- as.numeric(Sys.time())
+                            tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time))
+                            cat(paste0("\nPROCESS ", process.id, " ENDED | LOOP ", format(i4, big.mark=","), " / ", format(length(x), big.mark=","), " | TIME SPENT: ", tempo.lapse, "\n\n"))
+                        }
+                    }
+                }
+                wind <- wind[x, ]
+                if(length(output) != nrow(wind)){
+                    tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 4")
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+                }else{
+                    output <- data.frame(wind, value = output, stringsAsFactors = TRUE)
+                    return(output)
+                }
+            }
+        )
+        parallel::stopCluster(Clust)
+        # result assembly
+        output <- data.frame()
+        for(i2 in 1:length(paral.output.list)){ # compartment relatives to each parallelization
+            output <- rbind(output, paral.output.list[[i2]], stringsAsFactors = TRUE)
+        }
+        # end result assembly
+        if(nrow(output) != nrow(wind)){
+            tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 5\nlength(output): ", length(output), "\nnrow(wind): ", nrow(wind))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            output <- output[order(output$left), ]
+        }
+    }
+    if(verbose == TRUE){
+        end.date <- Sys.time()
+        end.time <- as.numeric(end.date)
+        total.lapse <- round(lubridate::seconds_to_period(end.time - ini.time))
+        cat(paste0("\nfun_slide JOB END\n\nTIME: ", end.date, "\n\nTOTAL TIME LAPSE: ", total.lapse, "\n\n\n"))
+    }
+    return(output)
 }
 
-# test if lapply can be used
-if(parall == FALSE){
-# new environment
-env.name <- paste0("env", ini.time)
-if(exists(env.name, where = -1)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ENVIRONMENT env.name ALREADY EXISTS. PLEASE RERUN ONCE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-assign(env.name, new.env())
-assign("wind", wind, envir = get(env.name, env = sys.nframe(), inherit = FALSE))
-assign("data", data, envir = get(env.name, env = sys.nframe(), inherit = FALSE))
-}
-# end new environment
-tempo.message <- fun_get_message(data="lapply(X = wind$left, Y = data, FUN = function(X, Y){res <- get(left)(Y, X) ; return(res)})", kind = "error", header = FALSE, env = get(env.name, env = sys.nframe(), inherit = FALSE), print.no = FALSE) # no env = sys.nframe(), inherit = FALSE in get(left) because look for function in the classical scope
-rm(env.name) # optional, because should disappear at the end of the function execution
-}else{
-tempo.message <- "ERROR" # with this, force the parallelization by default
-}
-# end test if lapply can be used
-if( ! any(grepl(x = tempo.message, pattern = "ERROR.*"))){
-left.log <- lapply(X = wind$left, Y = data, FUN = function(X, Y){
-res <- get(left)(Y, X) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-return(res)
-})
-right.log <- lapply(X = wind$right, Y = data, FUN = function(X, Y){
-res <- get(right)(Y, X) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-return(res)
-})
-log <- mapply(FUN = "&", left.log, right.log, SIMPLIFY = FALSE)
-output <- eval(parse(text = paste0("sapply(lapply(log, FUN = function(X){(data[X])}), FUN = fun", if( ! is.null(args)){paste0(", ", args)}, ")"))) # take the values of the data vector according to log (list of logical, each compartment of length(data)) and apply fun with args of fun
-if(length(output) != nrow(wind)){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 3")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-output <- data.frame(wind, value = output, stringsAsFactors = TRUE)
-}
-}else{
-if(verbose == TRUE){
-tempo.cat <- paste0("PARALLELIZATION INITIATED AT: ", ini.date)
-cat(paste0("\n", tempo.cat, "\n"))
-}
-tempo.thread.nb = parallel::detectCores(all.tests = FALSE, logical = TRUE) # detect the number of threads
-if( ! is.null(thread.nb)){
-if(tempo.thread.nb < thread.nb){
-thread.nb <- tempo.thread.nb
-if(verbose == TRUE){
-tempo.cat <- paste0("ONLY: ", tempo.thread.nb, " THREADS AVAILABLE")
-cat(paste0("\n", tempo.cat, "\n"))
-}
-}
-}else{
-thread.nb <- tempo.thread.nb
-}
-if(verbose == TRUE){
-tempo.cat <- paste0("NUMBER OF THREADS USED: ", thread.nb)
-cat(paste0("\n    ", tempo.cat, "\n"))
-}
-Clust <- parallel::makeCluster(thread.nb, outfile = paste0(res.path, "/fun_slide_parall_log.txt")) # outfile to print or cat during parallelization (only possible in a file, outfile = "" do not work on windows)
-cluster.list <- parallel::clusterSplit(Clust, 1:nrow(wind)) # split according to the number of cluster
-if(verbose == TRUE){
-tempo.cat <- paste0("SPLIT OF TEST NUMBERS IN PARALLELISATION:")
-cat(paste0("\n    ", tempo.cat, "\n"))
-str(cluster.list) # using print(str()) add a NULL below the result
-cat("\n")
-}
-paral.output.list <- parallel::clusterApply( #
-cl = Clust,
-x = cluster.list,
-function.name = function.name, 
-data = data, 
-FUN = fun, # because fun argument of clusterApply
-args = args, 
-thread.nb = thread.nb, 
-print.count = print.count, 
-wind = wind, 
-left = left, 
-right = right, 
-res.path = res.path, 
-lib.path = lib.path, 
-verbose = verbose, 
-env = env, 
-cute.path = cute.path, 
-fun = function(
-x, 
-function.name, 
-data, 
-FUN, 
-args, 
-thread.nb, 
-print.count, 
-wind, 
-left, 
-right, 
-res.path, 
-lib.path, 
-verbose, 
-env, 
-cute.path
-){
-# check again: very important because another R
-process.id <- Sys.getpid()
-cat(paste0("\nPROCESS ID ", process.id, " -> TESTS ", x[1], " TO ", x[length(x)], "\n"))
-source(cute.path, local = .GlobalEnv)
-fun_pack(req.package = "lubridate", lib.path = lib.path, load = TRUE) # load = TRUE to be sure that functions are present in the environment. And this prevent to use R.lib.path argument of fun_python_pack()
-# end check again: very important because another R
-ini.date <- Sys.time()
-ini.time <- as.numeric(ini.date) # time of process begin, converted into 
-output <- NULL
-print.count.loop <- 0
-for(i4 in 1:length(x)){
-print.count.loop <- print.count.loop + 1
-log <- get(left)(data, wind$left[x[i4]]) & get(right)(data, wind$right[x[i4]]) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-output <- c(output, eval(parse(text = paste0("FUN(data[log]", if( ! is.null(args)){paste0(", ", args)}, ")"))))
-if(verbose == TRUE){
-if(print.count.loop == print.count){
-print.count.loop <- 0
-tempo.time <- as.numeric(Sys.time())
-tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time))
-final.loop <- (tempo.time - ini.time) / i4 * length(x) # expected duration in seconds # intra nb.compar loop lapse: time lapse / cycles done * cycles remaining
-final.exp <- as.POSIXct(final.loop, origin = ini.date)
-cat(paste0("\nIN PROCESS ", process.id, " | LOOP ", format(i4, big.mark=","), " / ", format(length(x), big.mark=","), " | TIME SPENT: ", tempo.lapse, " | EXPECTED END: ", final.exp))
-}
-if(i4 == length(x)){
-tempo.time <- as.numeric(Sys.time())
-tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time))
-cat(paste0("\nPROCESS ", process.id, " ENDED | LOOP ", format(i4, big.mark=","), " / ", format(length(x), big.mark=","), " | TIME SPENT: ", tempo.lapse, "\n\n"))
-}
-}
-}
-wind <- wind[x, ]
-if(length(output) != nrow(wind)){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 4")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-output <- data.frame(wind, value = output, stringsAsFactors = TRUE)
-return(output)
-}
-}
-)
-parallel::stopCluster(Clust)
-# result assembly
-output <- data.frame()
-for(i2 in 1:length(paral.output.list)){ # compartment relatives to each parallelization
-output <- rbind(output, paral.output.list[[i2]], stringsAsFactors = TRUE)
-}
-# end result assembly
-if(nrow(output) != nrow(wind)){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 5\nlength(output): ", length(output), "\nnrow(wind): ", nrow(wind))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-output <- output[order(output$left), ]
-}
-}
-if(verbose == TRUE){
-end.date <- Sys.time()
-end.time <- as.numeric(end.date)
-total.lapse <- round(lubridate::seconds_to_period(end.time - ini.time))
-cat(paste0("\nfun_slide JOB END\n\nTIME: ", end.date, "\n\nTOTAL TIME LAPSE: ", total.lapse, "\n\n\n"))
-}
-return(output)
-}
-
-
-
-
-######## fun_codon2aa() #### convert codon to amino acid using standard genetic code
-
-
-fun_codon2aa <- function(
-data,
-display = FALSE
-){
-# AIM
-# Convert codon to amino acid using standard genetic code indicated in https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables
-# WARNINGS
-# None
-# ARGUMENTS
-# data: single caracter string of three characters, or vector of three caracters, indicating the DNA codon (only "A", "T", "G" and "C" allowed). Case insensitive. Omitted if display argument is TRUE
-# display: logical. Display the whole genetic table? if TRUE, override data
-# RETURN
-# The 1 letter uppercase amino acid of the submitted codon or the whole table if display argument is TRUE
-# REQUIRED PACKAGES
-# None
-# REQUIRED FUNCTIONS FROM THE cute PACKAGE
-# fun_check()
-# EXAMPLE
-# fun_codon2aa(data = "ATC", display = TRUE)
-# see http
-# DEBUGGING
-# data = "atg" ; display = FALSE
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
-arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
-# end function name
-# required function checking
-req.function <- c(
-"fun_check"
-)
-tempo <- NULL
-for(i1 in req.function){
-if(length(find(i1, mode = "function")) == 0L){
-tempo <- c(tempo, i1)
-}
-}
-if( ! is.null(tempo)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# reserved words
-# end reserved words
-# arg with no default values
-mandat.args <- c(
-"data"
-)
-tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
-if(any(tempo)){ # normally no NA for missing() output
-tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(length(mandat.args) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end arg with no default values
-# argument primary checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = data, class = "vector", typeof = "character", fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = display, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){ # normally no NA
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between == #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument primary checking
-# second round of checking and data preparation
-# management of NA arguments
-tempo.arg <- names(arg.user.setting) # values provided by the user
-tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
-if(any(tempo.log) == TRUE){ # normally no NA because is.na() used here
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT JUST BE NA")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NA arguments
-# management of NULL arguments
-tempo.arg <-c(
-"data", 
-"display"
-)
-tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
-if(any(tempo.log) == TRUE){# normally no NA with is.null()
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NULL arguments
-# code that protects set.seed() in the global environment
-# end code that protects set.seed() in the global environment
-# warning initiation
-# end warning initiation
-# other checkings
-if(length(data) == 1L){
-data <- unlist(strsplit(data, split = ""))
-}else if(length(data) != 3L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data ARGUMENT MUST BE A STRING OF THREE CHARACTERS OR A VECTOR OF THREE CHARACTERS, MADE OF \"A\", \"C\", \"G\", \"T\" ONLY")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! all(toupper(data) %in% c("A", "C", "G","T"))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data ARGUMENT MUST BE A STRING OF THREE CHARACTERS OR A VECTOR OF THREE CHARACTERS, MADE OF \"A\", \"C\", \"G\", \"T\" ONLY")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end other checkings
-# reserved word checking
-# end reserved word checking
-# end second round of checking and data preparation
-# package checking
-# end package checking
-# main code
-# standard genetic code
-sgc <- array(
-c(
-"F", "L", "I", "V",
-"S", "P", "T", "A",
-"Y", "H", "N", "D",
-"C", "R", "S", "G",
-
-"F", "L", "I", "V",
-"S", "P", "T", "A",
-"Y", "H", "N", "D",
-"C", "R", "S", "G",
-
-"L", "L", "I", "V",
-"S", "P", "T", "A",
-"stop", "Q", "K", "E",
-"stop", "R", "R", "G",
-
-"L", "L", "M", "V",
-"S", "P", "T", "A",
-"stop", "Q", "K", "E",
-"W", "R", "R", "G"
-), 
-dim = c(4, 4, 4),
-dimnames = list(
-first = c("T", "C", "A", "G"), 
-second = c("T", "C", "A", "G"), 
-third = c("T", "C", "A", "G")
-)
-)
-# end standard genetic code
-if(display == TRUE){
-output <- sgc
-}else{
-data <- toupper(data)
-output <- eval(parse(text = paste0("sgc['", paste0(data, collapse = "','"), "']")))
-}
-return(output)
+
+
+
+######## fun_codon2aa() #### convert codon to amino acid using standard genetic code
+
+
+fun_codon2aa <- function(
+    data,
+    display = FALSE
+){
+    # AIM
+    # Convert codon to amino acid using standard genetic code indicated in https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables
+    # WARNINGS
+    # None
+    # ARGUMENTS
+    # data: single caracter string of three characters, or vector of three caracters, indicating the DNA codon (only "A", "T", "G" and "C" allowed). Case insensitive. Omitted if display argument is TRUE
+    # display: logical. Display the whole genetic table? if TRUE, override data
+    # RETURN
+    # The 1 letter uppercase amino acid of the submitted codon or the whole table if display argument is TRUE
+    # REQUIRED PACKAGES
+    # None
+    # REQUIRED FUNCTIONS FROM THE cute PACKAGE
+    # fun_check()
+    # EXAMPLE
+    # fun_codon2aa(data = "ATC", display = TRUE)
+    # see http
+    # DEBUGGING
+    # data = "atg" ; display = FALSE
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
+    arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
+    # end function name
+    # required function checking
+    req.function <- c(
+        "fun_check"
+    )
+    tempo <- NULL
+    for(i1 in req.function){
+        if(length(find(i1, mode = "function")) == 0L){
+            tempo <- c(tempo, i1)
+        }
+    }
+    if( ! is.null(tempo)){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # reserved words
+    # end reserved words
+    # arg with no default values
+    mandat.args <- c(
+        "data"
+    )
+    tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
+    if(any(tempo)){ # normally no NA for missing() output
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(length(mandat.args) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args, collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end arg with no default values
+    # argument primary checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = data, class = "vector", typeof = "character", fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = display, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){ # normally no NA
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between == #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument primary checking
+    # second round of checking and data preparation
+    # management of NA arguments
+    tempo.arg <- names(arg.user.setting) # values provided by the user
+    tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
+    if(any(tempo.log) == TRUE){ # normally no NA because is.na() used here
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT JUST BE NA")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NA arguments
+    # management of NULL arguments
+    tempo.arg <-c(
+        "data", 
+        "display"
+    )
+    tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
+    if(any(tempo.log) == TRUE){# normally no NA with is.null()
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NULL arguments
+    # code that protects set.seed() in the global environment
+    # end code that protects set.seed() in the global environment
+    # warning initiation
+    # end warning initiation
+    # other checkings
+    if(length(data) == 1L){
+        data <- unlist(strsplit(data, split = ""))
+    }else if(length(data) != 3L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": data ARGUMENT MUST BE A STRING OF THREE CHARACTERS OR A VECTOR OF THREE CHARACTERS, MADE OF \"A\", \"C\", \"G\", \"T\" ONLY")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! all(toupper(data) %in% c("A", "C", "G","T"))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": data ARGUMENT MUST BE A STRING OF THREE CHARACTERS OR A VECTOR OF THREE CHARACTERS, MADE OF \"A\", \"C\", \"G\", \"T\" ONLY")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end other checkings
+    # reserved word checking
+    # end reserved word checking
+    # end second round of checking and data preparation
+    # package checking
+    # end package checking
+    # main code
+    # standard genetic code
+    sgc <- array(
+        c(
+            "F", "L", "I", "V",
+            "S", "P", "T", "A",
+            "Y", "H", "N", "D",
+            "C", "R", "S", "G",
+            
+            "F", "L", "I", "V",
+            "S", "P", "T", "A",
+            "Y", "H", "N", "D",
+            "C", "R", "S", "G",
+            
+            "L", "L", "I", "V",
+            "S", "P", "T", "A",
+            "stop", "Q", "K", "E",
+            "stop", "R", "R", "G",
+            
+            "L", "L", "M", "V",
+            "S", "P", "T", "A",
+            "stop", "Q", "K", "E",
+            "W", "R", "R", "G"
+        ), 
+        dim = c(4, 4, 4),
+        dimnames = list(
+            first = c("T", "C", "A", "G"), 
+            second = c("T", "C", "A", "G"), 
+            third = c("T", "C", "A", "G")
+        )
+    )
+    # end standard genetic code
+    if(display == TRUE){
+        output <- sgc
+    }else{
+        data <- toupper(data)
+        output <- eval(parse(text = paste0("sgc['", paste0(data, collapse = "','"), "']")))
+    }
+    return(output)
 }
 
 
@@ -4474,146 +4474,146 @@ return(output)
 
 
 fun_codon_finder <- function(
-pos, 
-begin, 
-end
+    pos, 
+    begin, 
+    end
 ){
-# AIM
-# gives the codon number and position in the codon of nucleotid positions
-# WARNINGS
-# Only for coding sequences (no introns): ((end - begin) + 1) / 3 must be an integer (i.e., modulo zero)
-# Negatives positions allowed but this implies that one base has the position 0 in the sequence
-# ARGUMENTS
-# pos: vector of integers indicating the positions of nucleotids in a sequence. Must be between begin and end arguments
-# begin: single integer indicating the position of the first base of the coding sequence
-# end: single indicating the position of the last base of the coding sequence
-# RETURN
-# a data frame with column names:
-# pos: values of the pos argument
-# codon_nb: the codon number in the CDS encompassing the pos value
-# codon_pos: the position of pos in the codon (either 1, 2 or 3)
-# codon_begin: the first base position of the codon
-# codon_end: the last base position of the codon
-# REQUIRED PACKAGES
-# None
-# REQUIRED FUNCTIONS FROM THE cute PACKAGE
-# fun_check()
-# EXAMPLE
-# fun_codon_finder(c(5, 6, 8, 10), begin = 5, end = 10)
-# fun_codon_finder(c(0, 5, 6, 8, 10), begin = -2, end = 12)
-# see http
-# DEBUGGING
-# pos = c(5, 6, 8, 10) ; begin = 5 ; end = 10
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
-arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
-# end function name
-# required function checking
-req.function <- c(
-"fun_check"
-)
-tempo <- NULL
-for(i1 in req.function){
-if(length(find(i1, mode = "function")) == 0L){
-tempo <- c(tempo, i1)
-}
-}
-if( ! is.null(tempo)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# reserved words
-# end reserved words
-# arg with no default values
-mandat.args <- c(
-"pos", 
-"begin", 
-"end"
-)
-tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
-if(any(tempo)){ # normally no NA for missing() output
-tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(length(mandat.args) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end arg with no default values
-# argument primary checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = pos, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = begin, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = end, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){ # normally no NA
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between == #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument primary checking
-# second round of checking and data preparation
-# management of NA arguments
-tempo.arg <- names(arg.user.setting) # values provided by the user
-tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
-if(any(tempo.log) == TRUE){ # normally no NA because is.na() used here
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT JUST BE NA")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NA arguments
-# management of NULL arguments
-tempo.arg <-c(
-"pos", 
-"begin", 
-"end"
-)
-tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
-if(any(tempo.log) == TRUE){# normally no NA with is.null()
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NULL arguments
-# code that protects set.seed() in the global environment
-# end code that protects set.seed() in the global environment
-# warning initiation
-# end warning initiation
-# other checkings
-if(begin >= end){
-tempo.cat <- paste0("ERROR IN ", function.name, ": end ARGUMENT MUST BE STRICTLY GREATER THAN begin ARGUMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if((end - begin + 1) %% 3 != 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ((end - begin) + 1) / 3 MUST BE AN INTEGER (I.E., MODULO ZERO)")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(pos < begin | pos > end)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": pos ARGUMENT VALUES MUST BE BETWEEN begin AND end ARGUMENT VALUES")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end other checkings
-# reserved word checking
-# end reserved word checking
-# end second round of checking and data preparation
-# package checking
-# end package checking
-# main code
-first <- seq.int(from = begin, to = end, by = 3)
-last <- seq.int(from = begin + 2, to = end, by = 3)
-tempo <- lapply(X = pos, FUN = function(x = X){
-tempo.log <- x >= first & x <= last
-if(sum(tempo.log, na.rm = TRUE) != 1){ # check that 1 possible TRUE
-tempo.cat <- paste0("ERROR IN ", function.name, ": INTERNAL ERROR. CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-codon_nb <- which(tempo.log)
-codon_pos <- as.integer((x - (begin + (codon_nb - 1) * 3) + 1))
-codon_begin <- as.integer(first[tempo.log])
-codon_end <- as.integer(last[tempo.log])
-}
-return(data.frame(codon_nb = codon_nb, codon_pos = codon_pos, codon_begin = codon_begin, codon_end = codon_end))
-})
-tempo <- do.call("rbind", tempo)
-output <- data.frame(pos = as.integer(pos), tempo)
-return(output)
+    # AIM
+    # gives the codon number and position in the codon of nucleotid positions
+    # WARNINGS
+    # Only for coding sequences (no introns): ((end - begin) + 1) / 3 must be an integer (i.e., modulo zero)
+    # Negatives positions allowed but this implies that one base has the position 0 in the sequence
+    # ARGUMENTS
+    # pos: vector of integers indicating the positions of nucleotids in a sequence. Must be between begin and end arguments
+    # begin: single integer indicating the position of the first base of the coding sequence
+    # end: single indicating the position of the last base of the coding sequence
+    # RETURN
+    # a data frame with column names:
+    # pos: values of the pos argument
+    # codon_nb: the codon number in the CDS encompassing the pos value
+    # codon_pos: the position of pos in the codon (either 1, 2 or 3)
+    # codon_begin: the first base position of the codon
+    # codon_end: the last base position of the codon
+    # REQUIRED PACKAGES
+    # None
+    # REQUIRED FUNCTIONS FROM THE cute PACKAGE
+    # fun_check()
+    # EXAMPLE
+    # fun_codon_finder(c(5, 6, 8, 10), begin = 5, end = 10)
+    # fun_codon_finder(c(0, 5, 6, 8, 10), begin = -2, end = 12)
+    # see http
+    # DEBUGGING
+    # pos = c(5, 6, 8, 10) ; begin = 5 ; end = 10
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
+    arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
+    # end function name
+    # required function checking
+    req.function <- c(
+        "fun_check"
+    )
+    tempo <- NULL
+    for(i1 in req.function){
+        if(length(find(i1, mode = "function")) == 0L){
+            tempo <- c(tempo, i1)
+        }
+    }
+    if( ! is.null(tempo)){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # reserved words
+    # end reserved words
+    # arg with no default values
+    mandat.args <- c(
+        "pos", 
+        "begin", 
+        "end"
+    )
+    tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
+    if(any(tempo)){ # normally no NA for missing() output
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(length(mandat.args) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args, collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end arg with no default values
+    # argument primary checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = pos, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = begin, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = end, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){ # normally no NA
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between == #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument primary checking
+    # second round of checking and data preparation
+    # management of NA arguments
+    tempo.arg <- names(arg.user.setting) # values provided by the user
+    tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
+    if(any(tempo.log) == TRUE){ # normally no NA because is.na() used here
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT JUST BE NA")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NA arguments
+    # management of NULL arguments
+    tempo.arg <-c(
+        "pos", 
+        "begin", 
+        "end"
+    )
+    tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
+    if(any(tempo.log) == TRUE){# normally no NA with is.null()
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NULL arguments
+    # code that protects set.seed() in the global environment
+    # end code that protects set.seed() in the global environment
+    # warning initiation
+    # end warning initiation
+    # other checkings
+    if(begin >= end){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": end ARGUMENT MUST BE STRICTLY GREATER THAN begin ARGUMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if((end - begin + 1) %% 3 != 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": ((end - begin) + 1) / 3 MUST BE AN INTEGER (I.E., MODULO ZERO)")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(any(pos < begin | pos > end)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": pos ARGUMENT VALUES MUST BE BETWEEN begin AND end ARGUMENT VALUES")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end other checkings
+    # reserved word checking
+    # end reserved word checking
+    # end second round of checking and data preparation
+    # package checking
+    # end package checking
+    # main code
+    first <- seq.int(from = begin, to = end, by = 3)
+    last <- seq.int(from = begin + 2, to = end, by = 3)
+    tempo <- lapply(X = pos, FUN = function(x = X){
+        tempo.log <- x >= first & x <= last
+        if(sum(tempo.log, na.rm = TRUE) != 1){ # check that 1 possible TRUE
+            tempo.cat <- paste0("ERROR IN ", function.name, ": INTERNAL ERROR. CODE HAS TO BE MODIFIED")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            codon_nb <- which(tempo.log)
+            codon_pos <- as.integer((x - (begin + (codon_nb - 1) * 3) + 1))
+            codon_begin <- as.integer(first[tempo.log])
+            codon_end <- as.integer(last[tempo.log])
+        }
+        return(data.frame(codon_nb = codon_nb, codon_pos = codon_pos, codon_begin = codon_begin, codon_end = codon_end))
+    })
+    tempo <- do.call("rbind", tempo)
+    output <- data.frame(pos = as.integer(pos), tempo)
+    return(output)
 }
 
 
@@ -4633,8798 +4633,8786 @@ return(output)
 
 
 fun_width <- function(
-class.nb, 
-inches.per.class.nb = 1, 
-ini.window.width = 7, 
-inch.left.space, 
-inch.right.space, 
-boundarie.space = 0.5
-){
-# AIM
-# rescale the width of a window to open depending on the number of classes to plot
-# can be used for height, considering that it is as if it was a width
-# this order can be used:
-# fun_width()
-# fun_open()
-# fun_prior_plot() # not for ggplot2
-# plot() or any other plotting
-# fun_post_plot() if fun_prior_plot() has been used # not for ggplot2
-# fun_close()
-# ARGUMENTS
-# class.nb: number of class to plot
-# inches.per.class.nb: number of inches per unit of class.nb. 2 means 2 inches for each boxplot for instance
-# ini.window.width:initial window width in inches
-# inch.left.space: left horizontal margin of the figure region (in inches)
-# inch.right.space: right horizontal margin of the figure region (in inches)
-# boundarie.space: space between the right and left limits of the plotting region and the plot (0.5 means half a class width)
-# RETURN
-# the new window width in inches
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# fun_width(class.nb = 10, inches.per.class.nb = 0.2, ini.window.width = 7, inch.left.space = 1, inch.right.space = 1, boundarie.space = 0.5)
-# DEBUGGING
-# class.nb = 10 ; inches.per.class.nb = 0.2 ; ini.window.width = 7 ; inch.left.space = 1 ; inch.right.space = 1 ; boundarie.space = 0.5 # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = class.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = inches.per.class.nb, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = ini.window.width, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = inch.left.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = inch.right.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = boundarie.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-range.max <- class.nb + boundarie.space # the max range of the future plot
-range.min <- boundarie.space # the min range of the future plot
-window.width <- inch.left.space + inch.right.space + inches.per.class.nb * (range.max - range.min)
-return(window.width)
-}
-
-
-######## fun_open() #### open a GUI or pdf graphic window
-
-
-fun_open <- function(
-pdf = TRUE, 
-pdf.path = "working.dir", 
-pdf.name = "graph", 
-width = 7, 
-height = 7, 
-paper = "special", 
-pdf.overwrite = FALSE, 
-rescale = "fixed", 
-remove.read.only = TRUE, 
-return.output = FALSE
-){
-# AIM
-# open a pdf or screen (GUI) graphic window and return initial graphic parameters
-# this order can be used:
-# fun_width()
-# fun_open()
-# fun_prior_plot() # not for ggplot2
-# plot() or any other plotting
-# fun_post_plot() if fun_prior_plot() has been used # not for ggplot2
-# fun_close()
-# WARNINGS
-# On Linux, use pdf = TRUE, if (GUI) graphic window is not always available, meaning that X is not installed (clusters for instance). Use X11() in R to test if available
-# ARGUMENTS:
-# pdf: logical. Use pdf display? If FALSE, a GUI is opened
-# pdf.path: where the pdf is saved (do not terminate by / or \\). Write "working.dir" if working directory is required (default). Ignored if pdf == FALSE
-# pdf.name: name of the pdf file containing the graphs (the .pdf extension is added by the function, if not detected in the name end). Ignored if pdf == FALSE
-# width: width of the window (in inches)
-# height: height of the window (in inches)
-# paper: paper argument of the pdf function (paper format). Only used for pdf(). Either "a4", "letter", "legal", "us", "executive", "a4r", "USr" or "special". If "special", means that the paper dimension will be width and height. With another paper format, if width or height is over the size of the paper, width or height will be modified such that the plot is adjusted to the paper dimension (see $dim in the returned list below to see the modified dimensions). Ignored if pdf == FALSE
-# pdf.overwrite: logical. Existing pdf can be overwritten? . Ignored if pdf == FALSE
-# rescale: kind of GUI. Either "R", "fit", or "fixed". Ignored on Mac and Linux OS. See ?windows for details
-# remove.read.only: logical. remove the read only (R.O.) graphical parameters? If TRUE, the graphical parameters are returned without the R.O. parameters. The returned $ini.par list can be used to set the par() of a new graphical device. If FALSE, graphical parameters are returned with the R.O. parameters, which provides information like text dimension (see ?par() ). The returned $ini.par list can be used to set the par() of a new graphical device, but generate a warning message. Ignored if return.output == FALSE. 
-# return.output: logical. Return output ? If TRUE the output list is displayed
-# RETURN
-# a list containing:
-# $pdf.loc: path of the pdf created
-# $ini.par: initial par() parameters
-# $zone.ini: initial window spliting
-# $dim: dimension of the graphical device (in inches)
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# fun_open(pdf = FALSE, pdf.path = "C:/Users/Gael/Desktop", pdf.name = "graph", width = 7, height = 7, paper = "special", pdf.overwrite = FALSE, return.output = TRUE)
-# DEBUGGING
-# pdf = TRUE ; pdf.path = "C:/Users/Gael/Desktop" ; pdf.name = "graphs" ; width = 7 ; height = 7 ; paper = "special" ; pdf.overwrite = FALSE ; rescale = "fixed" ; remove.read.only = TRUE ; return.output = TRUE # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = pdf, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = pdf.path, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = pdf.name, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = width, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = height, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = paper, options = c("a4", "letter", "legal", "us", "executive", "a4r", "USr", "special", "A4", "LETTER", "LEGAL", "US"), length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data =pdf.overwrite, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = rescale, options = c("R", "fit", "fixed"), length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = remove.read.only, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = return.output, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-if(pdf.path == "working.dir"){
-pdf.path <- getwd()
-}else{
-if(grepl(x = pdf.path, pattern = ".+/$")){
-pdf.path <- sub(x = pdf.path, pattern = "/$", replacement = "") # remove the last /
-}else if(grepl(x = pdf.path, pattern = ".+[\\]$")){ # or ".+\\\\$" # cannot be ".+\$" because \$ does not exist contrary to \n
-pdf.path <- sub(x = pdf.path, pattern = "[\\]$", replacement = "") # remove the last /
-}
-if(dir.exists(pdf.path) == FALSE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\npdf.path ARGUMENT DOES NOT CORRESPOND TO EXISTING DIRECTORY\n", pdf.path)
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# par.ini recovery
-# cannot use pdf(file = NULL), because some small differences between pdf() and other devices. For instance, differences with windows() for par()$fin, par()$pin and par()$plt
-if(Sys.info()["sysname"] == "Windows"){ # Note that .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
-open.fail <- NULL
-grDevices::windows()
-ini.par <- par(no.readonly = remove.read.only) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
-invisible(dev.off()) # close the new window
-}else if(Sys.info()["sysname"] == "Linux"){
-if(pdf == TRUE){# cannot use pdf(file = NULL), because some small differences between pdf() and other devices. For instance, differences with windows() for par()$fin, par()$pin and par()$plt
-if(exists(".Random.seed", envir = .GlobalEnv)){ # if .Random.seed does not exists, it means that no random operation has been performed yet in any R environment
-tempo.random.seed <- .Random.seed
-on.exit(assign(".Random.seed", tempo.random.seed, env = .GlobalEnv))
-}else{
-on.exit(set.seed(NULL)) # inactivate seeding -> return to complete randomness
-}
-set.seed(NULL)
-tempo.code <- sample(x = 1:1e7, size = 1)
-while(file.exists(paste0(pdf.path, "/recover_ini_par", tempo.code, ".pdf")) == TRUE){
-tempo.code <- tempo.code + 1
-}
-grDevices::pdf(width = width, height = height, file=paste0(pdf.path, "/recover_ini_par", tempo.code, ".pdf"), paper = paper)
-ini.par <- par(no.readonly = remove.read.only) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
-invisible(dev.off()) # close the pdf window
-file.remove(paste0(pdf.path, "/recover_ini_par", tempo.code, ".pdf")) # remove the pdf file
-}else{
-# test if X11 can be opened
-if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nTHIS FUNCTION CANNOT BE USED ON LINUX IF A Rplots.pdf FILE ALREADY EXISTS HERE\n", getwd())
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-open.fail <- suppressWarnings(try(grDevices::X11(), silent = TRUE))[] # try to open a X11 window. If open.fail == NULL, no problem, meaning that the X11 window is opened. If open.fail != NULL, a pdf can be opened here paste0(getwd(), "/Rplots.pdf")
-if(is.null(open.fail)){
-ini.par <- par(no.readonly = remove.read.only) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
-invisible(dev.off()) # close the new window
-}else if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
-file.remove(paste0(getwd(), "/Rplots.pdf")) # remove the pdf file
-tempo.cat <- ("ERROR IN fun_open()\nTHIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM\nTO OVERCOME THIS, EITHER SET THE X GRAPHIC INTERFACE OF THE SYSTEM OR SET THE pdf ARGUMENT OF THE fun_open() FUNCTION TO TRUE AND RERUN")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-}
-}else{
-open.fail <- NULL
-grDevices::quartz()
-ini.par <- par(no.readonly = remove.read.only) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
-invisible(dev.off()) # close the new window
-}
-# end par.ini recovery 
-zone.ini <- matrix(1, ncol=1) # to recover the initial parameters for next figure region when device region split into several figure regions
-if(pdf == TRUE){
-if(grepl(x = pdf.name, pattern = "\\.pdf$")){
-pdf.name <- sub(x = pdf.name, pattern = "\\.pdf$", replacement = "") # remove the last .pdf
-}
-pdf.loc <- paste0(pdf.path, "/", pdf.name, ".pdf")
-if(file.exists(pdf.loc) == TRUE & pdf.overwrite == FALSE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\npdf.loc FILE ALREADY EXISTS AND CANNOT BE OVERWRITTEN DUE TO pdf.overwrite ARGUMENT SET TO TRUE\n", pdf.loc)
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-grDevices::pdf(width = width, height = height, file=pdf.loc, paper = paper)
-}
-}else if(pdf == FALSE){
-pdf.loc <- NULL
-if(Sys.info()["sysname"] == "Windows"){ # .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
-grDevices::windows(width = width, height = height, rescale = rescale)
-}else if(Sys.info()["sysname"] == "Linux"){
-if( ! is.null(open.fail)){
-tempo.cat <- "ERROR IN fun_open()\nTHIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM\nTO OVERCOME THIS, EITHER SET THE X GRAPHIC INTERFACE OF THE SYSTEM OR SET THE pdf ARGUMENT OF THE fun_open() FUNCTION TO TRUE AND RERUN"
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-grDevices::X11(width = width, height = height)
-}
-}else{
-grDevices::quartz(width = width, height = height)
-}
-}
-if(return.output == TRUE){
-output <- list(pdf.loc = pdf.loc, ini.par = ini.par, zone.ini = zone.ini, dim = dev.size())
-return(output)
-}
-}
-
-
-######## fun_prior_plot() #### set graph param before plotting (erase axes for instance)
-
-
-fun_prior_plot <- function(
-param.reinitial = FALSE, 
-xlog.scale = FALSE, 
-ylog.scale = FALSE, 
-remove.label = TRUE, 
-remove.x.axis = TRUE, 
-remove.y.axis = TRUE, 
-std.x.range = TRUE, 
-std.y.range = TRUE, 
-down.space = 1, 
-left.space = 1, 
-up.space = 1, 
-right.space = 1, 
-orient = 1, 
-dist.legend = 3.5, 
-tick.length = 0.5, 
-box.type = "n", 
-amplif.label = 1, 
-amplif.axis = 1, 
-display.extend = FALSE, 
-return.par = FALSE
-){
-# AIM
-# very convenient to erase the axes for post plot axis redrawing using fun_post_plot()
-# reinitialize and set the graphic parameters before plotting
-# CANNOT be used if no graphic device already opened
-# ARGUMENTS
-# param.reinitial: reinitialize graphic parameters before applying the new ones, as defined by the other arguments? Either TRUE or FALSE
-# xlog.scale: Log scale for the x-axis? Either TRUE or FALSE. If TRUE, erases the x-axis, except legend, for further drawing by fun_post_plot()(xlog argument of par())
-# ylog.scale: Log scale for the y-axis? Either TRUE or FALSE. If TRUE, erases the y-axis, except legend, for further drawing by fun_post_plot()(ylog argument of par())
-# remove.label: remove labels (axis legend) of the two axes? Either TRUE or FALSE (ann argument of par())
-# remove.x.axis: remove x-axis except legend? Either TRUE or FALSE (control the xaxt argument of par()). Automately set to TRUE if xlog.scale == TRUE
-# remove.y.axis: remove y-axis except legend? Either TRUE or FALSE (control the yaxt argument of par()). Automately set to TRUE if ylog.scale == TRUE
-# std.x.range: standard range on the x-axis? TRUE (no range extend) or FALSE (4% range extend). Controls xaxs argument of par() (TRUE is xaxs = "i", FALSE is xaxs = "r")
-# std.y.range: standard range on the y-axis? TRUE (no range extend) or FALSE (4% range extend). Controls yaxs argument of par() (TRUE is yaxs = "i", FALSE is yaxs = "r")
-# down.space: lower vertical margin (in inches, mai argument of par())
-# left.space: left horizontal margin (in inches, mai argument of par())
-# up.space: upper vertical margin between plot region and grapical window (in inches, mai argument of par())
-# right.space: right horizontal margin (in inches, mai argument of par())
-# orient: scale number orientation (las argument of par()). 0, always parallel to the axis; 1, always horizontal; 2, always perpendicular to the axis; 3, always vertical
-# dist.legend: numeric value that moves axis legends away in inches (first number of mgp argument of par() but in inches thus / 0.2)
-# tick.length: length of the ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc. 0 means no tick
-# box.type: bty argument of par(). Either "o", "l", "7", "c", "u", "]", the resulting box resembles the corresponding upper case letter. A value of "n" suppresses the box
-# amplif.label: increase or decrease the size of the text in legends
-# amplif.axis: increase or decrease the size of the scale numbers in axis
-# display.extend: extend display beyond plotting region? Either TRUE or FALSE (xpd argument of par() without NA)
-# return.par: return graphic parameter modification?
-# RETURN
-# return graphic parameter modification
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# fun_prior_plot(param.reinitial = FALSE, xlog.scale = FALSE, ylog.scale = FALSE, remove.label = TRUE, remove.x.axis = TRUE, remove.y.axis = TRUE, std.x.range = TRUE, std.y.range = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 4.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = FALSE)
-# DEBUGGING
-# param.reinitial = FALSE ; xlog.scale = FALSE ; ylog.scale = FALSE ; remove.label = TRUE ; remove.x.axis = TRUE ; remove.y.axis = TRUE ; std.x.range = TRUE ; std.y.range = TRUE ; down.space = 1 ; left.space = 1 ; up.space = 1 ; right.space = 1 ; orient = 1 ; dist.legend = 4.5 ; tick.length = 0.5 ; box.type = "n" ; amplif.label = 1 ; amplif.axis = 1 ; display.extend = FALSE ; return.par = FALSE # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = param.reinitial, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = xlog.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = ylog.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = remove.label, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = remove.x.axis, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = remove.y.axis, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = std.x.range, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = std.y.range, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = down.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = left.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = up.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = right.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = orient, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = dist.legend, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = tick.length, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = box.type, options = c("o", "l", "7", "c", "u", "]", "n"), length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = amplif.label, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = amplif.axis, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = display.extend, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = return.par, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-if(is.null(dev.list())){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THIS FUNCTION CANNOT BE USED IF NO GRAPHIC DEVICE ALREADY OPENED (dev.list() IS CURRENTLY NULL)")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# par.ini recovery
-# cannot use pdf(file = NULL), because some small differences between pdf() and other devices. For instance, differences with windows() for par()$fin, par()$pin and par()$plt
-if(param.reinitial == TRUE){
-if( ! all(names(dev.cur()) == "null device")){
-active.wind.nb <- dev.cur()
-}else{
-active.wind.nb <- 0
-}
-if(Sys.info()["sysname"] == "Windows"){ # Note that .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
-grDevices::windows()
-ini.par <- par(no.readonly = FALSE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
-invisible(dev.off()) # close the new window
-}else if(Sys.info()["sysname"] == "Linux"){
-if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THIS FUNCTION CANNOT BE USED ON LINUX WITH param.reinitial SET TO TRUE IF A Rplots.pdf FILE ALREADY EXISTS HERE: ", getwd())
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-open.fail <- suppressWarnings(try(grDevices::X11(), silent = TRUE))[] # try to open a X11 window. If open.fail == NULL, no problem, meaning that the X11 window is opened. If open.fail != NULL, a pdf can be opened here paste0(getwd(), "/Rplots.pdf")
-if(is.null(open.fail)){
-ini.par <- par(no.readonly = FALSE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
-invisible(dev.off()) # close the new window
-}else if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
-ini.par <- par(no.readonly = FALSE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
-invisible(dev.off()) # close the new window
-file.remove(paste0(getwd(), "/Rplots.pdf")) # remove the pdf file
-}else{
-tempo.cat <- ("ERROR IN fun_prior_plot()\nTHIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM\nTO OVERCOME THIS, PLEASE USE A PDF GRAPHIC INTERFACE AND RERUN")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-}else{ # macOS
-grDevices::quartz()
-ini.par <- par(no.readonly = FALSE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened)
-invisible(dev.off()) # close the new window
-}
-if( ! all(names(dev.cur()) == "null device")){
-invisible(dev.set(active.wind.nb)) # go back to the active window if exists
-par(ini.par) # apply the initial par to current window
-}
-}
-# end par.ini recovery
-if(remove.x.axis == TRUE){
-par(xaxt = "n") # suppress the y-axis label
-}else{
-par(xaxt = "s")
-}
-if(remove.y.axis == TRUE){
-par(yaxt = "n") # suppress the y-axis label
-}else{
-par(yaxt = "s")
-}
-if(std.x.range == TRUE){
-par(xaxs = "i")
-}else{
-par(xaxs = "r")
-}
-if(std.y.range == TRUE){
-par(yaxs = "i")
-}else{
-par(yaxs = "r")
-}
-par(mai = c(down.space, left.space, up.space, right.space), ann = ! remove.label, las = orient, mgp = c(dist.legend/0.2, 1, 0), xpd = display.extend, bty= box.type, cex.lab = amplif.label, cex.axis = amplif.axis)
-par(tcl = -par()$mgp[2] * tick.length) # tcl gives the length of the ticks as proportion of line text, knowing that mgp is in text lines. So the main ticks are a 0.5 of the distance of the axis numbers by default. The sign provides the side of the tick (negative for outside of the plot region)
-if(xlog.scale == TRUE){
-par(xaxt = "n", xlog = TRUE) # suppress the x-axis label
-}else{
-par(xlog = FALSE)
-}
-if(ylog.scale == TRUE){
-par(yaxt = "n", ylog = TRUE) # suppress the y-axis label
-}else{
-par(ylog = FALSE)
-}
-if(return.par == TRUE){
-tempo.par <- par()
-return(tempo.par)
-}
-}
-
-
-######## fun_scale() #### select nice label numbers when setting number of ticks on an axis
-
-
- 
-
-
-fun_scale <- function(n, lim, kind = "approx", lib.path = NULL){
-# AIM
-# attempt to select nice scale numbers when setting n ticks on a lim axis range
-# ARGUMENTS
-# n: desired number of main ticks on the axis (integer above 0)
-# lim: vector of 2 numbers indicating the limit range of the axis. Order of the 2 values matters (for inverted axis). Can be log transformed values
-# kind: either "approx" (approximative), "strict" (strict) or "strict.cl" (strict clean). If "approx", use the scales::trans_breaks() function to provide an easy to read scale of approximately n ticks spanning the range of the lim argument. If "strict", cut the range of the lim argument into n + 1 equidistant part and return the n numbers at each boundary. This often generates numbers uneasy to read. If "strict.cl", provide an easy to read scale of exactly n ticks, but sometimes not completely spanning the range of the lim argument
-# lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
-# RETURN
-# a vector of numbers
-# REQUIRED PACKAGES
-# if kind = "approx":
-# ggplot2
-# scales
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# fun_round()
-# EXAMPLES
-# approximate number of main ticks
-# ymin = 2 ; ymax = 3.101 ; n = 5 ; scale <- fun_scale(n = n, lim = c(ymin, ymax), kind = "approx") ; scale ; par(yaxt = "n", yaxs = "i", las = 1) ; plot(ymin:ymax, ymin:ymax, xlim = range(scale, ymin, ymax)[order(c(ymin, ymax))], ylim = range(scale, ymin, ymax)[order(c(ymin, ymax))], xlab = "DEFAULT SCALE", ylab = "NEW SCALE") ; par(yaxt = "s") ; axis(side = 2, at = scale)
-# strict number of main ticks
-# ymin = 2 ; ymax = 3.101 ; n = 5 ; scale <- fun_scale(n = n, lim = c(ymin, ymax), kind = "strict") ; scale ; par(yaxt = "n", yaxs = "i", las = 1) ; plot(ymin:ymax, ymin:ymax, xlim = range(scale, ymin, ymax)[order(c(ymin, ymax))], ylim = range(scale, ymin, ymax)[order(c(ymin, ymax))], xlab = "DEFAULT SCALE", ylab = "NEW SCALE") ; par(yaxt = "s") ; axis(side = 2, at = scale)
-# strict "clean" number of main ticks
-# ymin = 2 ; ymax = 3.101 ; n = 5 ; scale <- fun_scale(n = n, lim = c(ymin, ymax), kind = "strict.cl") ; scale ; par(yaxt = "n", yaxs = "i", las = 1) ; plot(ymin:ymax, ymin:ymax, xlim = range(scale, ymin, ymax)[order(c(ymin, ymax))], ylim = range(scale, ymin, ymax)[order(c(ymin, ymax))], xlab = "DEFAULT SCALE", ylab = "NEW SCALE") ; par(yaxt = "s") ; axis(side = 2, at = scale)
-# approximate number of main ticks, scale inversion
-# ymin = 3.101 ; ymax = 2 ; n = 5 ; scale <- fun_scale(n = n, lim = c(ymin, ymax), kind = "approx") ; scale ; par(yaxt = "n", yaxs = "i", las = 1) ; plot(ymin:ymax, ymin:ymax, xlim = range(scale, ymin, ymax)[order(c(ymin, ymax))], ylim = range(scale, ymin, ymax)[order(c(ymin, ymax))], xlab = "DEFAULT SCALE", ylab = "NEW SCALE") ; par(yaxt = "s") ; axis(side = 2, at = scale)
-# DEBUGGING
-# n = 9 ; lim = c(2, 3.101) ; kind = "approx" ; lib.path = NULL # for function debugging
-# n = 10 ; lim = c(1e-4, 1e6) ; kind = "approx" ; lib.path = NULL # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# end initial argument checking
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_round", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_round() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = n, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & isTRUE(all.equal(n, 0))){ # isTRUE(all.equal(n, 0)) equivalent to n == 0 but deals with floats (approx ok)
-tempo.cat <- paste0("ERROR IN ", function.name, ": n ARGUMENT MUST BE A NON NULL AND POSITIVE INTEGER")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE) # 
-}
-tempo <- fun_check(data = lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & all(diff(lim) == 0L)){ # isTRUE(all.equal(diff(lim), rep(0, length(diff(lim))))) not used because we strictly need zero as a result
-tempo.cat <- paste0("ERROR IN ", function.name, ": lim ARGUMENT HAS A NULL RANGE (2 IDENTICAL VALUES)")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo$problem == FALSE & any(lim %in% c(Inf, -Inf))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": lim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo <- fun_check(data = kind, options = c("approx", "strict", "strict.cl"), length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(lib.path)){
-tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end argument checking with fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-lim.rank <- rank(lim) # to deal with inverted axis
-lim <- sort(lim)
-if(kind == "approx"){
-# package checking
-fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
-fun_pack(req.package = c("scales"), lib.path = lib.path)
-# end package checking
-output <- ggplot2::ggplot_build(ggplot2::ggplot() + ggplot2::scale_y_continuous(
-breaks = scales::trans_breaks(
-trans = "identity", 
-inv = "identity", 
-n = n
-), 
-limits = lim
-))$layout$panel_params[[1]]$y$breaks # pretty() alone is not appropriate: tempo.pret <-  pretty(seq(lim[1] ,lim[2], length.out = n)) ; tempo.pret[tempo.pret > = lim[1] & tempo.pret < = lim[2]]. # in ggplot 3.3.0, tempo.coord$y.major_source replaced by tempo.coord$y$breaks
-if( ! is.null(attributes(output))){ # layout$panel_params[[1]]$y$breaks can be characters (labels of the axis). In that case, it has attributes that corresponds to positions
-output <- unlist(attributes(output))
-}
-output <- output[ ! is.na(output)]
-}else if(kind == "strict"){
-output <- fun_round(seq(lim[1] ,lim[2], length.out = n), 2)
-}else if(kind == "strict.cl"){
-tempo.range <- diff(sort(lim))
-tempo.max <- max(lim)
-tempo.min <- min(lim)
-mid <- tempo.min + (tempo.range/2) # middle of axis
-tempo.inter <- tempo.range / (n + 1) # current interval between two ticks, between 0 and Inf
-if(tempo.inter == 0L){ # isTRUE(all.equal(tempo.inter, rep(0, length(tempo.inter)))) not used because we strictly need zero as a result
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE INTERVAL BETWEEN TWO TICKS OF THE SCALE IS NULL. MODIFY THE lim OR n ARGUMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-log10.abs.lim <- 200
-log10.range <- (-log10.abs.lim):log10.abs.lim
-log10.vec <- 10^log10.range
-round.vec <- c(5, 4, 3, 2.5, 2, 1.25, 1)
-dec.table <- outer(log10.vec, round.vec) # table containing the scale units (row: power of ten from -201 to +199, column: the 5, 2.5, 2, 1.25, 1 notches
-
- 
-
-# recover the number of leading zeros in tempo.inter
-ini.scipen <- options()$scipen
-options(scipen = -1000) # force scientific format
-if(any(grepl(pattern = "\\+", x = tempo.inter))){ # tempo.inter > 1
-power10.exp <- as.integer(substring(text = tempo.inter, first = (regexpr(pattern = "\\+", text = tempo.inter) + 1))) # recover the power of 10. Example recover 08 from 1e+08
-mantisse <- as.numeric(substr(x = tempo.inter, start = 1, stop = (regexpr(pattern = "\\+", text = tempo.inter) - 2))) # recover the mantisse. Example recover 1.22 from 1.22e+08
-}else if(any(grepl(pattern = "\\-", x = tempo.inter))){ # tempo.inter < 1
-power10.exp <- as.integer(substring(text = tempo.inter, first = (regexpr(pattern = "\\-", text = tempo.inter)))) # recover the power of 10. Example recover 08 from 1e+08
-mantisse <- as.numeric(substr(x = tempo.inter, start = 1, stop = (regexpr(pattern = "\\-", text = tempo.inter) - 2))) # recover the mantisse. Example recover 1.22 from 1.22e+08
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 1")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-tempo.scale <- dec.table[log10.range == power10.exp, ]
-# new interval 
-inter.select <- NULL
-for(i1 in 1:length(tempo.scale)){
-tempo.first.tick <- trunc((tempo.min + tempo.scale[i1]) / tempo.scale[i1]) * (tempo.scale[i1]) # this would be use to have a number not multiple of tempo.scale[i1]: ceiling(tempo.min) + tempo.scale[i1] * 10^power10.exp
-tempo.last.tick <- tempo.first.tick + tempo.scale[i1] * (n - 1)
-if((tempo.first.tick >= tempo.min) & (tempo.last.tick <= tempo.max)){
-inter.select <- tempo.scale[i1]
-break()
-}
-}
-if(is.null(inter.select)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 2")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-options(scipen = ini.scipen) # restore the initial scientific penalty
-# end new interval 
-# centering the new scale 
-tempo.mid <- trunc((mid + (-1:1) * inter.select) / inter.select) * inter.select # tempo middle tick closest to the middle axis
-mid.tick <- tempo.mid[which.min(abs(tempo.mid - mid))]
-if(isTRUE(all.equal(n, rep(1, length(n))))){ # isTRUE(all.equal(n, rep(1, length(n)))) is similar to n == 1L but deals with float
-output <- mid.tick
-}else if(isTRUE(all.equal(n, rep(2, length(n))))){ # isTRUE(all.equal(n, rep(0, length(n)))) is similar to n == 2L but deals with float
-output <- mid.tick
-tempo.min.dist <- mid.tick - inter.select - tempo.min
-tempo.max.dist <- tempo.max - mid.tick + inter.select
-if(tempo.min.dist <= tempo.max.dist){ # distance between lowest tick and bottom axis <= distance between highest tick and top axis. If yes, extra tick but at the top, otherwise at the bottom
-output <- c(mid.tick, mid.tick + inter.select)
-}else{
-output <- c(mid.tick - inter.select, mid.tick)
-}
-}else if((n / 2 - trunc(n / 2)) > 0.1){ # > 0.1 to avoid floating point. Because result can only be 0 or 0.5. Thus, > 0.1 means odd number
-output <- c(mid.tick - (trunc(n / 2):1) * inter.select, mid.tick, mid.tick + (1:trunc(n / 2)) * inter.select)
-}else if((n / 2 - trunc(n / 2)) < 0.1){ # < 0.1 to avoid floating point. Because result can only be 0 or 0.5. Thus, < 0.1 means even number
-tempo.min.dist <- mid.tick - trunc(n / 2) * inter.select - tempo.min
-tempo.max.dist <- tempo.max - mid.tick + trunc(n / 2) * inter.select
-if(tempo.min.dist <= tempo.max.dist){ # distance between lowest tick and bottom axis <= distance between highest tick and top axis. If yes, extra tick but at the bottom, otherwise at the top
-output <- c(mid.tick - ((trunc(n / 2) - 1):1) * inter.select, mid.tick, mid.tick + (1:trunc(n / 2)) * inter.select)
-}else{
-output <- c(mid.tick - (trunc(n / 2):1) * inter.select, mid.tick, mid.tick + (1:(trunc(n / 2) - 1)) * inter.select)
-}
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 3")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end centering the new scale 
-# last check
-if(min(output) < tempo.min){
-output <- c(output[-1], max(output) + inter.select) # remove the lowest tick and add a tick at the top
-}else if( max(output) > tempo.max){
-output <- c(min(output) - inter.select, output[-length(output)])
-}
-if(min(output) < tempo.min | max(output) > tempo.max){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 4")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(is.na(output))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 5 (NA GENERATION)")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end last check
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 6")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(diff(lim.rank) < 0){
-output <- rev(output)
-}
-return(output)
-}
-
-
-######## fun_inter_ticks() #### define coordinates of secondary ticks
-
-
-fun_inter_ticks <- function(
-lim, 
-log = "log10", 
-breaks = NULL, 
-n = NULL, 
-warn.print = TRUE
+    class.nb, 
+    inches.per.class.nb = 1, 
+    ini.window.width = 7, 
+    inch.left.space, 
+    inch.right.space, 
+    boundarie.space = 0.5
 ){
-# AIM
-# define coordinates and values of secondary ticks
-# ARGUMENTS
-# lim: vector of 2 numbers indicating the limit range of the axis. Order of the 2 values matters (for inverted axis). If log argument is "log2" or "log10", values in lim must be already log transformed. Thus, negative or zero values are allowed
-# log: either "log2" (values in the lim argument are log2 transformed) or "log10" (values in the lim argument are log10 transformed), or "no"
-# breaks: mandatory vector of numbers indicating the main ticks values/positions when log argument is "no". Ignored when log argument is "log2" or "log10"
-# n: number of secondary ticks between each main tick when log argument is "no". Ignored when log argument is "log2" or "log10"
-# warn.print: logical. Print potential warning messages at the end of the execution? If FALSE, warning messages are never printed, but can still be recovered in the returned list
-# RETURN
-# a list containing
-# $log: value of the log argument used
-# $coordinates: the coordinates of the secondary ticks on the axis, between the lim values
-# $values: the corresponding values associated to each coordinate (with log scale, 2^$values or 10^$values is equivalent to the labels of the axis)
-# $warn: the potential warning messages. Use cat() for proper display. NULL if no warning
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# no log scale
-# fun_inter_ticks(lim = c(-4,4), log = "no", breaks = c(-2, 0, 2), n = 3)
-# fun_inter_ticks(lim = c(10, 0), log = "no", breaks = c(10, 8, 6, 4, 2, 0), n = 4)
-# log2
-# fun_inter_ticks(lim = c(-4,4), log = "log2")
-# log10
-# fun_inter_ticks(lim = c(-2,3), log = "log10")
-# DEBUGGING
-# lim = c(2, 3.101) ; log = "no" ; breaks = NULL ; n = NULL ; warn.print = TRUE # for function debugging
-# lim = c(0, 26.5) ; log = "no" ; breaks = c(0, 10, 20) ; n = 3 # for function debugging
-# lim = c(10, 0); log = "no"; breaks = c(10, 8, 6, 4, 2, 0); n = 4 # for function debugging
-# lim = c(-10, -20); log = "no"; breaks = c(-20, -15, -10); n = 4 # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-req.function <- c(
-"fun_check"
-)
-for(i1 in req.function){
-if(length(find(i1, mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED ", i1, "() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end required function checking
-# argument primary checking
-# arg with no default values
-mandat.args <- c(
-"lim"
-)
-tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
-if(any(tempo)){ # normally no NA for missing() output
-tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end arg with no default values
-# using fun_check()
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = log, options = c("no", "log2", "log10"), length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(breaks)){
-tempo <- fun_check(data = breaks, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(n)){
-tempo <- fun_check(data = n, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = warn.print, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end using fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument primary checking
-# second round of checking and data preparation
-# management of NA
-if(any(is.na(lim)) | any(is.na(log)) | any(is.na(breaks)) | any(is.na(n)) | any(is.na(warn.print))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nNO ARGUMENT CAN HAVE NA VALUES")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NA
-# management of NULL
-if(is.null(lim) | is.null(log)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nTHESE ARGUMENTS\nlim\nlog\nCANNOT BE NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NULL
-if(all(diff(lim) == 0L)){ # isTRUE(all.equal(diff(lim), rep(0, length(diff(lim))))) not used because we strictly need zero as a result
-tempo.cat <- paste0("ERROR IN ", function.name, "\nlim ARGUMENT HAS A NULL RANGE (2 IDENTICAL VALUES): ", paste(lim, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(any(lim %in% c(Inf, -Inf))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nlim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(log == "no" & is.null(breaks)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nbreaks ARGUMENT CANNOT BE NULL IF log ARGUMENT IS \"no\"")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! is.null(breaks)){
-if(length(breaks) < 2){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nbreaks ARGUMENT MUST HAVE 2 VALUES AT LEAST (OTHERWISE, INTER TICK POSITIONS CANNOT BE COMPUTED): ", paste(breaks, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! isTRUE(all.equal(diff(sort(breaks)), rep(diff(sort(breaks))[1], length(diff(sort(breaks))))))){ # isTRUE(all.equal(n, 0)) equivalent to n == 0 but deals with floats (approx ok)
-tempo.cat <- paste0("ERROR IN ", function.name, "\nbreaks ARGUMENT MUST HAVE EQUIDISTANT VALUES (OTHERWISE, EQUAL NUMBER OF INTER TICK BETWEEN MAIN TICKS CANNOT BE COMPUTED): ", paste(breaks, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if( ! is.null(n)){
-if(n <= 0){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nn ARGUMENT MUST BE A POSITIVE AND NON NULL INTEGER: ", paste(n, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end second round of checking and data preparation
-# main code
-ini.warning.length <- options()$warning.length
-options(warning.length = 8170)
-warn <- NULL
-warn.count <- 0
-lim.rank <- rank(lim) # to deal with inverse axis
-if(log != "no"){
-ini.scipen <- options()$scipen
-options(scipen = -1000) # force scientific format
-power10.exp <- as.integer(substring(text = 10^lim, first = (regexpr(pattern = "\\+|\\-", text = 10^lim)))) # recover the power of 10, i.e., integer part of lim. Example recover 08 from 1e+08. Works for log2
-# mantisse <- as.numeric(substr(x = 10^lim, start = 1, stop = (regexpr(pattern = "\\+|\\-", text = 10^lim) - 2))) # recover the mantisse. Example recover 1.22 from 1.22e+08
-options(scipen = ini.scipen) # restore the initial scientific penalty
-tick.pos <- unique(as.vector(outer(2:10, ifelse(log == "log2", 2, 10)^((power10.exp[1] - ifelse(diff(lim.rank) > 0, 1, -1)):(power10.exp[2] + ifelse(diff(lim.rank) > 0, 1, -1)))))) # use log10(2:10) even if log2: it is to get log values between 0 and 1
-tick.pos <- sort(tick.pos, decreasing = ifelse(diff(lim.rank) > 0, FALSE, TRUE))
-if(log == "log2"){
-tick.values <- tick.pos[tick.pos >= min(2^lim) & tick.pos <= max(2^lim)]
-tick.pos <- log2(tick.values)
-}else if(log == "log10"){
-tick.values <- tick.pos[tick.pos >= min(10^lim) & tick.pos <= max(10^lim)]
-tick.pos <- log10(tick.values)
-}
-}else{
-# if(length(breaks) > 1){ # not required because already checked above
-breaks.rank <- rank(c(breaks[1], breaks[length(breaks)]))
-if(diff(breaks.rank) != diff(lim.rank)){
-breaks <- sort(breaks, decreasing = ifelse(diff(lim.rank) < 0, TRUE, FALSE))
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") VALUES IN breaks ARGUMENT NOT IN THE SAME ORDER AS IN lim ARGUMENT -> VALUES REORDERED AS IN lim: ", paste(breaks, collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-breaks.rank <- rank(c(breaks[1], breaks[length(breaks)]))
-}
-# }
-main.tick.dist <- mean(diff(breaks), na.rm = TRUE)
-tick.dist <- main.tick.dist / (n + 1)
-tempo.extra.margin <- max(abs(diff(breaks)), na.rm = TRUE)
-tick.pos <- seq(
-if(diff(breaks.rank) > 0){breaks[1] - tempo.extra.margin}else{breaks[1] + tempo.extra.margin}, 
-if(diff(breaks.rank) > 0){breaks[length(breaks)] + tempo.extra.margin}else{breaks[length(breaks)] - tempo.extra.margin}, 
-by = tick.dist
-)
-tick.pos <- tick.pos[tick.pos >= min(lim) & tick.pos <= max(lim)]
-tick.values <- tick.pos
-}
-if(any(is.na(tick.pos) | ! is.finite(tick.pos))){ 
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, ": NA or Inf GENERATED FOR THE INTER TICK POSITIONS: ", paste(tick.pos, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(tick.pos) == 0L){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NO INTER TICKS COMPUTED BETWEEN THE LIMITS INDICATED: ", paste(lim, collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-output <- list(log = log, coordinates = tick.pos, values = tick.values, warn = warn)
-if(warn.print == TRUE & ! is.null(warn)){
-on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE)) # to recover the warning messages, see $warn
-}
-on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
-return(output)
-}
-
-
-######## fun_post_plot() #### set graph param after plotting (axes redesign for instance)
-
-
- 
-
-
-fun_post_plot <- function(
-x.side = 0, 
-x.log.scale = FALSE, 
-x.categ = NULL, 
-x.categ.pos = NULL, 
-x.lab = "", 
-x.axis.size = 1.5, 
-x.label.size = 1.5, 
-x.dist.legend = 0.5, 
-x.nb.inter.tick = 1, 
-y.side = 0, 
-y.log.scale = FALSE, 
-y.categ = NULL, 
-y.categ.pos = NULL, 
-y.lab = "", 
-y.axis.size = 1.5, 
-y.label.size = 1.5, 
-y.dist.legend = 0.5, 
-y.nb.inter.tick = 1, 
-text.angle = 90, 
-tick.length = 0.5, 
-sec.tick.length = 0.3, 
-bg.color = NULL, 
-grid.lwd = NULL, 
-grid.col = "white", 
-corner.text = "", 
-corner.text.size = 1, 
-just.label.add = FALSE, 
-par.reset = FALSE, 
-custom.par = NULL
-){
-# AIM
-# redesign axis. If x.side = 0, y.side = 0, the function just adds text at topright of the graph and reset par() for next graphics and provides outputs (see below)
-# provide also positions for legend or additional text on the graph
-# use fun_prior_plot() before this function for initial inactivation of the axis drawings
-# ARGUMENTS
-# x.side: axis at the bottom (1) or top (3) of the region figure. Write 0 for no change
-# x.log.scale: Log scale for the x-axis? Either TRUE or FALSE
-# x.categ: character vector representing the classes (levels()) to specify when the x-axis is qualititative(stripchart, boxplot)
-# x.categ.pos: position of the classes names (numeric vector of identical length than x.categ). If left NULL, this will be 1:length(levels())
-# x.lab: label of the x-axis. If x.side == 0 and x.lab != "", then x.lab is printed
-# x.axis.size: positive numeric. Increase or decrease the size of the x axis numbers. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2. Also control the size of displayed categories
-# x.label.size: positive numeric. Increase or decrease the size of the x axis legend text. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2
-# x.dist.legend: increase the number to move x-axis legends away in inches (first number of mgp argument of par() but in inches)
-# x.nb.inter.tick: number of secondary ticks between main ticks on x-axis (only if not log scale). 0 means no secondary ticks
-# y.side: axis at the left (2) or right (4) of the region figure. Write 0 for no change
-# y.log.scale: Log scale for the y-axis? Either TRUE or FALSE
-# y.categ: classes (levels()) to specify when the y-axis is qualititative(stripchart, boxplot)
-# y.categ.pos: position of the classes names (numeric vector of identical length than y.categ). If left NULL, this will be 1:length(levels())
-# y.lab: label of the y-axis. If y.side == 0 and y.lab != "", then y.lab is printed
-# y.axis.size: positive numeric. Increase or decrease the size of the y axis numbers. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2. Also control the size of displayed categories
-# y.label.size: positive numeric. Increase or decrease the size of the y axis legend text. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2
-# y.dist.legend: increase the number to move y-axis legends away in inches (first number of mgp argument of par() but in inches)
-# y.nb.inter.tick: number of secondary ticks between main ticks on y-axis (only if not log scale). 0 means non secondary ticks
-# text.angle: angle of the text when axis is qualitative
-# tick.length: length of the main ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc., 0 for no ticks)
-# sec.tick.length: length of the secondary ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc., 0 for no ticks)
-# bg.color: background color of the plot region. NULL for no color. BEWARE: cover/hide an existing plot !
-# grid.lwd: if non NULL, activate the grid line (specify the line width)
-# grid.col: grid line color (only if grid.lwd non NULL)
-# corner.text: text to add at the top right corner of the window
-# corner.text.size: positive numeric. Increase or decrease the size of the text. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2
-# par.reset: to reset all the graphics parameters. BEWARE: TRUE can generate display problems, mainly in graphic devices with multiple figure regions
-# just.label.add: just add axis labels (legend)? Either TRUE or FALSE. If TRUE, at least (x.side == 0 & x.lab != "") or (y.side == 0 & y.lab != "") must be set to display the corresponding x.lab or y.lab
-# custom.par: list that provides the parameters that reset all the graphics parameters. BEWARE: if NULL and par.reset == TRUE, the default par() parameters are used
-# RETURN
-# a list containing: 
-# $x.mid.left.dev.region: middle of the left margin of the device region, in coordinates of the x-axis
-# $x.left.dev.region: left side of the left margin (including the potential margin of the device region), in coordinates of the x-axis
-# $x.mid.right.dev.region: middle of the right margin of the device region, in coordinates of the x-axis
-# $x.right.dev.region: right side of the right margin (including the potential margin of the device region), in coordinates of the x-axis
-# $x.mid.left.fig.region: middle of the left margin of the figure region, in coordinates of the x-axis
-# $x.left.fig.region: left side of the left margin, in coordinates of the x-axis
-# $x.mid.right.fig.region: middle of the right margin of the figure region, in coordinates of the x-axis
-# $x.right.fig.region: right side of the right margin, in coordinates of the x-axis
-# $x.left.plot.region: left side of the plot region, in coordinates of the x-axis
-# $x.right.plot.region: right side of the plot region, in coordinates of the x-axis
-# $x.mid.plot.region: middle of the plot region, in coordinates of the x-axis
-# $y.mid.bottom.dev.region: middle of the bottom margin of the device region, in coordinates of the y-axis
-# $y.bottom.dev.region: bottom side of the bottom margin (including the potential margin of the device region), in coordinates of the y-axis
-# $y.mid.top.dev.region: middle of the top margin of the device region, in coordinates of the y-axis
-# $y.top.dev.region: top side of the top margin (including the potential margin of the device region), in coordinates of the y-axis
-# $y.mid.bottom.fig.region: middle of the bottom margin of the figure region, in coordinates of the y-axis
-# $y.bottom.fig.region: bottom of the bottom margin of the figure region, in coordinates of the y-axis
-# $y.mid.top.fig.region: middle of the top margin of the figure region, in coordinates of the y-axis
-# $y.top.fig.region: top of the top margin of the figure region, in coordinates of the y-axis
-# $y.top.plot.region: top of the plot region, in coordinates of the y-axis
-# $y.bottom.plot.region: bottom of the plot region, in coordinates of the y-axis
-# $y.mid.plot.region: middle of the plot region, in coordinates of the y-axis
-# $text: warning text
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# fun_open() to reinitialize graph parameters if par.reset = TRUE and custom.par = NULL
-# EXAMPLES
-# Example of log axis with log y-axis and unmodified x-axis:
-# prior.par <- fun_prior_plot(param.reinitial = TRUE, xlog.scale = FALSE, ylog.scale = TRUE, remove.label = TRUE, remove.x.axis = FALSE, remove.y.axis = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 0.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = TRUE) ; plot(1:100, log = "y") ; fun_post_plot(y.side = 2, y.log.scale = prior.par$ylog, x.lab = "Values", y.lab = "TEST", y.axis.size = 1.25, y.label.size = 1.5, y.dist.legend = 0.7, just.label.add = ! prior.par$ann)
-# Example of log axis with redrawn x-axis and y-axis:
-# prior.par <- fun_prior_plot(param.reinitial = TRUE) ; plot(1:100) ; fun_post_plot(x.side = 1, x.lab = "Values", y.side = 2, y.lab = "TEST", y.axis.size = 1, y.label.size = 2, y.dist.legend = 0.6)
-# Example of title easily added to a plot:
-# plot(1:100) ; para <- fun_post_plot(corner.text = "TITLE ADDED") # try also: par(xpd = TRUE) ; text(x = para$x.mid.left.fig.region, y = para$y.mid.top.fig.region, labels = "TITLE ADDED", cex = 0.5)
-# example with margins in the device region:
-# windows(5,5) ; fun_prior_plot(box.type = "o") ; par(mai=c(0.5,0.5,0.5,0.5), omi = c(0.25,0.25,1,0.25), xaxs = "i", yaxs = "i") ; plot(0:10) ; a <- fun_post_plot(x.side = 0, y.side = 0) ; x <- c(a$x.mid.left.dev.region, a$x.left.dev.region, a$x.mid.right.dev.region, a$x.right.dev.region, a$x.mid.left.fig.region, a$x.left.fig.region, a$x.mid.right.fig.region, a$x.right.fig.region, a$x.right.plot.region, a$x.left.plot.region, a$x.mid.plot.region) ; y <- c(a$y.mid.bottom.dev.region, a$y.bottom.dev.region, a$y.mid.top.dev.region, a$y.top.dev.region, a$y.mid.bottom.fig.region, a$y.bottom.fig.region, a$y.mid.top.fig.region, a$y.top.fig.region, a$y.top.plot.region, a$y.bottom.plot.region, a$y.mid.plot.region) ; par(xpd = NA) ; points(x = rep(5, length(y)), y = y, pch = 16, col = "red") ; text(x = rep(5, length(y)), y = y, c("y.mid.bottom.dev.region", "y.bottom.dev.region", "y.mid.top.dev.region", "y.top.dev.region", "y.mid.bottom.fig.region", "y.bottom.fig.region", "y.mid.top.fig.region", "y.top.fig.region", "y.top.plot.region", "y.bottom.plot.region", "y.mid.plot.region"), cex = 0.65, col = grey(0.25)) ; points(y = rep(5, length(x)), x = x, pch = 16, col = "blue") ; text(y = rep(5, length(x)), x = x, c("x.mid.left.dev.region", "x.left.dev.region", "x.mid.right.dev.region", "x.right.dev.region", "x.mid.left.fig.region", "x.left.fig.region", "x.mid.right.fig.region", "x.right.fig.region", "x.right.plot.region", "x.left.plot.region", "x.mid.plot.region"), cex = 0.65, srt = 90, col = grey(0.25))
-# DEBUGGING
-# x.side = 0 ; x.log.scale = FALSE ; x.categ = NULL ; x.categ.pos = NULL ; x.lab = "" ; x.axis.size = 1.5 ; x.label.size = 1.5 ; x.dist.legend = 1 ; x.nb.inter.tick = 1 ; y.side = 0 ; y.log.scale = FALSE ; y.categ = NULL ; y.categ.pos = NULL ; y.lab = "" ; y.axis.size = 1.5 ; y.label.size = 1.5 ; y.dist.legend = 0.7 ; y.nb.inter.tick = 1 ; text.angle = 90 ; tick.length = 0.5 ; sec.tick.length = 0.3 ; bg.color = NULL ; grid.lwd = NULL ; grid.col = "white" ; corner.text = "" ; corner.text.size = 1 ; just.label.add = FALSE ; par.reset = FALSE ; custom.par = NULL # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_open", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_open() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = x.side, options = c(0, 1, 3), length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = x.log.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(x.categ)){
-tempo <- fun_check(data = x.categ, class = "character", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(x.categ.pos)){
-tempo <- fun_check(data = x.categ.pos, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = x.lab, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = x.axis.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = x.label.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = x.dist.legend, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = x.nb.inter.tick, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y.side, options = c(0, 2, 4), length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y.log.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(y.categ)){
-tempo <- fun_check(data = y.categ, class = "character", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(y.categ.pos)){
-tempo <- fun_check(data = y.categ.pos, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = y.lab, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y.axis.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y.label.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y.dist.legend, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y.nb.inter.tick, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = text.angle, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = tick.length, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = sec.tick.length, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
-if( ! is.null(bg.color)){
-tempo <- fun_check(data = bg.color, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-if( ! (bg.color %in% colors() | grepl(pattern = "^#", bg.color))){ # check color
-tempo.cat <- paste0("ERROR IN ", function.name, ": bg.color ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # OR A COLOR NAME GIVEN BY colors()")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-if( ! is.null(grid.lwd)){
-tempo <- fun_check(data = grid.lwd, class = "vector", mode = "numeric", neg.values = FALSE, fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(grid.col)){
-tempo <- fun_check(data = grid.col, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-if( ! (grid.col %in% colors() | grepl(pattern = "^#", grid.col))){ # check color
-tempo.cat <- paste0("ERROR IN ", function.name, ": grid.col ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # OR A COLOR NAME GIVEN BY colors()")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-tempo <- fun_check(data = corner.text, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = corner.text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = just.label.add, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = par.reset, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(custom.par)){
-tempo <- fun_check(data = custom.par, typeof = "list", length = 1, fun.name = function.name) ; eval(ee)
-}
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-text <- NULL
-par(tcl = -par()$mgp[2] * tick.length)
-if(x.log.scale == TRUE){
-grid.coord.x <- c(10^par("usr")[1], 10^par("usr")[2])
-}else{
-grid.coord.x <- c(par("usr")[1], par("usr")[2])
-}
-if(y.log.scale == TRUE){
-grid.coord.y <- c(10^par("usr")[3], 10^par("usr")[4])
-}else{
-grid.coord.y <- c(par("usr")[3], par("usr")[4])
-}
-if( ! is.null(bg.color)){
-rect(grid.coord.x[1], grid.coord.y[1], grid.coord.x[2], grid.coord.y[2], col = bg.color, border = NA)
-}
-if( ! is.null(grid.lwd)){
-grid(nx = NA, ny = NULL, col = grid.col, lty = 1, lwd = grid.lwd)
-}
-if(x.log.scale == TRUE){
-x.mid.left.dev.region <- 10^(par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1] / 2) # in x coordinates, to position axis labeling at the bottom of the graph (according to x scale)
-x.left.dev.region <- 10^(par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1]) # in x coordinates
-x.mid.right.dev.region <- 10^(par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) + ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * (1 - par("omd")[2]) / 2) # in x coordinates, to position axis labeling at the top of the graph (according to x scale)
-x.right.dev.region <- 10^(par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) + ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * (1 - par("omd")[2])) # in x coordinates
-x.mid.left.fig.region <- 10^(par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] / 2) # in x coordinates, to position axis labeling at the bottom of the graph (according to x scale)
-x.left.fig.region <- 10^(par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1]) # in x coordinates
-x.mid.right.fig.region <- 10^(par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) / 2) # in x coordinates, to position axis labeling at the top of the graph (according to x scale)
-x.right.fig.region <- 10^(par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2])) # in x coordinates
-x.left.plot.region <- 10^par("usr")[1] # in x coordinates, left of the plot region (according to x scale)
-x.right.plot.region <- 10^par("usr")[2] # in x coordinates, right of the plot region (according to x scale)
-x.mid.plot.region <- 10^((par("usr")[2] + par("usr")[1]) / 2) # in x coordinates, right of the plot region (according to x scale)
-}else{
-x.mid.left.dev.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1] / 2) # in x coordinates, to position axis labeling at the bottom of the graph (according to x scale)
-x.left.dev.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1]) # in x coordinates
-x.mid.right.dev.region <- (par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) + ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * (1 - par("omd")[2]) / 2) # in x coordinates, to position axis labeling at the top of the graph (according to x scale)
-x.right.dev.region <- (par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) + ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * (1 - par("omd")[2])) # in x coordinates
-x.mid.left.fig.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] / 2) # in x coordinates, to position axis labeling at the bottom of the graph (according to x scale)
-x.left.fig.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1]) # in x coordinates
-x.mid.right.fig.region <- (par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) / 2) # in x coordinates, to position axis labeling at the top of the graph (according to x scale)
-x.right.fig.region <- (par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2])) # in x coordinates
-x.left.plot.region <- par("usr")[1] # in x coordinates, left of the plot region (according to x scale)
-x.right.plot.region <- par("usr")[2] # in x coordinates, right of the plot region (according to x scale)
-x.mid.plot.region <- (par("usr")[2] + par("usr")[1]) / 2 # in x coordinates, right of the plot region (according to x scale)
-}
-if(y.log.scale == TRUE){
-y.mid.bottom.dev.region <- 10^(par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] - ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (par("omd")[3] / 2)) # in y coordinates, to position axis labeling at the bottom of the graph (according to y scale). Ex mid.bottom.space
-y.bottom.dev.region <- 10^(par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] - ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * par("omd")[3]) # in y coordinates
-y.mid.top.dev.region <- 10^(par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4]) / 2) # in y coordinates, to position axis labeling at the top of the graph (according to y scale). Ex mid.top.space
-y.top.dev.region <- 10^(par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4])) # in y coordinates
-y.mid.bottom.fig.region <- 10^(par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] / 2) # in y coordinates, to position axis labeling at the bottom of the graph (according to y scale). Ex mid.bottom.space
-y.bottom.fig.region <- 10^(par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3]) # in y coordinates
-y.mid.top.fig.region <- 10^(par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) / 2) # in y coordinates, to position axis labeling at the top of the graph (according to y scale). Ex mid.top.space
-y.top.fig.region <- 10^(par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4])) # in y coordinates
-y.top.plot.region <- 10^par("usr")[4] # in y coordinates, top of the plot region (according to y scale)
-y.bottom.plot.region <- 10^par("usr")[3] # in y coordinates, bottom of the plot region (according to y scale)
-y.mid.plot.region <- (par("usr")[3] + par("usr")[4]) / 2 # in x coordinates, right of the plot region (according to x scale)
-}else{
-y.mid.bottom.dev.region <- (par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] - ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (par("omd")[3] / 2)) # in y coordinates, to position axis labeling at the bottom of the graph (according to y scale). Ex mid.bottom.space
-y.bottom.dev.region <- (par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] - ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * par("omd")[3]) # in y coordinates
-y.mid.top.dev.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4]) / 2) # in y coordinates, to position axis labeling at the top of the graph (according to y scale). Ex mid.top.space
-y.top.dev.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4])) # in y coordinates
-y.mid.bottom.fig.region <- (par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] / 2) # in y coordinates, to position axis labeling at the bottom of the graph (according to y scale). Ex mid.bottom.space
-y.bottom.fig.region <- (par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3]) # in y coordinates
-y.mid.top.fig.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) / 2) # in y coordinates, to position axis labeling at the top of the graph (according to y scale). Ex mid.top.space
-y.top.fig.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4])) # in y coordinates
-y.top.plot.region <- par("usr")[4] # in y coordinates, top of the plot region (according to y scale)
-y.bottom.plot.region <- par("usr")[3] # in y coordinates, bottom of the plot region (according to y scale)
-y.mid.plot.region <- ((par("usr")[3] + par("usr")[4]) / 2) # in x coordinates, right of the plot region (according to x scale)
-}
-if(any(sapply(FUN = all.equal, c(1, 3), x.side) == TRUE)){
-par(xpd=FALSE, xaxt="s")
-if(is.null(x.categ) & x.log.scale == TRUE){
-if(any(par()$xaxp[1:2] == 0L)){ # any(sapply(FUN = all.equal, par()$xaxp[1:2], 0) == TRUE) not used because we strictly need zero as a result. Beware: write "== TRUE", because the result is otherwise character and a warning message appears using any()
-if(par()$xaxp[1] == 0L){ # isTRUE(all.equal(par()$xaxp[1], 0)) not used because we strictly need zero as a result
-par(xaxp = c(10^-30, par()$xaxp[2:3])) # because log10(par()$xaxp[1] == 0) == -Inf
-}
-if(par()$xaxp[2] == 0L){ # isTRUE(all.equal(par()$xaxp[1], 0)) not used because we strictly need zero as a result
-par(xaxp = c(par()$xaxp[1], 10^-30, par()$xaxp[3])) # because log10(par()$xaxp[2] == 0) == -Inf
-}
-}
-axis(side = x.side, at = c(10^par()$usr[1], 10^par()$usr[2]), labels=rep("", 2), lwd=1, lwd.ticks = 0) # draw the axis line
-mtext(side = x.side, text = x.lab, line = x.dist.legend / 0.2, las = 0, cex = x.label.size)
-par(tcl = -par()$mgp[2] * sec.tick.length) # length of the secondary ticks are reduced
-suppressWarnings(rug(10^outer(c((log10(par("xaxp")[1]) -1):log10(par("xaxp")[2])), log10(1:10), "+"), ticksize = NA, side = x.side)) # ticksize = NA to allow the use of par()$tcl value
-par(tcl = -par()$mgp[2] * tick.length) # back to main ticks
-axis(side = x.side, at = c(1e-15, 1e-14, 1e-13, 1e-12, 1e-11, 1e-10, 1e-9, 1e-8, 1e-7, 1e-6, 1e-5, 1e-4, 1e-3, 1e-2, 1e-1, 1e0, 1e1, 1e2, 1e3, 1e4, 1e5, 1e6, 1e7, 1e8, 1e9, 1e10), labels = expression(10^-15, 10^-14, 10^-13, 10^-12, 10^-11, 10^-10, 10^-9, 10^-8, 10^-7, 10^-6, 10^-5, 10^-4, 10^-3, 10^-2, 10^-1, 10^0, 10^1, 10^2, 10^3, 10^4, 10^5, 10^6, 10^7, 10^8, 10^9, 10^10), lwd = 0, lwd.ticks = 1, cex.axis = x.axis.size)
-x.text <- 10^par("usr")[2]
-}else if(is.null(x.categ) & x.log.scale == FALSE){
-axis(side=x.side, at=c(par()$usr[1], par()$usr[2]), labels=rep("", 2), lwd=1, lwd.ticks=0) # draw the axis line
-axis(side=x.side, at=round(seq(par()$xaxp[1], par()$xaxp[2], length.out=par()$xaxp[3]+1), 2), cex.axis = x.axis.size) # axis(side=x.side, at=round(seq(par()$xaxp[1], par()$xaxp[2], length.out=par()$xaxp[3]+1), 2), labels = format(round(seq(par()$xaxp[1], par()$xaxp[2], length.out=par()$xaxp[3]+1), 2), big.mark=','), cex.axis = x.axis.size) # to get the 1000 comma separator
-mtext(side = x.side, text = x.lab, line = x.dist.legend / 0.2, las = 0, cex = x.label.size)
-if(x.nb.inter.tick > 0){
-inter.tick.unit <- (par("xaxp")[2] - par("xaxp")[1]) / par("xaxp")[3]
-par(tcl = -par()$mgp[2] * sec.tick.length) # length of the ticks are reduced
-suppressWarnings(rug(seq(par("xaxp")[1] - 10 * inter.tick.unit, par("xaxp")[2] + 10 * inter.tick.unit, by = inter.tick.unit / (1 + x.nb.inter.tick)), ticksize = NA, x.side)) # ticksize = NA to allow the use of par()$tcl value
-par(tcl = -par()$mgp[2] * tick.length) # back to main ticks
-}
-x.text <- par("usr")[2]
-}else if(( ! is.null(x.categ)) & x.log.scale == FALSE){
-if(is.null(x.categ.pos)){
-x.categ.pos <- 1:length(x.categ)
-}else if(length(x.categ.pos) != length(x.categ)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x.categ.pos MUST BE THE SAME LENGTH AS x.categ")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-par(xpd = TRUE)
-if(isTRUE(all.equal(x.side, 1))){ #isTRUE(all.equal(x.side, 1)) is similar to x.side == 1L but deals with float
-segments(x0 = x.left.plot.region, x1 = x.right.plot.region, y0 = y.bottom.plot.region, y1 = y.bottom.plot.region) # draw the line of the axis
-text(x = x.categ.pos, y = y.mid.bottom.fig.region, labels = x.categ, srt = text.angle, cex = x.axis.size)
-}else if(isTRUE(all.equal(x.side, 3))){ #isTRUE(all.equal(x.side, 1)) is similar to x.side == 3L but deals with float
-segments(x0 = x.left.plot.region, x1 = x.right.plot.region, y0 = y.top.plot.region, y1 = y.top.plot.region) # draw the line of the axis
-text(x = x.categ.pos, y = y.mid.top.fig.region, labels = x.categ, srt = text.angle, cex = x.axis.size)
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": ARGUMENT x.side CAN ONLY BE 1 OR 3")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-par(xpd = FALSE)
-x.text <- par("usr")[2]
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": PROBLEM WITH THE x.side (", x.side ,") OR x.log.scale (", x.log.scale,") ARGUMENTS")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}else{
-x.text <- par("usr")[2]
-}
-if(any(sapply(FUN = all.equal, c(2, 4), y.side) == TRUE)){
-par(xpd=FALSE, yaxt="s")
-if(is.null(y.categ) & y.log.scale == TRUE){
-if(any(par()$yaxp[1:2] == 0L)){ # any(sapply(FUN = all.equal, par()$yaxp[1:2], 0) == TRUE) not used because we strictly need zero as a result. Beware: write "== TRUE", because the result is otherwise character and a warning message appears using any()
-if(par()$yaxp[1] == 0L){ # strict zero needed
-par(yaxp = c(10^-30, par()$yaxp[2:3])) # because log10(par()$yaxp[1] == 0) == -Inf
-}
-if(par()$yaxp[2] == 0L){ # strict zero needed
-par(yaxp = c(par()$yaxp[1], 10^-30, par()$yaxp[3])) # because log10(par()$yaxp[2] == 0) == -Inf
-}
-}
-axis(side=y.side, at=c(10^par()$usr[3], 10^par()$usr[4]), labels=rep("", 2), lwd=1, lwd.ticks=0) # draw the axis line
-par(tcl = -par()$mgp[2] * sec.tick.length) # length of the ticks are reduced
-suppressWarnings(rug(10^outer(c((log10(par("yaxp")[1])-1):log10(par("yaxp")[2])), log10(1:10), "+"), ticksize = NA, side = y.side)) # ticksize = NA to allow the use of par()$tcl value
-par(tcl = -par()$mgp[2] * tick.length) # back to main tick length
-axis(side = y.side, at = c(1e-15, 1e-14, 1e-13, 1e-12, 1e-11, 1e-10, 1e-9, 1e-8, 1e-7, 1e-6, 1e-5, 1e-4, 1e-3, 1e-2, 1e-1, 1e0, 1e1, 1e2, 1e3, 1e4, 1e5, 1e6, 1e7, 1e8, 1e9, 1e10), labels = expression(10^-15, 10^-14, 10^-13, 10^-12, 10^-11, 10^-10, 10^-9, 10^-8, 10^-7, 10^-6, 10^-5, 10^-4, 10^-3, 10^-2, 10^-1, 10^0, 10^1, 10^2, 10^3, 10^4, 10^5, 10^6, 10^7, 10^8, 10^9, 10^10), lwd = 0, lwd.ticks = 1, cex.axis = y.axis.size)
-y.text <- 10^(par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
-mtext(side = y.side, text = y.lab, line = y.dist.legend / 0.2, las = 0, cex = y.label.size)
-}else if(is.null(y.categ) & y.log.scale == FALSE){
-axis(side=y.side, at=c(par()$usr[3], par()$usr[4]), labels=rep("", 2), lwd=1, lwd.ticks=0) # draw the axis line
-axis(side=y.side, at=round(seq(par()$yaxp[1], par()$yaxp[2], length.out=par()$yaxp[3]+1), 2), cex.axis = y.axis.size)
-mtext(side = y.side, text = y.lab, line = y.dist.legend / 0.2, las = 0, cex = y.label.size)
-if(y.nb.inter.tick > 0){
-inter.tick.unit <- (par("yaxp")[2] - par("yaxp")[1]) / par("yaxp")[3]
-par(tcl = -par()$mgp[2] * sec.tick.length) # length of the ticks are reduced
-suppressWarnings(rug(seq(par("yaxp")[1] - 10 * inter.tick.unit, par("yaxp")[2] + 10 * inter.tick.unit, by = inter.tick.unit / (1 + y.nb.inter.tick)), ticksize = NA, side=y.side)) # ticksize = NA to allow the use of par()$tcl value
-par(tcl = -par()$mgp[2] * tick.length) # back to main tick length
-}
-y.text <- (par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
-}else if(( ! is.null(y.categ)) & y.log.scale == FALSE){
-if(is.null(y.categ.pos)){
-y.categ.pos <- 1:length(y.categ)
-}else if(length(y.categ.pos) != length(y.categ)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": y.categ.pos MUST BE THE SAME LENGTH AS y.categ")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-axis(side = y.side, at = y.categ.pos, labels = rep("", length(y.categ)), lwd=0, lwd.ticks=1) # draw the line of the axis
-par(xpd = TRUE)
-if(isTRUE(all.equal(y.side, 2))){ #isTRUE(all.equal(y.side, 2)) is similar to y.side == 2L but deals with float
-text(x = x.mid.left.fig.region, y = y.categ.pos, labels = y.categ, srt = text.angle, cex = y.axis.size)
-}else if(isTRUE(all.equal(y.side, 4))){ # idem
-text(x = x.mid.right.fig.region, y = y.categ.pos, labels = y.categ, srt = text.angle, cex = y.axis.size)
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": ARGUMENT y.side CAN ONLY BE 2 OR 4")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-par(xpd = FALSE)
-y.text <- (par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": PROBLEM WITH THE y.side (", y.side ,") OR y.log.scale (", y.log.scale,") ARGUMENTS")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}else{
-y.text <- (par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
-}
-par(xpd=NA)
-text(x = x.mid.right.fig.region, y = y.text, corner.text, adj=c(1, 1.1), cex = corner.text.size) # text at the topright corner. Replace x.right.fig.region by x.text if text at the right edge of the plot region
-if(just.label.add == TRUE & isTRUE(all.equal(x.side, 0)) & x.lab != ""){
-text(x = x.mid.plot.region, y = y.mid.bottom.fig.region, x.lab, adj=c(0.5, 0.5), cex = x.label.size) # x label
-}
-if(just.label.add == TRUE & isTRUE(all.equal(y.side, 0)) & y.lab != ""){
-text(x = y.mid.plot.region, y = x.mid.left.fig.region, y.lab, adj=c(0.5, 0.5), cex = y.label.size) # x label
-}
-par(xpd=FALSE)
-if(par.reset == TRUE){
-tempo.par <- fun_open(pdf = FALSE, return.output = TRUE)
-invisible(dev.off()) # close the new window
-if( ! is.null(custom.par)){
-if( ! names(custom.par) %in% names(tempo.par$ini.par)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": custom.par ARGUMENT SHOULD HAVE THE NAMES OF THE COMPARTMENT LIST COMING FROM THE par() LIST")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-par(custom.par)
-text <- c(text, "\nGRAPH PARAMETERS SET TO VALUES DEFINED BY custom.par ARGUMENT\n")
-}else{
-par(tempo.par$ini.par)
-text <- c(text, "\nGRAPH PARAMETERS RESET TO par() DEFAULT VALUES\n")
-}
-}
-output <- list(x.mid.left.dev.region = x.mid.left.dev.region, x.left.dev.region = x.left.dev.region, x.mid.right.dev.region = x.mid.right.dev.region, x.right.dev.region = x.right.dev.region, x.mid.left.fig.region = x.mid.left.fig.region, x.left.fig.region = x.left.fig.region, x.mid.right.fig.region = x.mid.right.fig.region, x.right.fig.region = x.right.fig.region, x.left.plot.region = x.left.plot.region, x.right.plot.region = x.right.plot.region, x.mid.plot.region = x.mid.plot.region, y.mid.bottom.dev.region = y.mid.bottom.dev.region, y.bottom.dev.region = y.bottom.dev.region, y.mid.top.dev.region = y.mid.top.dev.region, y.top.dev.region = y.top.dev.region, y.mid.bottom.fig.region = y.mid.bottom.fig.region, y.bottom.fig.region = y.bottom.fig.region, y.mid.top.fig.region = y.mid.top.fig.region, y.top.fig.region = y.top.fig.region, y.top.plot.region = y.top.plot.region, y.bottom.plot.region = y.bottom.plot.region, y.mid.plot.region = y.mid.plot.region, text = text)
-return(output)
-}
-
-
-######## fun_close() #### close specific graphic windows
-
-
-fun_close <- function(kind = "pdf", return.text = FALSE){
-# AIM
-# close only specific graphic windows (devices)
-# ARGUMENTS:
-# kind: vector, among c("windows", "quartz", "x11", "X11", "pdf", "bmp", "png", "tiff"), indicating the kind of graphic windows (devices) to close. BEWARE: either "windows", "quartz", "x11" or "X11" means that all the X11 GUI graphics devices will be closed, whatever the OS used
-# return.text: print text regarding the kind parameter and the devices that were finally closed?
-# RETURN
-# text regarding the kind parameter and the devices that were finally closed
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# windows() ; windows() ; pdf() ; dev.list() ; fun_close(kind = c("pdf", "x11"), return.text = TRUE) ; dev.list()
-# DEBUGGING
-# kind = c("windows", "pdf") ; return.text = FALSE # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = kind, options = c("windows", "quartz", "x11", "X11", "pdf", "bmp", "png", "tiff"), fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = return.text, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-text <- paste0("THE REQUIRED KIND OF GRAPHIC DEVICES TO CLOSE ARE ", paste(kind, collapse = " "))
-if(Sys.info()["sysname"] == "Windows"){ # Note that .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
-if(any(kind %in% c("windows", "quartz", "x11", "X11"))){
-tempo <- kind %in% c("windows", "quartz", "x11", "X11")
-kind[tempo] <- "windows" # term are replaced by what is displayed when using a <- dev.list() ; names(a)
-}
-}else if(Sys.info()["sysname"] == "Linux"){
-if(any(kind %in% c("windows", "quartz", "x11", "X11"))){
-tempo.device <- suppressWarnings(try(X11(), silent = TRUE))[] # open a X11 window to try to recover the X11 system used
-if( ! is.null(tempo.device)){
-text <- paste0(text, "\nCANNOT CLOSE GUI GRAPHIC DEVICES AS REQUIRED BECAUSE THIS LINUX SYSTEM DOES NOT HAVE IT")
-}else{
-tempo <- kind %in% c("windows", "quartz", "x11", "X11")
-kind[tempo] <- names(dev.list()[length(dev.list())]) # term are replaced by what is displayed when using a <- dev.list() ; names(a)
-invisible(dev.off()) # close the X11 opened by tempo
-}
-}
-}else{ # for macOS
-if(any(kind %in% c("windows", "quartz", "x11", "X11"))){
-tempo <- kind %in% c("windows", "quartz", "x11", "X11")
-kind[tempo] <- "quartz" # term are replaced by what is displayed when using a <- dev.list() ; names(a)
-}
-}
-kind <- unique(kind)
-if(length(dev.list()) != 0){
-for(i in length(names(dev.list())):1){
-if(names(dev.list())[i] %in% kind){
-text <- paste0(text, "\n", names(dev.list())[i], " DEVICE NUMBER ", dev.list()[i], " HAS BEEN CLOSED")
-invisible(dev.off(dev.list()[i]))
-}
-}
-}
-if(return.text == TRUE){
-return(text)
-}
-}
-
-
-################ Standard graphics
-
-
-######## fun_empty_graph() #### text to display for empty graphs
-
-
- 
-
-
-fun_empty_graph <- function(
-text = NULL, 
-text.size = 1, 
-title = NULL, 
-title.size = 1.5
-){
-# AIM
-# display an empty plot with a text in the middle of the window (for instance to specify that no plot can be drawn)
-# ARGUMENTS
-# text: character string of the message to display
-# text.size: numeric value of the text size
-# title: character string of the graph title
-# title.size: numeric value of the title size (in points)
-# RETURN
-# an empty plot
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# simple example
-# fun_empty_graph(text = "NO GRAPH")
-# white page
-# fun_empty_graph() # white page
-# all the arguments
-# fun_empty_graph(text = "NO GRAPH", text.size = 2, title = "GRAPH1", title.size = 1)
-# DEBUGGING
-# text = "NO GRAPH" ; title = "GRAPH1" ; text.size = 1
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-if( ! is.null(text)){
-tempo <- fun_check(data = text, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(title)){
-tempo <- fun_check(data = title, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = title.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
-par(ann=FALSE, xaxt="n", yaxt="n", mar = rep(1, 4), bty = "n", xpd = NA)
-plot(1, 1, type = "n") # no display with type = "n"
-x.left.dev.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1])
-y.top.dev.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4]))
-if( ! is.null(text)){
-text(x = 1, y = 1, labels = text, cex = text.size)
-}
-if( ! is.null(title)){
-text(x = x.left.dev.region, y = y.top.dev.region, labels = title, adj=c(0, 1), cex = title.size)
-}
-par(ini.par)
-}
-
-
-################ gg graphics
-
-
-######## fun_gg_palette() #### ggplot2 default color palette
-
-
- 
-
-
-fun_gg_palette <- function(n, kind = "std"){
-# AIM
-# provide colors used by ggplot2
-# the interest is to use another single color that is not the red one used by default
-# for ggplot2 specifications, see: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html
-# ARGUMENTS
-# n: number of groups on the graph
-# kind: either "std" for standard gg colors, "dark" for darkened gg colors, or "light" for pastel gg colors
-# RETURN
-# the vector of hexadecimal colors
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# output of the function
-# fun_gg_palette(n = 2)
-# the ggplot2 palette when asking for 7 different colors
-# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7))
-# selection of the 5th color of the ggplot2 palette made of 7 different colors
-# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7)[5])
-# the ggplot2 palette made of 7 darkened colors
-# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7, kind = "dark"))
-# the ggplot2 palette made of 7 lighten colors
-# plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7, kind = "light"))
-# DEBUGGING
-# n = 0
-# kind = "std"
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = n, class = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & isTRUE(all.equal(n, 0))){ # isTRUE(all.equal(n, 0))) is similar to n == 0 but deals with float
-tempo.cat <- paste0("ERROR IN ", function.name, ": n ARGUMENT MUST BE A NON ZERO INTEGER. HERE IT IS: ", paste(n, collapse = " "))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-tempo <- fun_check(data = kind, options = c("std", "dark", "light"), length = 1, fun.name = function.name) ; eval(ee)
-}
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-hues = seq(15, 375, length = n + 1)
-hcl(h = hues, l = if(kind == "std"){65}else if(kind == "dark"){35}else if(kind == "light"){85}, c = 100)[1:n]
-}
-
-
-######## fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle
-
-
- 
-
-
-fun_gg_just <- function(angle, pos, kind = "axis"){
-# AIM
-# provide correct justification for text labeling, depending on the chosen angle
-# WARNINGS
-# justification behave differently on plot, depending whether it is used for annotayed text or for axis labelling. Indeed the latter has labelling constrained
-# Of note, a bug in ggplot2: vjust sometimes does not work, i.e., the same justification result is obtained whatever the value used. This is the case with angle = 90, pos = "top", kind = "axis". While everything is fine with angle = 90, pos = "bottom", kind = "axis". At least, everything seems fine for kind = "axis" and pos = c("left", "bottom")
-# ARGUMENTS
-# angle: integer value of the text angle, using the same rules as in ggplot2. Positive values for counterclockwise rotation: 0 for horizontal, 90 for vertical, 180 for upside down etc. Negative values for clockwise rotation: 0 for horizontal, -90 for vertical, -180 for upside down etc. 
-# pos: where text is? Either "top", "right", "bottom" or "left" of the elements to justify from
-# kind: kind of text? Either "axis" or "text". In the first case, the pos argument refers to the axis position, and in the second to annotated text (using ggplot2::annotate() or ggplot2::geom_text())
-# RETURN
-# a list containing:
-# $angle: the submitted angle (value potentially reduced to fit the [-360 ; 360] interval, e.g., 460 -> 100, without impact on the final angle displayed)
-# $pos: the selected position (argument pos)
-# $kind: the selected kind of text (argument kind)
-# $hjust: the horizontal justification
-# $vjust: the vertical justification
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# fun_gg_just(angle = 45, pos = "bottom")
-# fun_gg_just(angle = (360*2 + 45), pos = "left")
-# output <- fun_gg_just(angle = 45, pos = "bottom") ; obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10), stringsAsFactors = TRUE) ; ggplot2::ggplot() + ggplot2::geom_bar(data = obs1, mapping = ggplot2::aes(x = group, y = time), stat = "identity") + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = output$angle, hjust = output$hjust, vjust = output$vjust))
-# output <- fun_gg_just(angle = -45, pos = "left") ; obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10), stringsAsFactors = TRUE) ; ggplot2::ggplot() + ggplot2::geom_bar(data = obs1, mapping = ggplot2::aes(x = group, y = time), stat = "identity") + ggplot2::theme(axis.text.y = ggplot2::element_text(angle = output$angle, hjust = output$hjust, vjust = output$vjust)) + ggplot2::coord_flip()
-# output1 <- fun_gg_just(angle = 90, pos = "bottom") ; output2 <- fun_gg_just(angle = -45, pos = "left") ; obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10), stringsAsFactors = TRUE) ; ggplot2::ggplot() + ggplot2::geom_bar(data = obs1, mapping = ggplot2::aes(x = group, y = time), stat = "identity") + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = output1$angle, hjust = output1$hjust, vjust = output1$vjust), axis.text.y = ggplot2::element_text(angle = output2$angle, hjust = output2$hjust, vjust = output2$vjust))
-# output <- fun_gg_just(angle = -45, pos = "left") ; obs1 <- data.frame(time = 1, km = 1, bird = "pigeon", stringsAsFactors = FALSE) ; ggplot2::ggplot(data = obs1, mapping = ggplot2::aes(x = time, y = km)) + ggplot2::geom_point() + ggplot2::geom_text(mapping = ggplot2::aes(label = bird), angle = output$angle, hjust = output$hjust, vjust = output$vjust)
-# obs1 <- data.frame(time = 1:10, km = 1:10, bird = c(NA, NA, NA, "pigeon", NA, "cat", NA, NA, NA, NA), stringsAsFactors = FALSE) ; fun_open(width = 4, height = 4) ; for(i0 in c("text", "axis")){for(i1 in c("top", "right", "bottom", "left")){for(i2 in c(0, 45, 90, 135, 180, 225, 270, 315, 360)){output <- fun_gg_just(angle = i2, pos = i1, kind = i0) ; title <- paste0("kind: ", i0, " | pos: ", i1, " | angle = ", i2, " | hjust: ", output$hjust, " | vjust: ", output$vjust) ; if(i0 == "text"){print(ggplot2::ggplot(data = obs1, mapping = ggplot2::aes(x = time, y = km)) + ggplot2::geom_point(color = fun_gg_palette(1), alpha = 0.5) + ggplot2::ggtitle(title) + ggplot2::geom_text(mapping = ggplot2::aes(label = bird), angle = output$angle, hjust = output$hjust, vjust = output$vjust) + ggplot2::theme(title = ggplot2::element_text(size = 5)))}else{print(ggplot2::ggplot(data = obs1, mapping = ggplot2::aes(x = time, y = km)) + ggplot2::geom_point(color = fun_gg_palette(1), alpha = 0.5) + ggplot2::ggtitle(title) + ggplot2::geom_text(mapping = ggplot2::aes(label = bird)) + ggplot2::scale_x_continuous(position = ifelse(i1 == "top", "top", "bottom")) + ggplot2::scale_y_continuous(position = ifelse(i1 == "right", "right", "left")) + ggplot2::theme(title = ggplot2::element_text(size = 5), axis.text.x = if(i1 %in% c("top", "bottom")){ggplot2::element_text(angle = output$angle, hjust = output$hjust, vjust = output$vjust)}, axis.text.y = if(i1 %in% c("right", "left")){ggplot2::element_text(angle = output$angle, hjust = output$hjust, vjust = output$vjust)}))}}}} ; dev.off()
-# DEBUGGING
-# angle = 45 ; pos = "left" ; kind = "axis"
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument primary checking
-# arg with no default values
-mandat.args <- c(
-"angle", 
-"pos"
-)
-tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
-if(any(tempo)){ # normally no NA for missing() output
-tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end arg with no default values
-# using fun_check()
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = angle, class = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = pos, options = c("left", "top", "right", "bottom"), length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = kind, options = c("axis", "text"), length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end using fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument primary checking
-# second round of checking and data preparation
-# management of NA arguments
-tempo.arg <- names(arg.user.setting) # values provided by the user
-tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
-if(any(tempo.log) == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT JUST BE NA")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NA arguments
-# management of NULL arguments
-tempo.arg <- c(
-"angle", 
-"pos", 
-"kind"
-)
-tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
-if(any(tempo.log) == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NULL arguments
-# end second round of checking and data preparation
-# main code
-# to get angle between -360 and 360
-while(angle > 360){
-angle <- angle - 360
-}
-while(angle < -360){
-angle <- angle + 360
-}
-# end to get angle between -360 and 360
-# justifications
-if(pos %in% c("bottom", "top")){
-# code below is for if(pos == "bottom"){
-if(any(sapply(FUN = all.equal, c(-360, -180, 0, 180, 360), angle) == TRUE)){ # equivalent of angle == -360 | angle == -180 | angle == 0 | angle == 180 | angle == 360 but deals with floats
-hjust <- 0.5
-if(kind == "text"){
-if(any(sapply(FUN = all.equal, c(-360, 0, 360), angle) == TRUE)){
-vjust <- 1
-}else if(any(sapply(FUN = all.equal, c(-180, 180), angle) == TRUE)){
-vjust <- 0
-}
-}else{
-vjust <- 0.5
-}
-}else if(any(sapply(FUN = all.equal, c(-270, 90), angle) == TRUE)){
-hjust <- 1
-vjust <- 0.5
-}else if(any(sapply(FUN = all.equal, c(-90, 270), angle) == TRUE)){
-hjust <- 0
-vjust <- 0.5
-}else if((angle > -360 & angle < -270) | (angle > 0 & angle < 90)){
-hjust <- 1
-vjust <- 1
-}else if((angle > -270 & angle < -180) | (angle > 90 & angle < 180)){
-hjust <- 1
-vjust <- 0
-}else if((angle > -180 & angle < -90) | (angle > 180 & angle < 270)){
-hjust <- 0
-vjust <- 0
-if(kind == "text" & pos == "top"){
-hjust <- 1
-}
-}else if((angle > -90 & angle < 0) | (angle > 270 & angle < 360)){
-hjust <- 0
-vjust <- 1
-}
-if(pos == "top"){
-if( ! ((angle > -180 & angle < -90) | (angle > 180 & angle < 270))){
-hjust <- 1 - hjust
-}
-vjust <- 1 - vjust
-}
-}else if(pos %in% c("left", "right")){
-# code below is for if(pos == "left"){
-if(any(sapply(FUN = all.equal, c(-270, -90, 90, 270), angle) == TRUE)){ # equivalent of angle == -270 | angle == -90 | angle == 90 | angle == 270 but deals with floats
-hjust <- 0.5
-if(kind == "text"){
-if(any(sapply(FUN = all.equal, c(-90, 90), angle) == TRUE)){
-vjust <- 0
-}else if(any(sapply(FUN = all.equal, c(-270, 270), angle) == TRUE)){
-vjust <- 1
-}
-}else{
-vjust <- 0.5
-}
-}else if(any(sapply(FUN = all.equal, c(-360, 0, 360), angle) == TRUE)){
-hjust <- 1
-vjust <- 0.5
-}else if(any(sapply(FUN = all.equal, c(-180, 180), angle) == TRUE)){
-hjust <- 0
-vjust <- 0.5
-}else if((angle > -360 & angle < -270) | (angle > 0 & angle < 90)){
-hjust <- 1
-vjust <- 0
-}else if((angle > -270 & angle < -180) | (angle > 90 & angle < 180)){
-hjust <- 0
-vjust <- 0
-}else if((angle > -180 & angle < -90) | (angle > 180 & angle < 270)){
-hjust <- 0
-vjust <- 1
-}else if((angle > -90 & angle < 0) | (angle > 270 & angle < 360)){
-hjust <- 1
-vjust <- 1
-}
-if(pos == "right"){
-hjust <- 1 - hjust
-if( ! (((angle > -270 & angle < -180) | (angle > 90 & angle < 180)) | ((angle > -180 & angle < -90) | (angle > 180 & angle < 270)))){
-vjust <- 1 - vjust
-}
-}
-}
-# end justifications
-output <- list(angle = angle, pos = pos, kind = kind, hjust = hjust, vjust = vjust)
-return(output)
-}
-
-
-######## fun_gg_get_legend() #### get the legend of ggplot objects
-
-
- 
-
-
-fun_gg_get_legend <- function(ggplot_built, fun.name = NULL, lib.path = NULL){
-# AIM
-# get legend of ggplot objects
-# # from https://stackoverflow.com/questions/12539348/ggplot-separate-legend-and-plot
-# ARGUMENTS
-# ggplot_built: a ggplot build object
-# fun.name: single character string indicating the name of the function using fun_gg_get_legend() for warning and error messages. Ignored if NULL
-# lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
-# RETURN
-# a list of class c("gtable", "gTree", "grob", "gDesc"), providing legend information of ggplot_built objet, or NULL if the ggplot_built object has no legend
-# REQUIRED PACKAGES
-# ggplot2
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# fun_pack()
-# EXAMPLES
-# Simple example
-# obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10), stringsAsFactors = TRUE) ; p <- ggplot2::ggplot() + ggplot2::geom_point(data = obs1, mapping = ggplot2::aes(x = group, y = time, fill = group)) ; fun_gg_get_legend(ggplot_built = ggplot2::ggplot_build(p))
-# Error message because no legend in the ggplot
-# obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10), stringsAsFactors = TRUE) ; p <- ggplot2::ggplot() + ggplot2::geom_point(data = obs1, mapping = ggplot2::aes(x = group, y = time)) ; fun_gg_get_legend(ggplot_built = ggplot2::ggplot_build(p))
-# DEBUGGING
-# obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10), stringsAsFactors = TRUE) ; p <- ggplot2::ggplot() + ggplot2::geom_point(data = obs1, mapping = ggplot2::aes(x = group, y = time)) ; ggplot_built = ggplot2::ggplot_build(p) ; fun.name = NULL ; lib.path = NULL
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-req.function <- c(
-"fun_check",
-"fun_pack"
-)
-for(i1 in req.function){
-if(length(find(i1, mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED ", i1, "() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end required function checking
-# argument primary checking
-# arg with no default values
-mandat.args <- c(
-"ggplot_built"
-)
-tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
-if(any(tempo)){ # normally no NA for missing() output
-tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end arg with no default values
-# using fun_check()
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = ggplot_built, class = "ggplot_built", mode = "list", fun.name = function.name) ; eval(ee)
-if( ! is.null(fun.name)){
-tempo <- fun_check(data = fun.name, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(lib.path)){
-tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(arg.check)){
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-}
-# end using fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument primary checking
-# second round of checking
-# management of NA
-if(any(is.na(ggplot_built)) | any(is.na(fun.name)) | any(is.na(lib.path))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": NO ARGUMENT CAN HAVE NA VALUES")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NA
-# management of NULL
-if(is.null(ggplot_built)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nggplot_built ARGUMENT CANNOT BE NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NULL
-if( ! is.null(lib.path)){
-if( ! all(dir.exists(lib.path))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end second round of checking
-# package checking
-fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
-# end package checking
-# main code
-win.nb <- dev.cur()
-pdf(file = NULL)
-tmp <- ggplot2::ggplot_gtable(ggplot_built)
-# BEWARE with ggplot_gtable : open a blanck device https://stackoverflow.com/questions/17012518/why-does-this-r-ggplot2-code-bring-up-a-blank-display-device
-invisible(dev.off())
-if(win.nb > 1){ # to go back to the previous active device, if == 1 means no opened device
-dev.set(win.nb)
-}
-leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
-if(length(leg) == 0L){
-legend <- NULL
-}else{
-legend <- tmp$grobs[[leg]]
-}
-return(legend)
-}
-
-
-######## fun_gg_point_rast() #### ggplot2 raster scatterplot layer
-
-
- 
-
-
-fun_gg_point_rast <- function(
-data = NULL, 
-mapping = NULL, 
-stat = "identity", 
-position = "identity", 
-..., 
-na.rm = FALSE, 
-show.legend = NA, 
-inherit.aes = TRUE, 
-raster.width = NULL, 
-raster.height = NULL, 
-raster.dpi = 300, 
-inactivate = TRUE, 
-lib.path = NULL
-){
-# AIM
-# equivalent to ggplot2::geom_point() but in raster mode
-# use it like ggplot2::geom_point() with the main raster.dpi additional argument
-# WARNINGS
-# can be long to generate the plot
-# use a square plot region. Otherwise, the dots will have ellipsoid shape
-# solve the transparency problems with some GUI
-# this function is derived from the geom_point_rast() function, created by Viktor Petukhov , and present in the ggrastr package (https://rdrr.io/github/VPetukhov/ggrastr/src/R/geom-point-rast.R, MIT License, Copyright (c) 2017 Viktor Petukhov). Has been placed here to minimize package dependencies
-# ARGUMENTS
-# classical arguments of geom_point(), shown here https://rdrr.io/github/VPetukhov/ggrastr/man/geom_point_rast.html
-# raster.width : width of the result image (in inches). Default: deterined by the current device parameters
-# raster.height: height of the result image (in inches). Default: deterined by the current device parameters
-# raster.dpi: resolution of the result image
-# inactivate: logical. Inactivate the fun.name argument of the fun_check() function? If TRUE, the name of the fun_check() function in error messages coming from this function. Use TRUE if fun_gg_point_rast() is used like this: eval(parse(text = "fun_gg_point_rast"))
-# lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
-# RETURN
-# a raster scatter plot
-# REQUIRED PACKAGES
-# ggplot2
-# grid (included in the R installation packages but not automatically loaded)
-# Cairo
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# fun_pack()
-# EXAMPLES
-# Two pdf in the current directory
-# set.seed(1) ; data1 = data.frame(x = rnorm(100000), y = rnorm(10000), stringsAsFactors = TRUE) ; fun_open(pdf.name = "Raster") ; ggplot2::ggplot() + fun_gg_point_rast(data = data1, mapping = ggplot2::aes(x = x, y = y)) ; fun_open(pdf.name = "Vectorial") ; ggplot2::ggplot() + ggplot2::geom_point(data = data1, mapping = ggplot2::aes(x = x, y = y)) ; dev.off() ; dev.off()
-# DEBUGGING
-# 
-# function name
-if(all(inactivate == FALSE)){ # inactivate has to be used here but will be fully checked below
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-}else if(all(inactivate == TRUE)){
-function.name <- NULL
-}else{
-tempo.cat <- paste0("ERROR IN fun_gg_point_rast(): CODE INCONSISTENCY 1")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_pack", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-if( ! is.null(data)){
-tempo <- fun_check(data = data, class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(mapping)){
-tempo <- fun_check(data = mapping, class = "uneval", typeof = "list", fun.name = function.name) ; eval(ee) # aes() is tested
-}
-# stat and position not tested because too complicate
-tempo <- fun_check(data = na.rm, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = show.legend, class = "vector", mode = "logical", length = 1, na.contain = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = inherit.aes, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(raster.width)){
-tempo <- fun_check(data = raster.width, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(raster.height)){
-tempo <- fun_check(data = raster.height, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = raster.dpi, class = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = inactivate, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(lib.path)){
-tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# package checking
-fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
-fun_pack(req.package = c("grid"), lib.path = lib.path)
-fun_pack(req.package = c("Cairo"), lib.path = lib.path)
-# end package checking
-# additional functions
-DrawGeomPointRast <- function(data, panel_params, coord, na.rm = FALSE, raster.width = NULL, raster.height= NULL, raster.dpi = raster.dpi){
-if (is.null(raster.width)){
-raster.width <- par('fin')[1]
-}
-if (is.null(raster.height)){
- raster.height <- par('fin')[2]
-}
-prev_dev_id <- dev.cur()
-p <- ggplot2::GeomPoint$draw_panel(data, panel_params, coord)
-dev_id <- Cairo::Cairo(type='raster', width = raster.width*raster.dpi, height = raster.height*raster.dpi, dpi = raster.dpi, units = 'px', bg = "transparent")[1]
-grid::pushViewport(grid::viewport(width = 1, height = 1))
-grid::grid.points(x = p$x, y = p$y, pch = p$pch, size = p$size,
-name = p$name, gp = p$gp, vp = p$vp, draw = T)
-grid::popViewport()
-cap <- grid::grid.cap()
-invisible(dev.off(dev_id))
-invisible(dev.set(prev_dev_id))
-grid::rasterGrob(cap, x = 0, y = 0, width = 1, height = 1, default.units = "native", just = c("left","bottom"))
-}
-# end additional functions
-# main code
-GeomPointRast <- ggplot2::ggproto("GeomPointRast", ggplot2::GeomPoint, draw_panel = DrawGeomPointRast)
-ggplot2::layer(
-data = data, 
-mapping = mapping, 
-stat = stat, 
-geom = GeomPointRast, 
-position = position, 
-show.legend = show.legend, 
-inherit.aes = inherit.aes, 
-params = list(
-na.rm = na.rm, 
-raster.width = raster.width, 
-raster.height = raster.height, 
-raster.dpi = raster.dpi, 
-...
-)
-)
-# end main code
-}
-
-
-######## fun_gg_boxplot() #### ggplot2 boxplot + background dots if required
-
-
-
-
-######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally)
-
-
-
-
-######## fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required
-
-
-#test plot.margin = margin(up.space.mds, right.space.mds, down.space.mds, left.space.mds, "inches") to set the dim of the region plot ?
-# if matrix is full of zero (or same value I guess), heatmap is complicate. Test it and error message
-
-fun_gg_heatmap <- function(
-data1, 
-legend.name1 = "", 
-low.color1 = "blue", 
-mid.color1 = "white", 
-high.color1 = "red", 
-limit1 = NULL, 
-midpoint1 = NULL, 
-data2 = NULL, 
-color2 = "black", 
-alpha2 = 0.5, 
-invert2 = FALSE, 
-text.size = 12, 
-title = "", 
-title.text.size = 12, 
-show.scale = TRUE, 
-rotate = FALSE, 
-return = FALSE, 
-plot = TRUE, 
-add = NULL, 
-warn.print = FALSE, 
-lib.path = NULL
-){
-# AIM
-# ggplot2 heatmap with the possibility to overlay a mask
-# see also:
-# draw : http://www.sthda.com/english/wiki/ggplot2-quick-correlation-matrix-heatmap-r-software-and-data-visualization
-# same range scale : https://stackoverflow.com/questions/44655723/r-ggplot2-heatmap-fixed-scale-color-between-graphs 
-# for ggplot2 specifications, see: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html
-# ARGUMENTS
-# data1: numeric matrix or data frame resulting from the conversion of the numeric matrix by reshape2::melt()
-# legend.name1: character string of the data1 heatmap scale legend
-# low.color1: character string of the color (i.e., "blue" or "#0000FF") of the lowest scale value
-# mid.color1: same as low.color1 but for the middle scale value. If NULL, the middle color is the default color between low.color1 and high.color1. BEWARE: argument midpoint1 is not ignored, even if mid.color1 is NULL, meaning that the default mid color can still be controled
-# high.color1: same as low.color1 but for the highest scale value
-# limit1: 2 numeric values defining the lowest and higest color scale values. If NULL, take the range of data1 values
-# midpoint1: single numeric value defining the value corresponding to the mid.color1 argument. A warning message is returned if midpoint1 does not correspond to the mean of limit1 values, because the color scale is not linear anymore. If NULL, takes the mean of limit1 values. Mean of data1, instead of mean of limit1, can be used here if required
-# data2: binary mask matrix (made of 0 and 1) of same dimension as data1 or a data frame resulting from the conversion of the binary mask matrix by reshape2::melt(). Value 1 of data2 will correspond to color2 argument (value 0 will be NA color), and the opposite if invert2 argument is TRUE (inverted mask)
-# color2: color of the 1 values of the binary mask matrix. The 0 values will be color NA
-# alpha2: numeric value (from 0 to 1) of the mask transparency
-# invert2: logical. Invert the mask (1 -> 0 and 0 -> 1)?
-# text.size: numeric value of the size of the texts in scale
-# title: character string of the graph title
-# title.text.size: numeric value of the title size (in points)
-# show.scale: logical. Show color scale?
-# rotate: logical. Rotate the heatmap 90° clockwise?
-# return: logical. Return the graph parameters?
-# plot: logical. Plot the graphic? If FALSE and return argument is TRUE, graphical parameters and associated warnings are provided without plotting
-# add: character string allowing to add more ggplot2 features (dots, lines, themes, etc.). BEWARE: (1) must start with "+" just after the simple or double opening quote (no space, end of line, carriage return, etc., allowed), (2) must finish with ")" just before the simple or double closing quote (no space, end of line, carriage return, etc., allowed) and (3) each function must be preceded by "ggplot2::" (for instance: "ggplot2::coord_flip()). If the character string contains the "ggplot2::theme" string, then internal ggplot2 theme() and theme_classic() functions will be inactivated to be reused by add. BEWARE: handle this argument with caution since added functions can create conflicts with the preexisting internal ggplot2 functions
-# warn.print: logical. Print warnings at the end of the execution? No print if no warning messages
-# lib.path: absolute path of the required packages, if not in the default folders
-# RETURN
-# a heatmap if plot argument is TRUE
-# a list of the graph info if return argument is TRUE:
-# $data: a list of the graphic info
-# $axes: a list of the axes info
-# $scale: the scale info (lowest, mid and highest values)
-# $warn: the warning messages. Use cat() for proper display. NULL if no warning
-# REQUIRED PACKAGES
-# ggplot2
-# reshape2
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# fun_pack()
-# fun_round()
-# EXAMPLES
-# fun_gg_heatmap(data1 = matrix(1:16, ncol = 4), title = "GRAPH 1")
-# fun_gg_heatmap(data1 = matrix(1:16, ncol = 4), return = TRUE)
-# fun_gg_heatmap(data1 = matrix(1:16, ncol = 4), legend.name1 = "VALUE", title = "GRAPH 1", text.size = 5, data2 = matrix(rep(c(1,0,0,0), 4), ncol = 4), invert2 = FALSE, return = TRUE)
-# diagonal matrix
-# fun_gg_heatmap(data1 = matrix(c(1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1), ncol = 4))
-# fun_gg_heatmap(data1 = reshape2::melt(matrix(c(1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1), ncol = 4)))
-# error message
-# fun_gg_heatmap(data1 = matrix(1:16, ncol = 4), data2 = matrix(rep(c(1,0,0,0), 5), ncol = 5))
-# fun_gg_heatmap(data1 = matrix(1:16, ncol = 4), data2 = reshape2::melt(matrix(rep(c(1,0,0,0), 4), ncol = 4)))
-# fun_gg_heatmap(data1 = reshape2::melt(matrix(1:16, ncol = 4)), data2 = reshape2::melt(matrix(rep(c(1,0,0,0), 4), ncol = 4)))
-# DEBUGGING
-# data1 = matrix(1:16, ncol = 4) ; legend.name1 = "" ; low.color1 = "blue" ; mid.color1 = "white" ; high.color1 = "red" ; limit1 = NULL ; midpoint1 = NULL ; data2 = matrix(rep(c(1,0,0,0), 4), ncol = 4) ; color2 = "black" ; alpha2 = 0.5 ; invert2 = FALSE ; text.size = 12 ; title = "" ; title.text.size = 12 ; show.scale = TRUE ; rotate = FALSE ; return = FALSE ; plot = TRUE ; add = NULL ; warn.print = TRUE ; lib.path = NULL
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_pack", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_round", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_round() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# no reserved words required for this function
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-if(all(is.matrix(data1))){
-tempo <- fun_check(data = data1, class = "matrix", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-}else if(all(is.data.frame(data1))){
-tempo <- fun_check(data = data1, class = "data.frame", length = 3, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-# structure of reshape2::melt() data frame
-tempo <- fun_check(data = data1[, 1], data.name = "COLUMN 1 OF data1 (reshape2::melt() DATA FRAME)", typeof = "integer", fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = data1[, 2], data.name = "COLUMN 2 OF data1 (reshape2::melt() DATA FRAME)", typeof = "integer", fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = data1[, 3], data.name = "COLUMN 3 OF data1 (reshape2::melt() DATA FRAME)", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-}
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 ARGUMENT MUST BE A NUMERIC MATRIX OR A DATA FRAME OUTPUT OF THE reshape::melt() FUNCTION")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo <- fun_check(data = legend.name1, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = low.color1, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & ! (all(low.color1 %in% colors() | grepl(pattern = "^#", low.color1)))){ # check that all strings of low.color1 start by #
-tempo.cat <- paste0("ERROR IN ", function.name, ": low.color1 ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors()")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-if( ! is.null(mid.color1)){
-tempo <- fun_check(data = mid.color1, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & ! (all(mid.color1 %in% colors() | grepl(pattern = "^#", mid.color1)))){ # check that all strings of mid.color1 start by #
-tempo.cat <- paste0("ERROR IN ", function.name, ": mid.color1 ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors()")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-tempo <- fun_check(data = high.color1, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & ! (all(high.color1 %in% colors() | grepl(pattern = "^#", high.color1)))){ # check that all strings of high.color1 start by #
-tempo.cat <- paste0("ERROR IN ", function.name, ": high.color1 ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors()")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-if( ! is.null(limit1)){
-tempo <- fun_check(data = limit1, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & any(limit1 %in% c(Inf, -Inf))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": limit1 ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-if( ! is.null(midpoint1)){
-tempo <- fun_check(data = midpoint1, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(data2)){
-if(all(is.matrix(data2))){
-tempo <- fun_check(data = data2, class = "matrix", mode = "numeric", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & ! all(unique(data2) %in% c(0,1))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": MATRIX IN data2 MUST BE MADE OF 0 AND 1 ONLY (MASK MATRIX)")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo$problem == FALSE & all(is.matrix(data1)) & ! identical(dim(data1), dim(data2))){ # matrix and matrix
-tempo.cat <- paste0("ERROR IN ", function.name, ": MATRIX DIMENSION IN data2 MUST BE IDENTICAL AS MATRIX DIMENSION IN data1. HERE IT IS RESPECTIVELY:\n", paste(dim(data2), collapse = " "), "\n", paste(dim(data1), collapse = " "))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo$problem == FALSE & all(is.data.frame(data1)) & nrow(data1) != prod(dim(data2))){ # reshape2 and matrix
-tempo.cat <- paste0("ERROR IN ", function.name, ": DATA FRAME IN data2 MUST HAVE ROW NUMBER EQUAL TO PRODUCT OF DIMENSIONS OF data1 MATRIX. HERE IT IS RESPECTIVELY:\n", paste(nrow(data1), collapse = " "), "\n", paste(prod(dim(data2)), collapse = " "))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else if(all(is.data.frame(data2))){
-tempo <- fun_check(data = data2, class = "data.frame", length = 3, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-# structure of reshape2::melt() data frame
-tempo <- fun_check(data = data2[, 1], data.name = "COLUMN 1 OF data2 (reshape2::melt() DATA FRAME)", typeof = "integer", fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = data2[, 2], data.name = "COLUMN 2 OF data2 (reshape2::melt() DATA FRAME)", typeof = "integer", fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = data2[, 3], data.name = "COLUMN 3 OF data2 (reshape2::melt() DATA FRAME)", mode = "numeric", fun.name = function.name) ; eval(ee)
-}
-if(tempo$problem == FALSE & ! all(unique(data2[, 3]) %in% c(0,1))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THIRD COLUMN OF DATA FRAME IN data2 MUST BE MADE OF 0 AND 1 ONLY (MASK DATA FRAME)")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo$problem == FALSE & all(is.data.frame(data1)) & ! identical(dim(data1), dim(data2))){ # data frame and data frame
-tempo.cat <- paste0("ERROR IN ", function.name, ": DATA FRAME DIMENSION IN data2 MUST BE IDENTICAL TO DATA FRAME DIMENSION IN data1. HERE IT IS RESPECTIVELY:\n", paste(dim(data2), collapse = " "), "\n", paste(dim(data1), collapse = " "))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo$problem == FALSE & all(is.matrix(data1)) & nrow(data2) != prod(dim(data1))){ # reshape2 and matrix
-tempo.cat <- paste0("ERROR IN ", function.name, ": DATA FRAME IN data2 MUST HAVE ROW NUMBER EQUAL TO PRODUCT OF DIMENSION OF data1 MATRIX. HERE IT IS RESPECTIVELY:\n", paste(nrow(data2), collapse = " "), "\n", paste(prod(dim(data1)), collapse = " "))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE data2 ARGUMENT MUST BE A NUMERIC MATRIX OR A DATA FRAME OUTPUT OF THE reshape::melt() FUNCTION")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-tempo <- fun_check(data = color2, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & ! (all(color2 %in% colors() | grepl(pattern = "^#", color2)))){ # check that all strings of color2 start by #
-tempo.cat <- paste0("ERROR IN ", function.name, ": color2 ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors()")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo <- fun_check(data = alpha2, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = invert2, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = title, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = title.text.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = show.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = return, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = plot, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(add)){
-tempo <- fun_check(data = add, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & ! grepl(pattern = "^\\+", add)){ # check that the add string start by +
-tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST START WITH \"+\": ", paste(unique(add), collapse = " "))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo$problem == FALSE & ! grepl(pattern = "ggplot2::", add)){ #
-tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST CONTAIN \"ggplot2::\" IN FRONT OF EACH GGPLOT2 FUNCTION: ", paste(unique(add), collapse = " "))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo$problem == FALSE & ! grepl(pattern = ")$", add)){ # check that the add string  finished by )
-tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST FINISH BY \")\": ", paste(unique(add), collapse = " "))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(lib.path)){
-tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# package checking
-fun_pack(req.package = c("reshape2", "ggplot2"), lib.path = lib.path)
-# end package checking
-# main code
-ini.warning.length <- options()$warning.length
-options(warning.length = 8170)
-warn <- NULL
-warn.count <- 0
-if(all(is.matrix(data1))){
-data1 <- reshape2::melt(data1) # transform a matrix into a data frame with 2 coordinates columns and the third intensity column
-}
-if(rotate == TRUE){
-data1[, 1] <- rev(data1[, 1])
-}
-if(is.null(limit1)){
-if(any(data1[, 3] %in% c(Inf, -Inf))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE data1 ARGUMENT CONTAINS -Inf OR Inf VALUES IN THE THIRD COLUMN, THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-limit1 <- range(data1[, 3], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE limit1 ARGUMENT IS NULL -> RANGE OF data1 ARGUMENT HAS BEEN TAKEN: ", paste(fun_round(limit1), collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-if(suppressWarnings(any(limit1 %in% c(Inf, -Inf)))){
-tempo.cat <- paste0("ERROR IN ", function.name, " COMPUTED LIMIT CONTAINS Inf VALUES, BECAUSE VALUES FROM data1 ARGUMENTS ARE NA OR Inf ONLY")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if(is.null(midpoint1)){
-midpoint1 <- mean(limit1, na.rm = TRUE)
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE midpoint1 ARGUMENT IS NULL -> MEAN OF limit1 ARGUMENT HAS BEEN TAKEN: ", paste(fun_round(midpoint1), collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else if(fun_round(midpoint1, 9) != fun_round(mean(limit1), 9)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE midpoint1 ARGUMENT (", fun_round(mean(midpoint1), 9), ") DOES NOT CORRESPOND TO THE MEAN OF THE limit1 ARGUMENT (", fun_round(mean(limit1), 9), "). COLOR SCALE IS NOT LINEAR")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if( ! is.null(data2)){
-if(all(is.matrix(data2))){
-data2 <- reshape2::melt(data2) # transform a matrix into a data frame with 2 coordinates columns and the third intensity column
-}
-if(rotate == TRUE){
-data2[, 1] <- rev(data2[, 1])
-}
-data2[, 3] <- factor(data2[, 3]) # to converte continuous scale into discrete scale
-}
-tempo.gg.name <- "gg.indiv.plot."
-tempo.gg.count <- 0 # to facilitate debugging
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggplot())
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_raster(data = data1, mapping = ggplot2::aes_string(x = names(data1)[ifelse(rotate == FALSE, 2, 1)], y = names(data1)[ifelse(rotate == FALSE, 1, 2)], fill = names(data1)[3]), show.legend = show.scale)) # show.legend option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_fill_gradient2(low = low.color1, high = high.color1, mid = mid.color1, midpoint = midpoint1, limit = limit1, breaks = c(limit1[1], midpoint1, limit1[2]), labels = fun_round(c(limit1[1], midpoint1, limit1[2])), name = legend.name1))
-if( ! is.null(data2)){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_raster(data = data2, mapping = ggplot2::aes_string(x = names(data2)[ifelse(rotate == FALSE, 2, 1)], y = names(data2)[ifelse(rotate == FALSE, 1, 2)], alpha = names(data2)[3]), fill = color2, show.legend = FALSE))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "alpha", values = if(invert2 == FALSE){c(0, alpha2)}else{c(alpha2, 0)}, guide = FALSE))
-# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_raster(data = data2, mapping = ggplot2::aes_string(x = names(data2)[ifelse(rotate == FALSE, 2, 1)], y = names(data2)[ifelse(rotate == FALSE, 1, 2)], group = names(data2)[3]), fill = data2[, 3], alpha = alpha2, show.legend = FALSE)) # BEWARE: this does not work if NA present, because geom_raster() has a tendency to complete empty spaces, and thus, behave differently than geom_tile(). See https://github.com/tidyverse/ggplot2/issues/3025
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::coord_fixed()) # x = y
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_y_reverse())
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggtitle(title))
-add.check <- TRUE
-if( ! is.null(add)){ # if add is NULL, then = 0
-if(grepl(pattern = "ggplot2::theme", add) == TRUE){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") \"ggplot2::theme\" STRING DETECTED IN THE add ARGUMENT -> INTERNAL GGPLOT2 THEME FUNCTIONS theme() AND theme_classic() HAVE BEEN INACTIVATED, TO BE USED BY THE USER")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-add.check <- FALSE
-}
-}
-if(add.check == TRUE){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::theme_classic(base_size = text.size))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::theme(
-text = ggplot2::element_text(size = text.size), 
-plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
-line = ggplot2::element_blank(),
-axis.title = ggplot2::element_blank(),
-axis.text = ggplot2::element_blank(),
-axis.ticks = ggplot2::element_blank(),
-panel.background = ggplot2::element_blank()
-))
-}
-if(plot == TRUE){
-# suppressWarnings(
-print(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if(is.null(add)){NULL}else{add}))))
-# )
-}else{
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") PLOT NOT SHOWN AS REQUESTED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if(warn.print == TRUE & ! is.null(warn)){
-on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
-}
-on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
-if(return == TRUE){
-output <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))
-output <- output$data
-names(output)[1] <- "heatmap"
-if( ! is.null(data2)){
-names(output)[2] <- "mask"
-}
-return(list(data = output, axes = output$layout$panel_params[[1]], scale = c(limit1[1],  midpoint1, limit1[2]), warn = warn))
-}
-}
-
-
-######## fun_gg_empty_graph() #### text to display for empty graphs
-
-
- 
-
-
-fun_gg_empty_graph <- function(
-text = NULL, 
-text.size = 12, 
-title = NULL, 
-title.size = 8, 
-lib.path = NULL
-){
-# AIM
-# display an empty ggplot2 plot with a text in the middle of the window (for instance to specify that no plot can be drawn)
-# ARGUMENTS
-# text: character string of the message to display
-# text.size: numeric value of the text size (in points)
-# title: character string of the graph title
-# title.size: numeric value of the title size (in points)
-# lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
-# RETURN
-# an empty plot
-# REQUIRED PACKAGES
-# ggplot2
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# fun_pack()
-# EXAMPLES
-### simple example
-# fun_gg_empty_graph(text = "NO GRAPH")
-### white page
-# fun_gg_empty_graph()
-### all the arguments
-# fun_gg_empty_graph(text = "NO GRAPH", text.size = 8, title = "GRAPH1", title.size = 10, lib.path = NULL)
-# DEBUGGING
-# text = "NO GRAPH" ; text.size = 12 ; title = "GRAPH1" ; title.size = 8 ; lib.path = NULL
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_pack", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-if( ! is.null(text)){
-tempo <- fun_check(data = text, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(title)){
-tempo <- fun_check(data = title, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = title.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# package checking
-fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
-# end package checking
-# main code
-tempo.gg.name <- "gg.indiv.plot."
-tempo.gg.count <- 0
-# no need loop part
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggplot())
-if( ! is.null(text)){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_text(data = data.frame(x = 1, y = 1, stringsAsFactors = TRUE), ggplot2::aes(x = x, y = y, label = text), size = text.size))
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggtitle(title))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::theme_void())
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
-plot.title = ggplot2::element_text(size = title.size) # stronger than text
-))
-suppressWarnings(print(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + ")))))
-}
-
-
-################ Graphic extraction
-
-
-######## fun_trim() #### display values from a quantitative variable and trim according to defined cut-offs
-
-# Add name of the variable in the graph
-# not max and min for boxplot but 1.5IQR
-fun_trim <- function(
-data, 
-displayed.nb = NULL, 
-single.value.display = FALSE, 
-trim.method = "", 
-trim.cutoffs = c(0.05, 
-0.975), 
-interval.scale.disp = TRUE, 
-down.space = 0.75, 
-left.space = 0.75, 
-up.space = 0.3, 
-right.space = 0.25, 
-orient = 1, 
-dist.legend = 0.37, 
-box.type = "l", 
-amplif.label = 1.25, 
-amplif.axis = 1.25, 
-std.x.range = TRUE, 
-std.y.range = TRUE, 
-cex.pt = 0.2, 
-col.box = hsv(0.55, 
-0.8, 
-0.8), 
-x.nb.inter.tick = 4, 
-y.nb.inter.tick = 0, 
-tick.length = 1, 
-sec.tick.length = 0.75, 
-corner.text = "", 
-amplif.legend = 1, 
-corner.text.size = 0.75, 
-trim.return = FALSE
-){
-# AIM
-# trim and display values from a numeric vector or matrix
-# plot 4 graphs: stripchart of values, stripchart of rank of values, histogram and normal QQPlot
-# different kinds of intervals are displayed on the top of graphes to facilitate the analysis of the variable and a trimming setting
-# the trimming interval chosen is displayed on top of graphs
-# both trimmed and not trimmed values are returned in a list
-# ARGUMENTS
-# data: values to plot (either a numeric vector or a numeric matrix)
-# displayed.nb: number of values displayed. If NULL, all the values are displayed. Otherwise, if the number of values is over displayed.nb, then displayed.nb values are displayed after random selection
-# single.value.display: provide the 4 graphs if data is made of a single (potentially repeated value)? If FALSE, an empty graph is displayed if data is made of a single (potentially repeated value). And the return list is made of NULL compartments
-# trim.method: Write "" if not required. write "mean.sd" if mean +/- sd has to be displayed as a trimming interval (only recommanded for normal distribution). Write "quantile" to display a trimming interval based on quantile cut-offs. No other possibility allowed. See trim.cutoffs below
-# trim.cutoffs: 2 values cutoff for the trimming interval displayed, each value between 0 and 1. Not used if trim.method == "".The couple of values c(lower, upper) represents the lower and upper boundaries of the trimming interval (in proportion), which represent the interval of distribution kept (between 0 and 1). Example: trim.cutoffs = c(0.05, 0.975). What is strictly kept for the display is ]lower , upper[, boundaries excluded. Using the "mean.sd" method, 0.025 and 0.975 represent 95% CI which is mean +/- 1.96 * sd
-# interval.scale.disp: display sd and quantiles intervals on top of graphs ?
-# down.space: lower vertical margin (in inches, mai argument of par())
-# left.space: left horizontal margin (in inches, mai argument of par())
-# up.space: upper vertical margin between plot region and grapical window (in inches, mai argument of par())
-# right.space: right horizontal margin (in inches, mai argument of par())
-# orient: scale number orientation (las argument of par()). 0, always parallel to the axis; 1, always horizontal; 2, always perpendicular to the axis; 3, always vertical
-# dist.legend: numeric value that moves axis legends away in inches (first number of mgp argument of par() but in inches thus / 0.2)
-# box.type: bty argument of par(). Either "o", "l", "7", "c", "u", "]", the resulting box resembles the corresponding upper case letter. A value of "n" suppresses the box
-# amplif.label: increase or decrease the size of the text in legends
-# amplif.axis: increase or decrease the size of the scale numbers in axis
-# std.x.range: standard range on the x-axis? TRUE (no range extend) or FALSE (4% range extend). Controls xaxs argument of par() (TRUE is xaxs = "i", FALSE is xaxs = "r")
-# std.y.range: standard range on the y-axis? TRUE (no range extend) or FALSE (4% range extend). Controls yaxs argument of par() (TRUE is yaxs = "i", FALSE is yaxs = "r")
-# cex.pt: size of points in stripcharts (in inches, thus cex.pt will be thereafter / 0.2)
-# col.box: color of boxplot
-# x.nb.inter.tick: number of secondary ticks between main ticks on x-axis (only if not log scale). Zero means non secondary ticks
-# y.nb.inter.tick: number of secondary ticks between main ticks on y-axis (only if not log scale). Zero means non secondary ticks
-# tick.length: length of the ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc. 0 means no tick
-# sec.tick.length: length of the secondary ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc., 0 for no ticks)
-# corner.text: text to add at the top right corner of the window
-# amplif.legend: increase or decrease the size of the text of legend
-# corner.text.size: positive numeric. Increase or decrease the size of the text. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2
-# trim.return: return the trimmed and non trimmed values? NULL returned for trimmed and non trimmed values if trim.method == ""
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# RETURN
-# a list containing:
-# $trim.method: correspond to trim.method above
-# $trim.cutoffs: correspond to trim.cutoffs above
-# $real.trim.cutoffs: the two boundary values (in the unit of the numeric vector or numeric matrix analyzed). NULL 
-# $trimmed.values: the values outside of the trimming interval as defined in trim.cutoffs above
-# $kept.values: the values inside the trimming interval as defined in trim.cutoffs above
-# EXAMPLES
-# fun_trim(data = c(1:100, 1:10), displayed.nb = NULL, single.value.display = FALSE, trim.method = "mean.sd", trim.cutoffs = c(0.05, 0.975), interval.scale.disp = TRUE, down.space = 0.75, left.space = 0.75, up.space = 0.3, right.space = 0.25, orient = 1, dist.legend = 0.37, box.type = "l", amplif.label = 1.25, amplif.axis = 1.25, std.x.range = TRUE, std.y.range = TRUE, cex.pt = 0.2, col.box = hsv(0.55, 0.8, 0.8), x.nb.inter.tick = 4, y.nb.inter.tick = 0, tick.length = 0.5, sec.tick.length = 0.3, corner.text = "", amplif.legend = 1, corner.text.size = 0.75, trim.return = TRUE)
-# DEBUGGING
-# data = c(1:100, 1:10) ; displayed.nb = NULL ; single.value.display = FALSE ; trim.method = "quantile" ; trim.cutoffs = c(0.05, 0.975) ; interval.scale.disp = TRUE ; down.space = 1 ; left.space = 1 ; up.space = 0.5 ; right.space = 0.25 ; orient = 1 ; dist.legend = 0.5 ; box.type = "l" ; amplif.label = 1 ; amplif.axis = 1 ; std.x.range = TRUE ; std.y.range = TRUE ; cex.pt = 0.1 ; col.box = hsv(0.55, 0.8, 0.8) ; x.nb.inter.tick = 4 ; y.nb.inter.tick = 0 ; tick.length = 0.5 ; sec.tick.length = 0.3 ; corner.text = "" ; amplif.legend = 1 ; corner.text.size = 0.75 ; trim.return = TRUE # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-# argument checking without fun_check()
-if( ! (all(class(data) == "numeric") | all(class(data) == "integer") | (all(class(data) %in% c("matrix", "array")) & base::mode(data) == "numeric"))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data ARGUMENT MUST BE A NUMERIC VECTOR OR NUMERIC MATRIX")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end argument checking without fun_check()
-# argument checking with fun_check()
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-if( ! is.null(displayed.nb)){
-tempo <- fun_check(data = displayed.nb, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-if(displayed.nb < 2){
-tempo.cat <- paste0("ERROR IN ", function.name, ": displayed.nb ARGUMENT MUST BE A SINGLE INTEGER VALUE GREATER THAN 1 AND NOT: ", paste(displayed.nb, collapse = " "))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-tempo <- fun_check(data = single.value.display, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = trim.method, options = c("", "mean.sd", "quantile"), length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = trim.cutoffs, class = "vector", mode = "numeric", length = 2, prop = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = interval.scale.disp, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = down.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = left.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = up.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = right.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = orient, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = dist.legend, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = box.type, options = c("o", "l", "7", "c", "u", "]", "n"), length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = amplif.label, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = amplif.axis, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = std.x.range, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = std.y.range, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = cex.pt, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = col.box, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = x.nb.inter.tick, class = "integer", length = 1, neg.values = FALSE, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y.nb.inter.tick, class = "integer", length = 1, neg.values = FALSE, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = tick.length, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = sec.tick.length, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = corner.text, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = amplif.legend, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = corner.text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = trim.return, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end argument checking with fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-if(all(is.na(data) | ! is.finite(data))){
-tempo.cat <- paste0("ERROR IN fun_trim FUNCTION\ndata ARGUMENT CONTAINS ONLY NA OR Inf")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end argument checking
-# main code
-if(all(class(data)%in% c("matrix", "array"))){
-data <- as.vector(data)
-}
-na.nb <- NULL
-if(any(is.na(data))){
-na.nb <- sum(c(is.na(data)))
-data <- data[ ! is.na(data)]
-}
-color.cut <- hsv(0.75, 1, 1) # color of interval selected
-col.mean <- hsv(0.25, 1, 0.8) # color of interval using mean+/-sd
-col.quantile <- "orange" # color of interval using quantiles
-quantiles.selection <- c(0.01, 0.025, 0.05, 0.1, 0.25, 0.5, 0.75, 0.9, 0.95, 0.975, 0.99) # quantiles used in axis to help for choosing trimming cutoffs
-if(single.value.display == FALSE & length(unique(data)) == 1L){
-par(bty = "n", xaxt = "n", yaxt = "n", xpd = TRUE)
-plot(1, pch = 16, col = "white", xlab = "", ylab = "")
-text(x = 1, y = 1, paste0("No graphic displayed\nBecause data made of a single different value (", formatC(as.double(table(data))), ")"), cex = 2)
-output <- list(trim.method = NULL, trim.cutoffs = NULL, real.trim.cutoffs = NULL, trimmed.values = NULL, kept.values = NULL)
-}else{
-output <- list(trim.method = trim.method, trim.cutoffs = trim.cutoffs, real.trim.cutoffs = NULL, trimmed.values = NULL, kept.values = NULL)
-fun.rug <- function(sec.tick.length.f = sec.tick.length, x.nb.inter.tick.f = x.nb.inter.tick, y.nb.inter.tick.f = y.nb.inter.tick){
-if(x.nb.inter.tick.f > 0){
-inter.tick.unit <- (par("xaxp")[2] - par("xaxp")[1]) / par("xaxp")[3]
-par.ini <- par()[c("xpd", "tcl")]
-par(xpd = FALSE)
-par(tcl = -par()$mgp[2] * sec.tick.length.f) # tcl gives the length of the ticks as proportion of line text, knowing that mgp is in text lines. So the main ticks are a 0.5 of the distance of the axis numbers by default. The sign provides the side of the tick (negative for outside of the plot region)
-suppressWarnings(rug(seq(par("xaxp")[1] - 10 * inter.tick.unit, par("xaxp")[2] + 10 * inter.tick.unit, by = inter.tick.unit / (1 + x.nb.inter.tick.f)), ticksize = NA, side = 1)) # ticksize = NA to allow the use of par()$tcl value
-par(par.ini)
-rm(par.ini)
-}
-if(y.nb.inter.tick.f > 0){
-inter.tick.unit <- (par("yaxp")[2] - par("yaxp")[1]) / par("yaxp")[3]
-par.ini <- par()[c("xpd", "tcl")]
-par(xpd = FALSE)
-par(tcl = -par()$mgp[2] * sec.tick.length.f) # tcl gives the length of the ticks as proportion of line text, knowing that mgp is in text lines. So the main ticks are a 0.5 of the distance of the axis numbers by default. The sign provides the side of the tick (negative for outside of the plot region)
-suppressWarnings(rug(seq(par("yaxp")[1] - 10 * inter.tick.unit, par("yaxp")[2] + 10 * inter.tick.unit, by = inter.tick.unit / (1 + y.nb.inter.tick.f)), ticksize = NA, side = 2)) # ticksize = NA to allow the use of par()$tcl value
-par(par.ini)
-rm(par.ini)
-}
-}
-fun.add.cut <- function(data.f, trim.method.f = trim.method, trim.cutoffs.f = trim.cutoffs, color.cut.f = color.cut, return.f = FALSE){
-# DEBUGGING
-# data.f = data ; trim.method.f = "mean.sd"; trim.cutoffs.f = trim.cutoffs ; color.cut.f = color.cut ; return.f = TRUE
-real.trim.cutoffs.f <- NULL
-if(trim.method.f != ""){
-data.f <- sort(data.f)
-par.ini <- par()$xpd
-par(xpd = FALSE)
-if(trim.method.f == "mean.sd"){
-real.trim.cutoffs.f <- qnorm(trim.cutoffs.f, mean(data.f, na.rm = TRUE), sd(data.f, na.rm = TRUE))
-abline(v = qnorm(trim.cutoffs.f, mean(data.f, na.rm = TRUE), sd(data.f, na.rm = TRUE)), col = color.cut.f)
-segments(qnorm(trim.cutoffs.f[1], mean(data.f, na.rm = TRUE), sd(data.f, na.rm = TRUE)), par()$usr[4] * 0.75, qnorm(trim.cutoffs.f[2], mean(data.f, na.rm = TRUE), sd(data.f, na.rm = TRUE)), par()$usr[4] * 0.75, col = color.cut.f)
-}
-if(trim.method.f == "quantile"){
-real.trim.cutoffs.f <- quantile(data.f, probs = trim.cutoffs.f, type = 7, na.rm = TRUE)
-abline(v = quantile(data.f, probs = trim.cutoffs.f, type = 7, na.rm = TRUE), col = color.cut.f)
-segments(quantile(data.f, probs = trim.cutoffs.f[1], type = 7, na.rm = TRUE), par()$usr[4] * 0.75, quantile(data.f, probs = trim.cutoffs.f[2], type = 7, na.rm = TRUE), par()$usr[4] * 0.75, col = color.cut.f)
-}
-par(par.ini)
-if(return.f == TRUE){
-trimmed.values.f <- data.f[data.f <= real.trim.cutoffs.f[1] | data.f >= real.trim.cutoffs.f[2]]
-kept.values.f <- data.f[data.f > real.trim.cutoffs.f[1] & data.f < real.trim.cutoffs.f[2]]
-}
-}else{
-real.trim.cutoffs.f <- NULL
-trimmed.values.f <- NULL
-kept.values.f <- NULL
-}
-if(return.f == TRUE){
-output <- list(trim.method = trim.method.f, trim.cutoffs = trim.cutoffs.f, real.trim.cutoffs = real.trim.cutoffs.f, trimmed.values = trimmed.values.f, kept.values = kept.values.f)
-return(output)
-}
-}
-fun.interval.scale.display <- function(data.f, col.quantile.f = col.quantile, quantiles.selection.f = quantiles.selection, col.mean.f = col.mean){ # intervals on top of graphs
-par.ini <- par()[c("mgp", "xpd")]
-par(mgp = c(0.25, 0.25, 0), xpd = NA)
-axis(side = 3, at = c(par()$usr[1], par()$usr[2]), labels = rep("", 2), col = col.quantile.f, lwd.ticks = 0)
-par(xpd = FALSE)
-axis(side = 3, at = quantile(as.vector(data.f), probs = quantiles.selection.f, type = 7, na.rm = TRUE), labels = quantiles.selection.f, col.axis = col.quantile.f, col = col.quantile.f)
-par(mgp = c(1.75, 1.75, 1.5), xpd = NA)
-axis(side = 3, at = c(par()$usr[1], par()$usr[2]), labels = rep("", 2), col = col.mean.f, lwd.ticks = 0)
-par(xpd = FALSE)
-axis(side = 3, at = m + s * qnorm(quantiles.selection.f), labels = formatC(round(qnorm(quantiles.selection.f), 2)), col.axis = col.mean.f, col = col.mean.f, lwd.ticks = 1)
-par(par.ini)
-}
-zone<-matrix(1:4, ncol=2)
-layout(zone)
-par(omi = c(0, 0, 1.5, 0), mai = c(down.space, left.space, up.space, right.space), las = orient, mgp = c(dist.legend / 0.2, 0.5, 0), xpd = FALSE, bty= box.type, cex.lab = amplif.label, cex.axis = amplif.axis, xaxs = ifelse(std.x.range, "i", "r"), yaxs = ifelse(std.y.range, "i", "r"))
-par(tcl = -par()$mgp[2] * tick.length) # tcl gives the length of the ticks as proportion of line text, knowing that mgp is in text lines. So the main ticks are a 0.5 of the distance of the axis numbers by default. The sign provides the side of the tick (negative for outside of the plot region)
-if(is.null(displayed.nb)){
-sampled.data <- as.vector(data)
-if(corner.text == ""){
-corner.text <- paste0("ALL VALUES OF THE DATASET DISPLAYED")
-}else{
-corner.text <- paste0(corner.text, "\nALL VALUES OF THE DATASET DISPLAYED")
-}
-}else{
-if(length(as.vector(data)) > displayed.nb){
-sampled.data <- sample(as.vector(data), displayed.nb, replace = FALSE)
-if(corner.text == ""){
-corner.text <- paste0("WARNING: ONLY ", displayed.nb, " VALUES ARE DISPLAYED AMONG THE ", length(as.vector(data)), " VALUES OF THE DATASET ANALYZED")
-}else{
-corner.text <- paste0(corner.text, "\nWARNING: ONLY ", displayed.nb, " VALUES ARE DISPLAYED AMONG THE ", length(as.vector(data)), " VALUES OF THE DATASET ANALYZED")
-}
-}else{
-sampled.data <- as.vector(data)
-if(corner.text == ""){
-corner.text <- paste0("WARNING: THE DISPLAYED NUMBER OF VALUES PARAMETER ", deparse(substitute(displayed.nb)), " HAS BEEN SET TO ", displayed.nb, " WHICH IS ABOVE THE NUMBER OF VALUES OF THE DATASET ANALYZED -> ALL VALUES DISPLAYED")
-}else{
-corner.text <- paste0(corner.text, "\nWARNING: THE DISPLAYED NUMBER OF VALUES PARAMETER ", deparse(substitute(displayed.nb)), " HAS BEEN SET TO ", displayed.nb, " WHICH IS ABOVE THE NUMBER OF VALUES OF THE DATASET ANALYZED -> ALL VALUES DISPLAYED")
-}
-}
-}
-if( ! is.null(na.nb)){
-if(corner.text == ""){
-corner.text <- paste0("WARNING: NUMBER OF NA REMOVED IS ", na.nb)
-}else{
-corner.text <- paste0("WARNING: NUMBER OF NA REMOVED IS ", na.nb)
-}
-}
-stripchart(sampled.data, method="jitter", jitter=0.4, vertical=FALSE, ylim=c(0.5, 1.5), group.names = "", xlab = "Value", ylab="", pch=1, cex = cex.pt / 0.2)
-fun.rug(y.nb.inter.tick.f = 0)
-boxplot(as.vector(data), horizontal=TRUE, add=TRUE, boxwex = 0.4, staplecol = col.box, whiskcol = col.box, medcol = col.box, boxcol = col.box, range = 0, whisklty = 1)
-m <- mean(as.vector(data), na.rm = TRUE)
-s <- sd(as.vector(data), na.rm = TRUE)
-segments(m, 0.8, m, 1, lwd=2, col="red") # mean 
-segments(m -1.96 * s, 0.9, m + 1.96 * s, 0.9, lwd=1, col="red") # mean 
-graph.xlim <- par()$usr[1:2] # for hist() and qqnorm() below
-if(interval.scale.disp == TRUE){
-fun.interval.scale.display(data.f = data)
-if(corner.text == ""){
-corner.text <- paste0("MULTIPLYING FACTOR DISPLAYED (MEAN +/- SD) ON SCALES: ", paste(formatC(round(qnorm(quantiles.selection), 2))[-(1:(length(quantiles.selection) - 1) / 2)], collapse = ", "), "\nQUANTILES DISPLAYED ON SCALES: ", paste(quantiles.selection, collapse = ", "))
-}else{
-corner.text <- paste0(corner.text, "\nMULTIPLYING FACTOR DISPLAYED (MEAN +/- SD) ON SCALES: ", paste(formatC(round(qnorm(quantiles.selection), 2))[-(1:(length(quantiles.selection) - 1) / 2)], collapse = ", "), "\nQUANTILES DISPLAYED ON SCALES: ", paste(quantiles.selection, collapse = ", "))
-}
-}
-output.tempo <- fun.add.cut(data.f = data, return.f = TRUE) # to recover real.trim.cutoffs
-if(trim.return == TRUE){
-output <- output.tempo
-}
-par(xpd = NA)
-if(trim.method != ""){
-if(corner.text == ""){
-corner.text <- paste0("SELECTED CUT-OFFS (PROPORTION): ", paste(trim.cutoffs, collapse = ", "), "\nSELECTED CUT-OFFS: ", paste(output.tempo$real.trim.cutoffs, collapse = ", "))
-}else{
-corner.text <- paste0(corner.text, "\nSELECTED CUT-OFFS (PROPORTION): ", paste(trim.cutoffs, collapse = ", "), "\nSELECTED CUT-OFFS: ", paste(output.tempo$real.trim.cutoffs, collapse = ", "))
-}
-if(interval.scale.disp == TRUE){
-legend(x = (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / (par("omd")[2] - par("omd")[1])) * par("omd")[1]), y = (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / (par("omd")[4] - par("omd")[3])) * (1 - par("omd")[4]) / 2), legend = c(c("min, Q1, Median, Q3, max"), "mean +/- 1.96sd", paste0("Trimming interval: ", paste0(trim.cutoffs, collapse = " , ")), "Mean +/- sd multiplying factor", "Quantile"), yjust = 0, lty=1, col=c(col.box, "red", color.cut, col.mean, col.quantile), bty="n", cex = amplif.legend)
-}else{
-legend(x = (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / (par("omd")[2] - par("omd")[1])) * par("omd")[1]), y = (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / (par("omd")[4] - par("omd")[3])) * (1 - par("omd")[4]) / 2), legend = c(c("min, Q1, Median, Q3, max"), "mean +/- 1.96sd", paste0("Trimming interval: ", paste0(trim.cutoffs, collapse = " , "))), yjust = 0, lty=1, col=c(col.box, "red", color.cut), bty="n", cex = amplif.legend, y.intersp=1.25)
-}
-}else{
-if(interval.scale.disp == TRUE){
-legend(x = (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / (par("omd")[2] - par("omd")[1])) * par("omd")[1]), y = (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / (par("omd")[4] - par("omd")[3])) * (1 - par("omd")[4]) / 2), legend = c(c("min, Q1, Median, Q3, max"), "mean +/- sd", "Mean +/- sd multiplying factor", "Quantile"), yjust = 0, lty=1, col=c(col.box, "red", col.mean, col.quantile), bty="n", cex = amplif.legend)
-}else{
-legend(x = (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / (par("omd")[2] - par("omd")[1])) * par("omd")[1]), y = (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / (par("omd")[4] - par("omd")[3])) * (1 - par("omd")[4]) / 2), legend = c(c("min, Q1, Median, Q3, max"), "mean +/- sd"), yjust = 0, lty=1, col=c(col.box, "red"), bty="n", cex = amplif.legend, y.intersp=1.25)
-}
-}
-par(xpd = FALSE, xaxs = ifelse(std.x.range, "i", "r"), yaxs = ifelse(std.y.range, "i", "r"))
-hist(as.vector(data), main = "", xlim = graph.xlim, xlab = "Value", ylab="Density", col = grey(0.25)) # removed: breaks = seq(min(as.vector(data), na.rm = TRUE), max(as.vector(data), na.rm = TRUE), length.out = length(as.vector(data)) / 10)
-abline(h = par()$usr[3])
-fun.rug()
-if(interval.scale.disp == TRUE){
-fun.interval.scale.display(data.f = data)
-}
-fun.add.cut(data.f = data)
-par(xaxs = ifelse(std.x.range, "i", "r"))
-stripchart(rank(sampled.data), method="stack", vertical=FALSE, ylim=c(0.99, 1.3), group.names = "", xlab = "Rank of values", ylab="", pch=1, cex = cex.pt / 0.2)
-fun.rug(y.nb.inter.tick.f = 0)
-x.text <- par("usr")[2] + (par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1]) * (1 - par("plt")[2]) / 2
-y.text <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par()$omd[4] / 2) * ((par("plt")[4] - par("plt")[3])))) * (1 - par("omd")[4])) # BEWARE. Here in "(par()$omd[4] / 2", division by two because there are 2 graphs staked on the y axis, and not one
-par(xpd=NA)
-text(x = x.text, y = y.text, paste0(corner.text), adj=c(1, 1.1), cex = corner.text.size) # text at the topright corner
-par(xpd=FALSE)
-par(xaxs = ifelse(std.x.range, "i", "r"), yaxs = ifelse(std.y.range, "i", "r"))
-qqnorm(as.vector(sampled.data), main = "", datax = TRUE, ylab = "Value", pch = 1, col = "red", cex = cex.pt / 0.2)
-fun.rug()
-if(diff(quantile(as.vector(data), probs = c(0.25, 0.75), na.rm = TRUE)) != 0){ # otherwise, error generated
-qqline(as.vector(data), datax = TRUE)
-}
-if(interval.scale.disp == TRUE){
-fun.interval.scale.display(data.f = data)
-}
-fun.add.cut(data.f = data)
-}
-if(trim.return == TRUE){
-return(output)
-}
-}
-
-
-######## fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation
-
-
-fun_segmentation <- function(
-data1, 
-x1, 
-y1, 
-x.range.split = NULL, 
-x.step.factor = 10, 
-y.range.split = NULL, 
-y.step.factor = 10, 
-error = 0, 
-data2 = NULL, 
-x2, 
-y2, 
-data2.pb.dot = "unknown", 
-xy.cross.kind = "&", 
-plot = FALSE, 
-graph.in.file = FALSE, 
-raster = TRUE, 
-warn.print = FALSE, 
-lib.path = NULL
-){
-# AIM
-# if data1 is a data frame corresponding to the data set of a scatterplot (with a x column for x-axis values and a y column for the y-axis column), then fun_segmentation() delimits a frame around the dots cloud using a sliding window set by x.range.split and x.step.factor to frame the top and bottom part of the cloud, and set by y.range.split and y.step.factor to frame the left and right part of the cloud
-# if a second data frame is provided, corresponding to the data set of a scatterplot (with a x column for x-axis values and a y column for the y-axis column), then fun_segmentation() defines the dots of this data frame, outside of the frame of the first data frame
-# WARNINGS
-# if dots from data2 look significant on the graph (outside the frame) but are not (not black on the last figure), this is probably because the frame is flat on the zero coordinate (no volume inside the frame at this position). Thus, no way to conclude that data2 dots here are significant. These dots are refered to as "unknown". The pb.dot argument deals with such dots
-# dots that are sometimes inside and outside the frame, depending on the sliding window, are treated differently: they are removed. Such dots are neither classified as "signif", "non signif" or "unknown", but as "inconsistent"
-# unknown dots are treated as finally significant, not significant, or unknown (data2.pb.dot argument) for each x-axis and y-axis separately. Then, the union or intersection of significant dots is performed (argument xy.cross.kind). See the example section
-# ARGUMENTS
-# data1: a data frame containing a column of x-axis values and a column of y-axis values
-# x1: character string of the data1 column name for x-axis (first column of data1 by default)
-# y1: character string of the data1 column name for y-axis (second column of data1 by default)
-# x.range.split: positive non null numeric value giving the number of interval on the x value range. if x.range is the range of the dots on the x-axis, then abs(diff(x.range) / x.range.split) gives the window size. Window size decreases when range.split increases. In unit of x-axis. Write NULL if not required. At least one of the x.range.split and y.range.split must be non NULL
-# x.step.factor: positive non null numeric value giving the shift step of the window. If x.step.factor = 1, no overlap during the sliding (when the window slides from position n to position n+1, no overlap between the two positions). If x.step.factor = 2, 50% of overlap (when the window slides from position n to position n+1, the window on position n+1 overlap 50% of the window when it was on position n)
-# y.range.split: same as x.range.split for the y-axis. At least one of the x.range.split and y.range.split must be non NULL
-# y.step.factor: same as x.step.factor for the y-axis
-# error: proportion (from 0 to 1) of false positives (i.e., proportion of dots from data1 outside of the frame). 0.05 means 5% of the dots from data1 outside of the frame
-# data2: a data frame containing a column of x-axis values and a column of y-axis values, for which outside dots of the data1 cloud has to be determined. Write NULL if not required
-# x2: character string of the data1 column name for x-axis (first column of data1 by default)
-# y2: character string of the data1 column name for y-axis (second column of data1 by default)
-# data2.pb.dot: unknown dots are explain in the warning section above. If "signif", then the unknown dots are finally considered as significant (outside the frame). If "not.signif", then the unknown dots are finally considered as non significant (inside the frame). If "unknown", no conclusion are drawn from these dots. See the examples below
-# xy.cross.kind: if data2 is non null and if both x.range.split and y.range.split are non null, which dots are finally significants? Write "&" for intersection of outside dots on x and on y. Write "|" for union of outside dots on x and on y. See the examples below
-# plot: logical. Print graphs that check the frame?
-# graph.in.file: logical. Graphs sent into a graphic device already opened? If FALSE, GUI are opened for each graph. If TRUE, no GUI are opended. The graphs are displayed on the current active graphic device. Ignored if plot is FALSE
-# raster: logical. Dots in raster mode? If FALSE, dots from each geom_point from geom argument are in vectorial mode (bigger pdf and long to display if millions of dots). If TRUE, dots from each geom_point from geom argument are in matricial mode (smaller pdf and easy display if millions of dots, but long to generate the layer). If TRUE, the region plot will be square to avoid a bug in fun_gg_point_rast(). If TRUE, solve the transparency problem with some GUI. Not considered if plot is FALSE
-# warn.print: logical. Print warnings at the end of the execution? No print if no warning messages
-# lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL. Ignored if plot is FALSE
-# RETURN
-# several graphs if plot is TRUE
-# a list containing:
-# $data1.removed.row.nb: which rows have been removed due to NA; NaN, -Inf or Inf detection in x1 or y1 columns (NULL if no row removed)
-# $data1.removed.rows: removed rows (NULL if no row removed)
-# $data2.removed.row.nb: which rows have been removed due to NA; NaN, -Inf or Inf detection in x2 or y2 columns (NULL if no row removed)
-# $data2.removed.rows: removed rows (NULL if no row removed)
-# $hframe: x and y coordinates of the bottom and top frames for frame plotting (frame1 for the left step and frame2 for the right step)
-# $vframe: x and y coordinates of the left and right frames for frame plotting (frame1 for the down step and frame2 for the top step)
-# $data1.signif.dot: the significant dots of data1 (i.e., dots outside the frame). A good segmentation should not have any data1.signif.dot
-# $data1.non.signif.dot: the non significant dots of data1 (i.e., dots inside the frame)
-# $data1.inconsistent.dot: see the warning section above
-# $data2.signif.dot: the significant dots of data2 if non NULL (i.e., dots outside the frame)
-# $data2.non.signif.dot: the non significant dots of data2 (i.e., dots inside the frame)
-# $data2.unknown.dot: the problematic dots of data2 (i.e., data2 dots outside of the range of data1, or data2 dots in a sliding window without data1 dots). Is systematically NULL except if argument data2.pb.dot = "unknown" and some data2 dots are in such situation. Modifying the segmentation x.range.split, x.step.factor, y.range.split, y.step.factor arguments can solve this problem
-# $data2.inconsistent.dot: see the warning section above
-# $axes: the x-axis and y-axis info
-# $warn: the warning messages. Use cat() for proper display. NULL if no warning
-# REQUIRED PACKAGES
-# ggplot2 if plot is TRUE
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# if plot is TRUE:
-# fun_pack()
-# fun_open()
-# fun_gg_palette()
-# fun_gg_scatter()
-# fun_gg_empty_graph()
-# fun_close()
-# EXAMPLES
-# example explaining the unknown and inconsistent dots, and the cross 
-
-# set.seed(1) ; data1 = data.frame(x = rnorm(500), y = rnorm(500), stringsAsFactors = TRUE) ; data1[5:7, 2] <- NA ; data2 = data.frame(x = rnorm(500, 0, 2), y = rnorm(500, 0, 2), stringsAsFactors = TRUE) ; data2[11:13, 1] <- Inf ; set.seed(NULL) ; fun_segmentation(data1 = data1, x1 = names(data1)[1], y1 = names(data1)[2], x.range.split = 20, x.step.factor = 10, y.range.split = 23, y.step.factor = 10, error = 0, data2 = data2, x2 = names(data2)[1], y2 = names(data2)[2], data2.pb.dot = "not.signif", xy.cross.kind = "|", plot = TRUE, graph.in.file = FALSE, raster = FALSE, lib.path = NULL)
-# set.seed(1) ; data1 = data.frame(x = rnorm(500), y = rnorm(500), stringsAsFactors = TRUE) ; data2 = data.frame(x = rnorm(500, 0, 2), y = rnorm(500, 0, 2), stringsAsFactors = TRUE) ; set.seed(NULL) ; fun_segmentation(data1 = data1, x1 = names(data1)[1], y1 = names(data1)[2], x.range.split = NULL, x.step.factor = 10, y.range.split = 23, y.step.factor = 10, error = 0, data2 = data2, x2 = names(data2)[1], y2 = names(data2)[2], data2.pb.dot = "unknown", xy.cross.kind = "|", plot = TRUE, graph.in.file = FALSE, raster = FALSE, lib.path = NULL)
-# set.seed(1) ; data1 = data.frame(x = rnorm(500), y = rnorm(500), stringsAsFactors = TRUE) ; data2 = data.frame(x = rnorm(500, 0, 2), y = rnorm(500, 0, 2), stringsAsFactors = TRUE) ; set.seed(NULL) ; fun_segmentation(data1 = data1, x1 = names(data1)[1], y1 = names(data1)[2], x.range.split = 20, x.step.factor = 10, y.range.split = NULL, y.step.factor = 10, error = 0, data2 = data2, x2 = names(data2)[1], y2 = names(data2)[2], data2.pb.dot = "unknown", xy.cross.kind = "&", plot = TRUE, graph.in.file = FALSE, raster = FALSE, lib.path = NULL)
-# DEBUGGING
-# set.seed(1) ; data1 = data.frame(x = rnorm(50), y = rnorm(50), stringsAsFactors = TRUE) ; data1[5:7, 2] <- NA ; x1 = names(data1)[1] ; y1 = names(data1)[2] ; x.range.split = 5 ; x.step.factor = 10 ; y.range.split = 5 ; y.step.factor = 10 ; error = 0 ; data2 = data.frame(x = rnorm(50, 0, 2), y = rnorm(50, 0, 2), stringsAsFactors = TRUE) ; set.seed(NULL) ; x2 = names(data2)[1] ; y2 = names(data2)[2] ; data2.pb.dot = "unknown" ; xy.cross.kind = "|" ; plot = TRUE ; graph.in.file = FALSE ; raster = FALSE ; warn.print = TRUE ; lib.path = NULL
-# set.seed(1) ; data1 = data.frame(x = rnorm(500), y = rnorm(500), stringsAsFactors = TRUE) ; data2 = data.frame(x = rnorm(500, 0, 2), y = rnorm(500, 0, 2), stringsAsFactors = TRUE) ; set.seed(NULL) ; x1 = names(data1)[1] ; y1 = names(data1)[2] ; x.range.split = 20 ; x.step.factor = 10 ; y.range.split = 23 ; y.step.factor = 10 ; error = 0 ; x2 = names(data2)[1] ; y2 = names(data2)[2] ; data2.pb.dot = "not.signif" ; xy.cross.kind = "|" ; plot = TRUE ; graph.in.file = FALSE ; raster = FALSE ; warn.print = TRUE ; lib.path = NULL
-# set.seed(1) ; data1 = data.frame(x = rnorm(500), y = rnorm(500), stringsAsFactors = TRUE) ; data2 = data.frame(x = rnorm(500, 0, 2), y = rnorm(500, 0, 2), stringsAsFactors = TRUE) ; set.seed(NULL) ; x1 = names(data1)[1] ; y1 = names(data1)[2] ; x.range.split = 20 ; x.step.factor = 10 ; y.range.split = NULL ; y.step.factor = 10 ; error = 0 ; x2 = names(data2)[1] ; y2 = names(data2)[2] ; data2.pb.dot = "unknown" ; xy.cross.kind = "&" ; plot = TRUE ; graph.in.file = FALSE ; raster = FALSE ; warn.print = TRUE ; lib.path = NULL
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-ini.warning.length <- options()$warning.length
-warn <- NULL
-warn.count <- 0
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = data1, class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & length(data1) < 2){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data1 ARGUMENT MUST BE A DATA FRAME OF AT LEAST 2 COLUMNS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo <- fun_check(data = x1, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & ! (x1 %in% names(data1))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x1 ARGUMENT MUST BE A COLUMN NAME OF data1")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo$problem == FALSE & x1 %in% names(data1)){
-tempo <- fun_check(data = data1[, x1], data.name = "x1 COLUMN OF data1", class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = y1, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & ! (y1 %in% names(data1))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": y1 ARGUMENT MUST BE A COLUMN NAME OF data1")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo$problem == FALSE & y1 %in% names(data1)){
-tempo <- fun_check(data = data1[, y1], data.name = "y1 COLUMN OF data1", class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-}
-if(is.null(x.range.split) & is.null(y.range.split)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": AT LEAST ONE OF THE x.range.split AND y.range.split ARGUMENTS MUST BE NON NULL")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-if( ! is.null(x.range.split)){
-tempo <- fun_check(data = x.range.split, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & x.range.split < 1){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x.range.split ARGUMENT CANNOT BE LOWER THAN 1")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-if( ! is.null(y.range.split)){
-tempo <- fun_check(data = y.range.split, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & y.range.split < 1){
-tempo.cat <- paste0("ERROR IN ", function.name, ": y.range.split ARGUMENT CANNOT BE LOWER THAN 1")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-tempo <- fun_check(data = x.step.factor, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & x.step.factor < 1){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x.step.factor ARGUMENT CANNOT BE LOWER THAN 1")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo <- fun_check(data = y.step.factor, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & y.step.factor < 1){
-tempo.cat <- paste0("ERROR IN ", function.name, ": y.step.factor ARGUMENT CANNOT BE LOWER THAN 1")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo <- fun_check(data = error, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(data2)){
-if(is.null(x2) | is.null(y2)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x2 AND y2 ARGUMENTS CANNOT BE NULL IF data2 ARGUMENT IS NON NULL")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo <- fun_check(data = data2, class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & length(data2) < 2){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data2 ARGUMENT MUST BE A DATA FRAME OF AT LEAST 2 COLUMNS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-if( ! is.null(x2)){
-tempo <- fun_check(data = x2, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & ! (x2 %in% names(data2))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x2 ARGUMENT MUST BE A COLUMN NAME OF data2")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo$problem == FALSE & x2 %in% names(data2)){
-tempo <- fun_check(data = data2[, x2], data.name = "x2 COLUMN OF data2", class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-}
-}
-if( ! is.null(y2)){
-tempo <- fun_check(data = y2, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & ! (y2 %in% names(data2))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": y2 ARGUMENT MUST BE A COLUMN NAME OF data2")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo$problem == FALSE & y2 %in% names(data2)){
-tempo <- fun_check(data = data2[, y2], data.name = "y2 COLUMN OF data2", class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-}
-}
-}
-if( ! is.null(data2)){
-tempo <- fun_check(data = data2.pb.dot, options = c("signif", "not.signif", "unknown"), length = 1, fun.name = function.name) ; eval(ee)
-}
-if( ! (is.null(x.range.split)) & ! (is.null(y.range.split))){
-tempo <- fun_check(data = xy.cross.kind, options = c("&", "|"), length = 1, fun.name = function.name) ; eval(ee)
-}
-tempo <- fun_check(data = plot, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & plot == TRUE){
-tempo <- fun_check(data = raster, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = graph.in.file, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & graph.in.file == TRUE & is.null(dev.list())){
-tempo.cat <- paste0("ERROR IN ", function.name, ": \ngraph.in.file PARAMETER SET TO TRUE BUT NO ACTIVE GRAPHIC DEVICE DETECTED")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo$problem == FALSE & graph.in.file == TRUE & ! is.null(dev.list())){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") GRAPHS PRINTED IN THE CURRENT DEVICE (TYPE ", toupper(names(dev.cur())), ")")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if( ! is.null(lib.path)){
-tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}
-}
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# other required function checking
-if(plot == TRUE){
-if(length(utils::find("fun_pack", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_open", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_open() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_gg_palette", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_gg_palette() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_gg_empty_graph", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_gg_empty_graph() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_gg_scatter", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_gg_scatter() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_close", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_close() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end other required function checking
-# package checking
-if(plot == TRUE){
-fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
-}
-# end package checking
-# main code
-# na and Inf detection and removal (done now to be sure of the correct length of categ)
-data1.removed.row.nb <- NULL
-data1.removed.rows <- NULL
-data2.removed.row.nb <- NULL
-data2.removed.rows <- NULL
-if(any(is.na(data1[, c(x1, y1)])) | any(is.infinite(data1[, x1])) | any(is.infinite(data1[, y1]))){
-tempo.na <- unlist(lapply(lapply(c(data1[c(x1, y1)]), FUN = is.na), FUN = which))
-tempo.inf <- unlist(lapply(lapply(c(data1[c(x1, y1)]), FUN = is.infinite), FUN = which))
-data1.removed.row.nb <- sort(unique(c(tempo.na, tempo.inf)))
-if(length(data1.removed.row.nb) > 0){
-data1.removed.rows <- data1[data1.removed.row.nb, ]
-}
-if(length(data1.removed.row.nb) == nrow(data1)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": AT LEAST ONE NA, NaN, -Inf OR Inf DETECTED IN EACH ROW OF data1. FUNCTION CANNOT BE USED ON EMPTY DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(data1.removed.row.nb) > 0){
-data1 <- data1[-data1.removed.row.nb, ]
-}
-if(nrow(data1) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 1")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NA, NaN, -Inf OR Inf DETECTED IN COLUMN ", paste(c(x1, y1), collapse = " "), " OF data1 AND CORRESPONDING ROWS REMOVED (SEE $data1.removed.row.nb AND $data1.removed.rows)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else{
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NO NA, NaN, -Inf OR Inf DETECTED IN COLUMN ", paste(c(x1, y1), collapse = " "), " OF data1. NO ROW REMOVED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if( ! is.null(data2)){
-if(any(is.na(data2[, c(x2, y2)])) | any(is.infinite(data2[, x2])) | any(is.infinite(data2[, y2]))){
-tempo.na <- unlist(lapply(lapply(c(data2[c(x2, y2)]), FUN = is.na), FUN = which))
-tempo.inf <- unlist(lapply(lapply(c(data2[c(x2, y2)]), FUN = is.infinite), FUN = which))
-data2.removed.row.nb <- sort(unique(c(tempo.na, tempo.inf)))
-if(length(data2.removed.row.nb) > 0){
-data2.removed.rows <- data2[data2.removed.row.nb, ]
-}
-if(length(data2.removed.row.nb) == nrow(data2)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": AT LEAST ONE NA, NaN, -Inf OR Inf DETECTED IN EACH ROW OF data2. FUNCTION CANNOT BE USED ON EMPTY DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(data2.removed.row.nb) > 0){
-data2 <- data2[-data2.removed.row.nb, ]
-}
-if(nrow(data2) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 2")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NA, NaN, -Inf OR Inf DETECTED IN COLUMN ", paste(c(x2, y2), collapse = " "), " OF data2 AND CORRESPONDING ROWS REMOVED (SEE $data2.removed.row.nb AND $data2.removed.rows)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else{
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NO NA, NaN, -Inf OR Inf DETECTED IN COLUMN ", paste(c(x2, y2), collapse = " "), " OF data2. NO ROW REMOVED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# end na and Inf detection and removal (done now to be sure of the correct length of categ)
-# row annotation (dot number)
-# data1 <- data1[ ! duplicated(data1[, c(x1, y1)]), ] # do not remove the dots that have same x and y values, because they will have different dot number -> not the same position on the matrices (so true for symmetric matrices)
-data1 <- cbind(data1, DOT_NB = 1:nrow(data1), stringsAsFactors = TRUE)
-if( ! is.null(data2)){
-# data2 <- data2[ ! duplicated(data2[, c(x2, y2)]), ] # do not remove the dots that have same x and y values, because they will have different dot number -> not the same position on the matrices (so true for symmetric matrices)
-data2 <- cbind(data2, DOT_NB = 1:nrow(data2), stringsAsFactors = TRUE)
-}
-# end row annotation (dot number)
-
-
-
-
-# Method using x unit interval 
-# may be create vector of each column to increase speed
-x.data1.l <- NULL # x coord of the y upper and lower limits defined on the data1 cloud for left step line
-x.data1.r <- NULL # x coord of the y upper and lower limits defined on the data1 cloud for right step line
-y.data1.down.limit.l <- NULL # lower limit of the data1 cloud for left step line
-y.data1.top.limit.l <- NULL # upper limit of the data1 cloud for left step line
-y.data1.down.limit.r <- NULL # lower limit of the data1 cloud for right step line
-y.data1.top.limit.r <- NULL # upper limit of the data1 cloud for left step line
-if(any(data1[, x1] %in% c(Inf, -Inf))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE data1 ARGUMENT CONTAINS -Inf OR Inf VALUES IN THE x1 COLUMN, THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-x.range <- range(data1[, x1], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
-if(suppressWarnings(any(x.range %in% c(Inf, -Inf)))){
-tempo.cat <- paste0("ERROR IN ", function.name, " COMPUTED x.range CONTAINS Inf VALUES, BECAUSE VALUES FROM data1 ARGUMENTS ARE NA OR Inf ONLY")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data1[, y1] %in% c(Inf, -Inf))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE data1 ARGUMENT CONTAINS -Inf OR Inf VALUES IN THE y1 COLUMN, THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-y.range <- range(data1[, y1], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
-if(suppressWarnings(any(x.range %in% c(Inf, -Inf)))){
-tempo.cat <- paste0("ERROR IN ", function.name, " COMPUTED y.range CONTAINS Inf VALUES, BECAUSE VALUES FROM data1 ARGUMENTS ARE NA OR Inf ONLY")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-x.range.plot <- range(data1[, x1], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
-y.range.plot <- range(data1[, y1], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
-if( ! is.null(data2)){
-if(any(data2[, x2] %in% c(Inf, -Inf))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE data2 ARGUMENT CONTAINS -Inf OR Inf VALUES IN THE x2 COLUMN, THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-x.range.plot <- range(data1[, x1], data2[, x2], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
-if(any(data2[, y2] %in% c(Inf, -Inf))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE data2 ARGUMENT CONTAINS -Inf OR Inf VALUES IN THE y2 COLUMN, THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-y.range.plot <- range(data1[, y1], data2[, y2], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
-}
-if(suppressWarnings(any(x.range.plot %in% c(Inf, -Inf)))){
-tempo.cat <- paste0("ERROR IN ", function.name, " COMPUTED x.range.plot CONTAINS Inf VALUES, BECAUSE VALUES FROM data1 (AND data2?) ARGUMENTS ARE NA OR Inf ONLY")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(suppressWarnings(any(y.range.plot %in% c(Inf, -Inf)))){
-tempo.cat <- paste0("ERROR IN ", function.name, " COMPUTED y.range.plot CONTAINS Inf VALUES, BECAUSE VALUES FROM data1 (AND data2?) ARGUMENTS ARE NA OR Inf ONLY")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! is.null(x.range.split)){
-# data.frame ordering to slide the window from small to big values + sliding window definition
-data1 <- data1[order(data1[, x1], na.last = TRUE), ]
-if( ! is.null(data2)){
-data2 <- data2[order(data2[, x2], na.last = TRUE), ]
-}
-x.win.size <- abs(diff(x.range) / x.range.split) # in unit of x-axis
-step <- x.win.size / x.step.factor
-# end data.frame ordering to slide the window from small to big values + sliding window definition
-# x-axis sliding and y-axis limits of the data1 cloud -> y significant data2
-loop.nb <- ceiling((diff(x.range) - x.win.size) / step) # x.win.size + n * step covers the x range if x.win.size + n * step >= diff(x.range), thus if n >= (diff(x.range) - x.win.size) / step 
-y.outside.data1.dot.nb <- integer() # vector that will contain the selected rows numbers of data1 that are upper or lower than the frame
-y.inside.data1.dot.nb <- integer() # vector that will contain the selected rows numbers of data1 that are not upper or lower than the frame
-y.data1.median <- median(data1[, y1], na.rm = TRUE) # will be used for sliding windows without data1 in it
-if( ! is.null(data2)){
-y.outside.data2.dot.nb <- integer() # vector that will contain the selected 1D coordinates (i.e., dots) of data2 that are upper or lower than the data1 frame
-y.inside.data2.dot.nb <- integer() # vector that will contain the 1D coordinates (i.e., dots) of data2 that are not upper or lower than the data1 frame
-y.unknown.data2.dot.nb <- integer() # vector that will contain the 1D coordinates (i.e., dots) of data2 that are problematic: data2 dots outside of the range of data1, or data2 dots in a sliding window without data1 dots
-# recover data2 dots outside the range of data1
-if(any(data2[, x2] < x.range[1])){
-y.unknown.data2.dot.nb <- c(y.unknown.data2.dot.nb, data2$DOT_NB[data2[, x2] < x.range[1]])
-#tempo.warn & indicate the interval
-}
-if(any(data2[, x2] > x.range[2])){
-y.unknown.data2.dot.nb <- c(y.unknown.data2.dot.nb, data2$DOT_NB[data2[, x2] > x.range[2]])
-#tempo.warn & indicate the interval
-}
-# end recover data2 dots outside the range of data1
-}
-# loop.ini.time <- as.numeric(Sys.time())
-for(i1 in 0:(loop.nb + 1)){
-min.pos <- x.range[1] + step * i1 # lower position of the sliding window in data1
-max.pos <- min.pos + x.win.size # upper position of the sliding window in data1
-x.data1.l <- c(x.data1.l, min.pos, min.pos + step) # min.pos + step to make the steps
-x.data1.r <- c(x.data1.r, max.pos, max.pos + step) # max.pos + step to make the steps
-x.data1.dot.here <- data1[, x1] >= min.pos & data1[, x1] < max.pos # is there data1 dot present in the sliding window, considering the x axis?
-if( ! is.null(data2)){
-x.data2.dot.here <- data2[, x2] >= min.pos & data2[, x2] < max.pos # is there data2 dot present in the sliding window, considering the x axis?
-}
-# recover the data1 dots outside the frame
-if(any(x.data1.dot.here == TRUE)){
-tempo.y.data1.top.limit <- quantile(data1[x.data1.dot.here, y1], probs = 1 - error, na.rm = TRUE)
-tempo.y.data1.down.limit <- quantile(data1[x.data1.dot.here, y1], probs = 0 + error, na.rm = TRUE)
-y.data1.top.limit.l <- c(y.data1.top.limit.l, tempo.y.data1.top.limit, tempo.y.data1.top.limit)
-y.data1.down.limit.l <- c(y.data1.down.limit.l, tempo.y.data1.down.limit, tempo.y.data1.down.limit)
-y.data1.top.limit.r <- c(y.data1.top.limit.r, tempo.y.data1.top.limit, tempo.y.data1.top.limit)
-y.data1.down.limit.r <- c(y.data1.down.limit.r, tempo.y.data1.down.limit, tempo.y.data1.down.limit)
-y.data1.dot.signif <- ( ! ((data1[, y1] <= tempo.y.data1.top.limit) & (data1[, y1] >= tempo.y.data1.down.limit))) & x.data1.dot.here # is there data1 dot present in the sliding window, above or below the data1 limits, considering the y axis?
-y.data1.dot.not.signif <- x.data1.dot.here & ! y.data1.dot.signif
-y.outside.data1.dot.nb <- c(y.outside.data1.dot.nb, data1$DOT_NB[y.data1.dot.signif]) # recover the row number of data1
-y.outside.data1.dot.nb <- unique(y.outside.data1.dot.nb)
-y.inside.data1.dot.nb <- c(y.inside.data1.dot.nb, data1$DOT_NB[y.data1.dot.not.signif])
-y.inside.data1.dot.nb <- unique(y.inside.data1.dot.nb)
-}else{
-y.data1.top.limit.l <- c(y.data1.top.limit.l, y.data1.median, y.data1.median)
-y.data1.down.limit.l <- c(y.data1.down.limit.l, y.data1.median, y.data1.median)
-y.data1.top.limit.r <- c(y.data1.top.limit.r, y.data1.median, y.data1.median)
-y.data1.down.limit.r <- c(y.data1.down.limit.r, y.data1.median, y.data1.median)
-}
-# end recover the data1 dots outside the frame
-# recover the data2 dots outside the frame
-if( ! is.null(data2)){
-if(any(x.data1.dot.here == TRUE) & any(x.data2.dot.here == TRUE)){ 
-y.data2.dot.signif <- ( ! ((data2[, y2] <= tempo.y.data1.top.limit) & (data2[, y2] >= tempo.y.data1.down.limit))) & x.data2.dot.here # is there data2 dot present in the sliding window, above or below the data1 limits, considering the y axis?
-y.data2.dot.not.signif <- x.data2.dot.here & ! y.data2.dot.signif
-y.outside.data2.dot.nb <- c(y.outside.data2.dot.nb, data2$DOT_NB[y.data2.dot.signif])
-y.outside.data2.dot.nb <- unique(y.outside.data2.dot.nb)
-y.inside.data2.dot.nb <- c(y.inside.data2.dot.nb, data2$DOT_NB[y.data2.dot.not.signif])
-y.inside.data2.dot.nb <- unique(y.inside.data2.dot.nb)
-}else if(any(x.data1.dot.here == FALSE) & any(x.data2.dot.here == TRUE)){ # problem: data2 dots in the the window but no data1 dots to generates the quantiles
-y.unknown.data2.dot.nb <- c(y.unknown.data2.dot.nb, data2$DOT_NB[x.data2.dot.here])
-y.unknown.data2.dot.nb <- unique(y.unknown.data2.dot.nb)
-#tempo.warn & indicate the interval
-
-
-
-
-# tempo.warn <- paste0("FROM FUNCTION ", function.name, ": THE [", round(min.pos, 3), " ; ", round(max.pos, 3), "] INTERVAL DOES NOT CONTAIN data1 X VALUES BUT CONTAINS data2 X VALUES WHICH CANNOT BE EVALUATED.\nTHE CONCERNED data2 ROW NUMBERS ARE:\n", paste(which(x.data1.dot.here == FALSE & x.data2.dot.here == TRUE), collapse = "\n"))
-# warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# end recover the data2 dots outside the frame
-# if(any(i1 == seq(1, loop.nb, 500))){
-# loop.fin.time <- as.numeric(Sys.time()) # time of process end
-# cat(paste0("COMPUTATION TIME OF LOOP ", i1, " / ", loop.nb, ": ", as.character(lubridate::seconds_to_period(round(loop.fin.time - loop.ini.time))), "\n"))
-# }
-}
-if(max.pos < x.range[2]){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE SLIDING WINDOW HAS NOT REACHED THE MAX VALUE OF data1 ON THE X-AXIS: ", max.pos, " VERSUS ", x.range[2])
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-y.incon.data1.dot.nb.final <- unique(c(y.outside.data1.dot.nb[y.outside.data1.dot.nb %in% y.inside.data1.dot.nb], y.inside.data1.dot.nb[y.inside.data1.dot.nb %in% y.outside.data1.dot.nb])) # inconsistent dots: if a row number of y.inside.data1.dot.nb is present in y.outside.data1.dot.nb (and vice versa), it means that during the sliding, a dot has been sometime inside, sometime outside -> removed from the outside list
-y.outside.data1.dot.nb.final <- y.outside.data1.dot.nb[ ! (y.outside.data1.dot.nb %in% y.incon.data1.dot.nb.final)] # inconsistent dots removed from the outside list
-y.inside.data1.dot.nb.final <- y.inside.data1.dot.nb[ ! (y.inside.data1.dot.nb %in% y.incon.data1.dot.nb.final)] # inconsistent dots removed from the inside list
-if( ! is.null(data2)){
-# if some unknown dots are also inside, and/or outside, they are put in the inside and/or outside. Ok, because then the intersection between inside and outside is treated -> inconsistent dots
-tempo.unknown.out <- y.unknown.data2.dot.nb[y.unknown.data2.dot.nb %in% y.outside.data2.dot.nb]
-y.outside.data2.dot.nb <- unique(c(y.outside.data2.dot.nb, tempo.unknown.out)) # if a row number of y.unknown.data2.dot.nb is present in y.outside.data2.dot.nb, it is put into outside
-tempo.unknown.in <- y.unknown.data2.dot.nb[y.unknown.data2.dot.nb %in% y.inside.data2.dot.nb]
-y.inside.data2.dot.nb <- unique(c(y.inside.data2.dot.nb, tempo.unknown.in)) # if a row number of y.unknown.data2.dot.nb is present in y.inside.data2.dot.nb, it is put into inside
-y.unknown.data2.dot.nb.final <- y.unknown.data2.dot.nb[ ! (y.unknown.data2.dot.nb %in% c(y.outside.data2.dot.nb, y.inside.data2.dot.nb))] # then dots also in inside and outside are remove from unknown
-y.incon.data2.dot.nb.final <- unique(c(y.outside.data2.dot.nb[y.outside.data2.dot.nb %in% y.inside.data2.dot.nb], y.inside.data2.dot.nb[y.inside.data2.dot.nb %in% y.outside.data2.dot.nb])) # inconsistent dots: if a row number of y.inside.data2.dot.nb is present in y.outside.data2.dot.nb (and vice versa), it means that during the sliding, a dot has been sometime inside, sometime outside -> removed from the outside list
-y.outside.data2.dot.nb.final <- y.outside.data2.dot.nb[ ! (y.outside.data2.dot.nb %in% y.incon.data2.dot.nb.final)] # inconsistent dots removed from the outside list
-y.inside.data2.dot.nb.final <- y.inside.data2.dot.nb[ ! (y.inside.data2.dot.nb %in% y.incon.data2.dot.nb.final)] # inconsistent dots removed from the inside list
-}
-# end x-axis sliding and y-axis limits of the data1 cloud -> y significant data2
-}
-# end Method using x unit interval 
-
-
-
-
-# Method using y unit interval 
-y.data1.d <- NULL # y coord of the x upper and lower limits defined on the data1 cloud for down step line
-y.data1.t <- NULL # y coord of the x upper and lower limits defined on the data1 cloud for top step line
-x.data1.left.limit.d <- NULL # left limit of the data1 cloud for down step line
-x.data1.right.limit.d <- NULL # right limit of the data1 cloud for down step line
-x.data1.left.limit.t <- NULL # left limit of the data1 cloud for top step line
-x.data1.right.limit.t <- NULL # right limit of the data1 cloud for top step line
-if( ! is.null(y.range.split)){
-# data.frame ordering to slide the window from small to big values + sliding window definition
-data1 <- data1[order(data1[, y1], na.last = TRUE), ]
-if( ! is.null(data2)){
-data2 <- data2[order(data2[, y2], na.last = TRUE), ]
-}
-y.win.size <- abs(diff(y.range) / y.range.split) # in unit of y-axis
-step <- y.win.size / y.step.factor
-# end data.frame ordering to slide the window from small to big values + sliding window definition
-# y-axis sliding and x-axis limits of the data1 cloud -> x significant data2
-loop.nb <- ceiling((diff(y.range) - y.win.size) / step) # y.win.size + n * step covers the y range if y.win.size + n * step >= diff(y.range), thus if n >= (diff(y.range) - y.win.size) / step 
-x.outside.data1.dot.nb <- integer() # vector that will contain the selected rows numbers of data1 that are upper or lower than the frame
-x.inside.data1.dot.nb <- integer() # vector that will contain the selected rows numbers of data1 that are not upper or lower than the frame
-x.data1.median <- median(data1[, x1], na.rm = TRUE) # will be used for sliding window without data1 in it
-if( ! is.null(data2)){
-x.outside.data2.dot.nb <- integer() # vector that will contain the selected 1D coordinates (i.e., dots) of data2 that are upper or lower than the data1 frame
-x.inside.data2.dot.nb <- integer() # vector that will contain the 1D coordinates (i.e., dots) of data2 that are not upper or lower than the data1 frame
-x.unknown.data2.dot.nb <- integer() # vector that will contain the 1D coordinates (i.e., dots) of data2 that are problematic: data2 dots outside of the range of data1, or data2 dots in a sliding window without data1 dots
-# recover data2 dots outside the range of data1
-if(any(data2[, y2] < y.range[1])){
-x.unknown.data2.dot.nb <- c(x.unknown.data2.dot.nb, data2$DOT_NB[data2[, y2] < y.range[1]])
-}
-if(any(data2[, y2] > y.range[2])){
-x.unknown.data2.dot.nb <- c(x.unknown.data2.dot.nb, data2$DOT_NB[data2[, y2] > y.range[2]])
-}
-# end recover data2 dots outside the range of data1
-}
-# loop.ini.time <- as.numeric(Sys.time())
-for(i1 in 0:(loop.nb + 1)){
-min.pos <- y.range[1] + step * i1 # lower position of the sliding window in data1
-max.pos <- min.pos + y.win.size # upper position of the sliding window in data1
-y.data1.d <- c(y.data1.d, min.pos, min.pos + step) # min.pos + step to make the steps
-y.data1.t <- c(y.data1.t, max.pos, max.pos + step) # max.pos + step to make the steps
-y.data1.dot.here <- data1[, y1] >= min.pos & data1[, y1] < max.pos # is there data1 dot present in the sliding window, considering the y axis?
-if( ! is.null(data2)){
-y.data2.dot.here <- data2[, y2] >= min.pos & data2[, y2] < max.pos # is there data2 dot present in the sliding window, considering the y axis?
-}
-# recover the data1 dots outside the frame
-if(any(y.data1.dot.here == TRUE)){
-tempo.x.data1.right.limit <- quantile(data1[y.data1.dot.here, x1], probs = 1 - error, na.rm = TRUE)
-tempo.x.data1.left.limit <- quantile(data1[y.data1.dot.here, x1], probs = 0 + error, na.rm = TRUE)
-x.data1.right.limit.d <- c(x.data1.right.limit.d, tempo.x.data1.right.limit, tempo.x.data1.right.limit)
-x.data1.left.limit.d <- c(x.data1.left.limit.d, tempo.x.data1.left.limit, tempo.x.data1.left.limit)
-x.data1.right.limit.t <- c(x.data1.right.limit.t, tempo.x.data1.right.limit, tempo.x.data1.right.limit)
-x.data1.left.limit.t <- c(x.data1.left.limit.t, tempo.x.data1.left.limit, tempo.x.data1.left.limit)
-x.data1.dot.signif <- ( ! ((data1[, x1] <= tempo.x.data1.right.limit) & (data1[, x1] >= tempo.x.data1.left.limit))) & y.data1.dot.here # is there data2 dot present in the sliding window, above or below the data1 limits, considering the x axis?
-x.data1.dot.not.signif <- y.data1.dot.here & ! x.data1.dot.signif
-x.outside.data1.dot.nb <- c(x.outside.data1.dot.nb, data1$DOT_NB[x.data1.dot.signif]) # recover the row number of data1
-x.outside.data1.dot.nb <- unique(x.outside.data1.dot.nb)
-x.inside.data1.dot.nb <- c(x.inside.data1.dot.nb, data1$DOT_NB[x.data1.dot.not.signif])
-x.inside.data1.dot.nb <- unique(x.inside.data1.dot.nb)
-}else{
-x.data1.right.limit.d <- c(x.data1.right.limit.d, x.data1.median, x.data1.median)
-x.data1.left.limit.d <- c(x.data1.left.limit.d, x.data1.median, x.data1.median)
-x.data1.right.limit.t <- c(x.data1.right.limit.t, x.data1.median, x.data1.median)
-x.data1.left.limit.t <- c(x.data1.left.limit.t, x.data1.median, x.data1.median)
-}
-# end recover the data1 dots outside the frame
-# recover the data2 dots outside the frame
-if( ! is.null(data2)){
-if(any(y.data1.dot.here == TRUE) & any(y.data2.dot.here == TRUE)){ 
-x.data2.dot.signif <- ( ! ((data2[, x2] <= tempo.x.data1.right.limit) & (data2[, x2] >= tempo.x.data1.left.limit))) & y.data2.dot.here # is there data2 dot present in the sliding window, above or below the data1 limits, considering the x axis?
-x.data2.dot.not.signif <- y.data2.dot.here & ! x.data2.dot.signif
-x.outside.data2.dot.nb <- c(x.outside.data2.dot.nb, data2$DOT_NB[x.data2.dot.signif])
-x.outside.data2.dot.nb <- unique(x.outside.data2.dot.nb)
-x.inside.data2.dot.nb <- c(x.inside.data2.dot.nb, data2$DOT_NB[x.data2.dot.not.signif])
-x.inside.data2.dot.nb <- unique(x.inside.data2.dot.nb)
-}else if(any(y.data1.dot.here == FALSE) & any(y.data2.dot.here == TRUE)){ # recover the data2 dots outside the range of the data1 cloud
-x.unknown.data2.dot.nb <- c(x.unknown.data2.dot.nb, data2$DOT_NB[y.data2.dot.here])
-x.unknown.data2.dot.nb <- unique(x.unknown.data2.dot.nb)
-
-
-
-# tempo.warn <- paste0("FROM FUNCTION ", function.name, ": THE [", round(min.pos, 3), " ; ", round(max.pos, 3), "] INTERVAL DOES NOT CONTAIN data1 Y VALUES BUT CONTAINS data2 Y VALUES WHICH CANNOT BE EVALUATED.\nTHE CONCERNED data2 ROW NUMBERS ARE:\n", paste(which(y.data1.dot.here == FALSE & y.data2.dot.here == TRUE), collapse = "\n"))
-# warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# end recover the data2 dots outside the frame
-# if(any(i1 == seq(1, loop.nb, 500))){
-# loop.fin.time <- as.numeric(Sys.time()) # time of process end
-# cat(paste0("COMPUTATION TIME OF LOOP ", i1, " / ", loop.nb, ": ", as.character(lubridate::seconds_to_period(round(loop.fin.time - loop.ini.time))), "\n"))
-# }
-}
-if(max.pos < y.range[2]){
-tempo.cat <- paste0("ERROR IN ", function.name, ": THE SLIDING WINDOW HAS NOT REACHED THE MAX VALUE OF data1 ON THE Y-AXIS: ", max.pos, " VERSUS ", y.range[2])
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-x.incon.data1.dot.nb.final <- unique(c(x.outside.data1.dot.nb[x.outside.data1.dot.nb %in% x.inside.data1.dot.nb], x.inside.data1.dot.nb[x.inside.data1.dot.nb %in% x.outside.data1.dot.nb])) # inconsistent dots: if a row number of x.inside.data1.dot.nb is present in x.outside.data1.dot.nb (and vice versa), it means that during the sliding, a dot has been sometime inside, sometime outside -> removed from the outside list
-x.outside.data1.dot.nb.final <- x.outside.data1.dot.nb[ ! (x.outside.data1.dot.nb %in% x.incon.data1.dot.nb.final)] # inconsistent dots removed from the outside list
-x.inside.data1.dot.nb.final <- x.inside.data1.dot.nb[ ! (x.inside.data1.dot.nb %in% x.incon.data1.dot.nb.final)] # inconsistent dots removed from the inside list
-if( ! is.null(data2)){
-# if some unknown dots are also inside, and/or outside, they are put in the inside and/or outside. Ok, because then the intersection between inside and outside is treated -> inconsistent dots
-tempo.unknown.out <- x.unknown.data2.dot.nb[x.unknown.data2.dot.nb %in% x.outside.data2.dot.nb]
-x.outside.data2.dot.nb <- unique(c(x.outside.data2.dot.nb, tempo.unknown.out)) # if a row number of x.unknown.data2.dot.nb is present in x.outside.data2.dot.nb, it is put into outside
-tempo.unknown.in <- x.unknown.data2.dot.nb[x.unknown.data2.dot.nb %in% x.inside.data2.dot.nb]
-x.inside.data2.dot.nb <- unique(c(x.inside.data2.dot.nb, tempo.unknown.in)) # if a row number of x.unknown.data2.dot.nb is present in x.inside.data2.dot.nb, it is put into inside
-x.unknown.data2.dot.nb.final <- x.unknown.data2.dot.nb[ ! (x.unknown.data2.dot.nb %in% c(x.outside.data2.dot.nb, x.inside.data2.dot.nb))] # then dots also in inside and outside are remove from unknown
-x.incon.data2.dot.nb.final <- unique(c(x.outside.data2.dot.nb[x.outside.data2.dot.nb %in% x.inside.data2.dot.nb], x.inside.data2.dot.nb[x.inside.data2.dot.nb %in% x.outside.data2.dot.nb])) # inconsistent dots: if a row number of x.inside.data2.dot.nb is present in x.outside.data2.dot.nb (and vice versa), it means that during the sliding, a dot has been sometime inside, sometime outside -> removed from the outside list
-x.outside.data2.dot.nb.final <- x.outside.data2.dot.nb[ ! (x.outside.data2.dot.nb %in% x.incon.data2.dot.nb.final)] # inconsistent dots removed from the outside list
-x.inside.data2.dot.nb.final <- x.inside.data2.dot.nb[ ! (x.inside.data2.dot.nb %in% x.incon.data2.dot.nb.final)] # inconsistent dots removed from the inside list
-}
-# end y-axis sliding and x-axis limits of the data1 cloud -> x significant data2
-}
-# end Method using y unit interval 
-
-
-
-# recovering the frame coordinates
-hframe = rbind(
-data.frame(
-x = if(is.null(x.data1.l)){NULL}else{x.data1.l}, 
-y = if(is.null(x.data1.l)){NULL}else{y.data1.down.limit.l}, 
-kind = if(is.null(x.data1.l)){NULL}else{"down.frame1"},
-stringsAsFactors = TRUE
-), 
-data.frame(
-x = if(is.null(x.data1.r)){NULL}else{x.data1.r}, 
-y = if(is.null(x.data1.r)){NULL}else{y.data1.down.limit.r}, 
-kind = if(is.null(x.data1.r)){NULL}else{"down.frame2"},
-stringsAsFactors = TRUE
-), 
-data.frame(
-x = if(is.null(x.data1.l)){NULL}else{x.data1.l}, 
-y = if(is.null(x.data1.l)){NULL}else{y.data1.top.limit.l}, 
-kind = if(is.null(x.data1.l)){NULL}else{"top.frame1"},
-stringsAsFactors = TRUE
-), 
-data.frame(
-x = if(is.null(x.data1.r)){NULL}else{x.data1.r}, 
-y = if(is.null(x.data1.r)){NULL}else{y.data1.top.limit.r}, 
-kind = if(is.null(x.data1.r)){NULL}else{"top.frame2"},
-stringsAsFactors = TRUE
-), 
-stringsAsFactors = TRUE
-)
-vframe = rbind(
-data.frame(
-x = if(is.null(y.data1.d)){NULL}else{x.data1.left.limit.d}, 
-y = if(is.null(y.data1.d)){NULL}else{y.data1.d}, 
-kind = if(is.null(y.data1.d)){NULL}else{"left.frame1"},
-stringsAsFactors = TRUE
-), 
-data.frame(
-x = if(is.null(y.data1.t)){NULL}else{x.data1.left.limit.t}, 
-y = if(is.null(y.data1.t)){NULL}else{y.data1.t}, 
-kind = if(is.null(y.data1.t)){NULL}else{"left.frame2"},
-stringsAsFactors = TRUE
-), 
-data.frame(
-x = if(is.null(y.data1.d)){NULL}else{x.data1.right.limit.d}, 
-y = if(is.null(y.data1.d)){NULL}else{y.data1.d}, 
-kind = if(is.null(y.data1.d)){NULL}else{"right.frame1"},
-stringsAsFactors = TRUE
-),
-data.frame(
-x = if(is.null(y.data1.t)){NULL}else{x.data1.right.limit.t}, 
-y = if(is.null(y.data1.t)){NULL}else{y.data1.t}, 
-kind = if(is.null(y.data1.t)){NULL}else{"right.frame2"},
-stringsAsFactors = TRUE
-), 
-stringsAsFactors = TRUE
-)
-# end recovering the frame coordinates
-# recovering the dot coordinates
-data1.signif.dot <- NULL
-data1.non.signif.dot <- NULL
-data1.incon.dot <- NULL
-data2.signif.dot <- NULL
-data2.non.signif.dot <- NULL
-data2.unknown.dot <- NULL
-data2.incon.dot <- NULL
-if(( ! is.null(x.range.split)) & ( ! is.null(y.range.split))){
-# inconsistent dots recovery 
-if(length(unique(c(x.incon.data1.dot.nb.final, y.incon.data1.dot.nb.final))) > 0){
-data1.incon.dot <- data1[data1$DOT_NB %in% unique(c(x.incon.data1.dot.nb.final, y.incon.data1.dot.nb.final)), ] # if a dot in inconsistent in x or y -> classified as inconsistent (so unique() used)
-# removal of the inconsistent dot in the other classifications
-x.inside.data1.dot.nb.final <- x.inside.data1.dot.nb.final[ ! x.inside.data1.dot.nb.final %in% data1.incon.dot$DOT_NB]
-y.inside.data1.dot.nb.final <- y.inside.data1.dot.nb.final[ ! y.inside.data1.dot.nb.final %in% data1.incon.dot$DOT_NB]
-x.outside.data1.dot.nb.final <- x.outside.data1.dot.nb.final[ ! x.outside.data1.dot.nb.final %in% data1.incon.dot$DOT_NB]
-y.outside.data1.dot.nb.final <- y.outside.data1.dot.nb.final[ ! y.outside.data1.dot.nb.final %in% data1.incon.dot$DOT_NB]
-x.unknown.data1.dot.nb.final <- x.unknown.data1.dot.nb.final[ ! x.unknown.data1.dot.nb.final %in% data1.incon.dot$DOT_NB]
-y.unknown.data1.dot.nb.final <- y.unknown.data1.dot.nb.final[ ! y.unknown.data1.dot.nb.final %in% data1.incon.dot$DOT_NB]
-# end removal of the inconsistent dot in the other classifications
-}
-if( ! is.null(data2)){
-if(length(unique(c(x.incon.data2.dot.nb.final, y.incon.data2.dot.nb.final))) > 0){
-data2.incon.dot <- data2[data2$DOT_NB %in% unique(c(x.incon.data2.dot.nb.final, y.incon.data2.dot.nb.final)), ]
-# removal of the inconsistent dot in the other classifications
-x.inside.data2.dot.nb.final <- x.inside.data2.dot.nb.final[ ! x.inside.data2.dot.nb.final %in% data2.incon.dot$DOT_NB]
-y.inside.data2.dot.nb.final <- y.inside.data2.dot.nb.final[ ! y.inside.data2.dot.nb.final %in% data2.incon.dot$DOT_NB]
-x.outside.data2.dot.nb.final <- x.outside.data2.dot.nb.final[ ! x.outside.data2.dot.nb.final %in% data2.incon.dot$DOT_NB]
-y.outside.data2.dot.nb.final <- y.outside.data2.dot.nb.final[ ! y.outside.data2.dot.nb.final %in% data2.incon.dot$DOT_NB]
-x.unknown.data2.dot.nb.final <- x.unknown.data2.dot.nb.final[ ! x.unknown.data2.dot.nb.final %in% data2.incon.dot$DOT_NB]
-y.unknown.data2.dot.nb.final <- y.unknown.data2.dot.nb.final[ ! y.unknown.data2.dot.nb.final %in% data2.incon.dot$DOT_NB]
-# end removal of the inconsistent dot in the other classifications
-}
-}
-# end inconsistent dots recovery 
-# unknown dots recovery 
-if( ! is.null(data2)){
-if(data2.pb.dot == "signif"){
-x.outside.data2.dot.nb.final <- unique(c(x.outside.data2.dot.nb.final, x.unknown.data2.dot.nb.final))
-x.inside.data2.dot.nb.final <- x.inside.data2.dot.nb.final[ ! x.inside.data2.dot.nb.final %in% x.unknown.data2.dot.nb.final] # remove x.unknown.data2.dot.nb.final from x.inside.data2.dot.nb.final
-y.outside.data2.dot.nb.final <- unique(c(y.outside.data2.dot.nb.final, y.unknown.data2.dot.nb.final))
-y.inside.data2.dot.nb.final <- y.inside.data2.dot.nb.final[ ! y.inside.data2.dot.nb.final %in% y.unknown.data2.dot.nb.final] # remove y.unknown.data2.dot.nb.final from y.inside.data2.dot.nb.final
-x.unknown.data2.dot.nb.final <- NULL
-y.unknown.data2.dot.nb.final <- NULL
-data2.unknown.dot <- NULL
-}else if(data2.pb.dot == "not.signif"){
-x.inside.data2.dot.nb.final <- unique(c(x.inside.data2.dot.nb.final, x.unknown.data2.dot.nb.final))
-x.outside.data2.dot.nb.final <- x.outside.data2.dot.nb.final[ ! x.outside.data2.dot.nb.final %in% x.unknown.data2.dot.nb.final] # remove x.unknown.data2.dot.nb.final from x.outside.data2.dot.nb.final
-y.inside.data2.dot.nb.final <- unique(c(y.inside.data2.dot.nb.final, y.unknown.data2.dot.nb.final))
-y.outside.data2.dot.nb.final <- y.outside.data2.dot.nb.final[ ! y.outside.data2.dot.nb.final %in% y.unknown.data2.dot.nb.final] # remove y.unknown.data2.dot.nb.final from y.outside.data2.dot.nb.final
-x.unknown.data2.dot.nb.final <- NULL
-y.unknown.data2.dot.nb.final <- NULL
-data2.unknown.dot <- NULL
-}else if(data2.pb.dot == "unknown"){
-if(length(unique(c(x.unknown.data2.dot.nb.final, y.unknown.data2.dot.nb.final))) > 0){
-data2.unknown.dot <- data2[data2$DOT_NB %in% unique(c(x.unknown.data2.dot.nb.final, y.unknown.data2.dot.nb.final)), ] # if a dot in unknown in x or y -> classified as unknown (so unique() used)
-x.outside.data2.dot.nb.final <- x.outside.data2.dot.nb.final[ ! x.outside.data2.dot.nb.final %in% data2.unknown.dot$DOT_NB] # remove x.unknown.data2.dot.nb.final from x.outside.data2.dot.nb.final
-x.inside.data2.dot.nb.final <- x.inside.data2.dot.nb.final[ ! x.inside.data2.dot.nb.final %in% data2.unknown.dot$DOT_NB] # remove x.unknown.data2.dot.nb.final from x.inside.data2.dot.nb.final
-y.outside.data2.dot.nb.final <- y.outside.data2.dot.nb.final[ ! y.outside.data2.dot.nb.final %in% data2.unknown.dot$DOT_NB] # remove y.unknown.data2.dot.nb.final from y.outside.data2.dot.nb.final
-y.inside.data2.dot.nb.final <- y.inside.data2.dot.nb.final[ ! y.inside.data2.dot.nb.final %in% data2.unknown.dot$DOT_NB] # remove y.unknown.data2.dot.nb.final from y.inside.data2.dot.nb.final
-}
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 3")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end unknown dots recovery 
-# sign and non sign dot recovery
-if(xy.cross.kind == "|"){ # here the problem is to deal with significant dots depending on x and y. Thus I start with that, recover dots finally non significant in outside and put them in inside (when &), and remove from inside the dots in outside
-if(length(unique(c(x.outside.data1.dot.nb.final, y.outside.data1.dot.nb.final))) > 0){
-tempo.outside <- unique(c(x.outside.data1.dot.nb.final, y.outside.data1.dot.nb.final)) # union so unique() used
-tempo.inside <- unique(c(x.inside.data1.dot.nb.final, y.inside.data1.dot.nb.final))
-tempo.inside <- tempo.inside[ ! tempo.inside %in% tempo.outside]
-data1.signif.dot <- data1[data1$DOT_NB %in% tempo.outside, ]
-data1.non.signif.dot <- data1[data1$DOT_NB %in% tempo.inside, ]
-}else{
-data1.non.signif.dot <- data1[unique(c(x.inside.data1.dot.nb.final, y.inside.data1.dot.nb.final)), ] # if no outside dots, I recover all the inside dots and that's it
-}
-}else if(xy.cross.kind == "&"){
-if(sum(x.outside.data1.dot.nb.final %in% y.outside.data1.dot.nb.final) > 0){ # that is intersection
-tempo.outside <- unique(x.outside.data1.dot.nb.final[x.outside.data1.dot.nb.final %in% y.outside.data1.dot.nb.final]) # intersection
-tempo.outside.removed <- unique(c(x.outside.data1.dot.nb.final, y.outside.data1.dot.nb.final))[ ! unique(c(x.outside.data1.dot.nb.final, y.outside.data1.dot.nb.final)) %in% tempo.outside]
-tempo.inside <- unique(c(x.inside.data1.dot.nb.final, y.inside.data1.dot.nb.final))
-data1.signif.dot <- data1[data1$DOT_NB %in% tempo.outside, ]
-data1.non.signif.dot <- data1[data1$DOT_NB %in% tempo.inside, ]
-}else{
-data1.non.signif.dot <- data1[unique(c(x.inside.data1.dot.nb.final, y.inside.data1.dot.nb.final)), ] # if no outside dots, I recover all the inside dots and that's it
-}
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 4")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! is.null(data2)){
-if(xy.cross.kind == "|"){ # here the problem is to deal with significant dots depending on x and y. Thus I start with that, recover dots finally non significant in outside and put them in inside (when &), and remove from inside the dots in outside
-if(length(unique(c(x.outside.data2.dot.nb.final, y.outside.data2.dot.nb.final))) > 0){
-tempo.outside <- unique(c(x.outside.data2.dot.nb.final, y.outside.data2.dot.nb.final)) # union so unique() used
-tempo.inside <- unique(c(x.inside.data2.dot.nb.final, y.inside.data2.dot.nb.final))
-tempo.inside <- tempo.inside[ ! tempo.inside %in% tempo.outside]
-data2.signif.dot <- data2[data2$DOT_NB %in% tempo.outside, ]
-data2.non.signif.dot <- data2[data2$DOT_NB %in% tempo.inside, ]
-}else{
-data2.non.signif.dot <- data2[unique(c(x.inside.data2.dot.nb.final, y.inside.data2.dot.nb.final)), ] # if no outside dots, I recover all the inside dots and that's it
-}
-}else if(xy.cross.kind == "&"){
-if(sum(x.outside.data2.dot.nb.final %in% y.outside.data2.dot.nb.final) > 0){ # that is intersection
-tempo.outside <- unique(x.outside.data2.dot.nb.final[x.outside.data2.dot.nb.final %in% y.outside.data2.dot.nb.final]) # intersection
-tempo.outside.removed <- unique(c(x.outside.data2.dot.nb.final, y.outside.data2.dot.nb.final))[ ! unique(c(x.outside.data2.dot.nb.final, y.outside.data2.dot.nb.final)) %in% tempo.outside]
-tempo.inside <- unique(c(x.inside.data2.dot.nb.final, y.inside.data2.dot.nb.final))
-data2.signif.dot <- data2[data2$DOT_NB %in% tempo.outside, ]
-data2.non.signif.dot <- data2[data2$DOT_NB %in% tempo.inside, ]
-}else{
-data2.non.signif.dot <- data2[unique(c(x.inside.data2.dot.nb.final, y.inside.data2.dot.nb.final)), ] # if no outside dots, I recover all the inside dots and that's it
-}
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 5")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end sign and non sign dot recovery
-}else if(( ! is.null(x.range.split)) & is.null(y.range.split)){
-# inconsistent dots recovery 
-if(length(y.incon.data1.dot.nb.final) > 0){
-data1.incon.dot <- data1[data1$DOT_NB %in% y.incon.data1.dot.nb.final, ]
-}
-if( ! is.null(data2)){
-if(length(y.incon.data2.dot.nb.final) > 0){
-data2.incon.dot <- data2[data2$DOT_NB %in% y.incon.data2.dot.nb.final, ]
-}
-}# end inconsistent dots recovery 
-# unknown dots recovery 
-if( ! is.null(data2)){
-if(data2.pb.dot == "signif"){
-y.outside.data2.dot.nb.final <- unique(c(y.outside.data2.dot.nb.final, y.unknown.data2.dot.nb.final))
-}else if(data2.pb.dot == "not.signif"){
-y.inside.data2.dot.nb.final <- unique(c(y.inside.data2.dot.nb.final, y.unknown.data2.dot.nb.final))
-}else if(data2.pb.dot == "unknown"){
-if(length(y.unknown.data2.dot.nb.final) > 0){
-data2.unknown.dot <- data2[data2$DOT_NB %in% y.unknown.data2.dot.nb.final, ]
-}
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 6")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end unknown dots recovery 
-# sign and non sign dot recovery
-if(length(y.outside.data1.dot.nb.final) > 0){
-data1.signif.dot <- data1[data1$DOT_NB %in% y.outside.data1.dot.nb.final, ]
-}
-if(length(y.inside.data1.dot.nb.final) > 0){
-data1.non.signif.dot <- data1[data1$DOT_NB %in% y.inside.data1.dot.nb.final, ]
-}
-if( ! is.null(data2)){
-if(length(y.outside.data2.dot.nb.final) > 0){
-data2.signif.dot <- data2[data2$DOT_NB %in% y.outside.data2.dot.nb.final, ]
-}
-if(length(y.inside.data2.dot.nb.final) > 0){
-data2.non.signif.dot <- data2[data2$DOT_NB %in% y.inside.data2.dot.nb.final, ]
-}
-}
-# end sign and non sign dot recovery
-}else if(is.null(x.range.split) & ( ! is.null(y.range.split))){
-# inconsistent dots recovery 
-if(length(x.incon.data1.dot.nb.final) > 0){
-data1.incon.dot <- data1[data1$DOT_NB %in% x.incon.data1.dot.nb.final, ]
-}
-if( ! is.null(data2)){
-if(length(x.incon.data2.dot.nb.final) > 0){
-data2.incon.dot <- data2[data2$DOT_NB %in% x.incon.data2.dot.nb.final, ]
-}
-}# end inconsistent dots recovery 
-# unknown dots recovery 
-if( ! is.null(data2)){
-if(data2.pb.dot == "signif"){
-x.outside.data2.dot.nb.final <- unique(c(x.outside.data2.dot.nb.final, x.unknown.data2.dot.nb.final))
-}else if(data2.pb.dot == "not.signif"){
-x.inside.data2.dot.nb.final <- unique(c(x.inside.data2.dot.nb.final, x.unknown.data2.dot.nb.final))
-}else if(data2.pb.dot == "unknown"){
-if(length(x.unknown.data2.dot.nb.final) > 0){
-data2.unknown.dot <- data2[data2$DOT_NB %in% x.unknown.data2.dot.nb.final, ]
-}
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 7")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end unknown dots recovery 
-# sign and non sign dot recovery
-if(length(x.outside.data1.dot.nb.final) > 0){
-data1.signif.dot <- data1[data1$DOT_NB %in% x.outside.data1.dot.nb.final, ]
-}
-if(length(x.inside.data1.dot.nb.final) > 0){
-data1.non.signif.dot <- data1[data1$DOT_NB %in% x.inside.data1.dot.nb.final, ]
-}
-if( ! is.null(data2)){
-if(length(x.outside.data2.dot.nb.final) > 0){
-data2.signif.dot <- data2[data2$DOT_NB %in% x.outside.data2.dot.nb.final, ]
-}
-if(length(x.inside.data2.dot.nb.final) > 0){
-data2.non.signif.dot <- data2[data2$DOT_NB %in% x.inside.data2.dot.nb.final, ]
-}
-}
-# end sign and non sign dot recovery
-}
-# end recovering the dot coordinates
-# verif
-if(any(data1.signif.dot$DOT_NB %in% data1.non.signif.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", FUNCTION.NAME, ": CODE INCONSISTENCY 8")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data1.non.signif.dot$DOT_NB %in% data1.signif.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", FUNCTION.NAME, ": CODE INCONSISTENCY 9")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data1.signif.dot$DOT_NB %in% data1.incon.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 10")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data1.incon.dot$DOT_NB %in% data1.signif.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 11")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data1.non.signif.dot$DOT_NB %in% data1.incon.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 12")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data1.incon.dot$DOT_NB %in% data1.non.signif.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 13")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! is.null(data2)){
-if(any(data2.signif.dot$DOT_NB %in% data2.non.signif.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 14")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data2.non.signif.dot$DOT_NB %in% data2.signif.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 15")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data2.signif.dot$DOT_NB %in% data2.unknown.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 16")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data2.unknown.dot$DOT_NB %in% data2.signif.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 17")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data2.signif.dot$DOT_NB %in% data2.incon.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 18")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data2.incon.dot$DOT_NB %in% data2.signif.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 19")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data2.non.signif.dot$DOT_NB %in% data2.unknown.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 20")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data2.unknown.dot$DOT_NB %in% data2.non.signif.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 21")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data2.non.signif.dot$DOT_NB %in% data2.incon.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 22")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data2.incon.dot$DOT_NB %in% data2.non.signif.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 23")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data2.unknown.dot$DOT_NB %in% data2.incon.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 24")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(data2.incon.dot$DOT_NB %in% data2.unknown.dot$DOT_NB)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 25")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end verif
-# plot
-# recovering the axes data whatever plot or not
-if(is.null(data2)){
-axes <- fun_gg_scatter(data1 = list(data1), x = list(x1), y = list(y1), categ = list(NULL), color = list(fun_gg_palette(2)[2]), geom = list("geom_point"), alpha = list(0.5), x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, plot = FALSE, return = TRUE)$axes
-}else{
-axes <- fun_gg_scatter(data1 = list(data1, data2), x = list(x1, x2), y = list(y1, y2), categ = list(NULL, NULL), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1]), geom = list("geom_point", "geom_point"), alpha = list(0.5, 0.5), x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, plot = FALSE, return = TRUE)$axes
-}
-# end recovering the axes data whatever plot or not
-if(plot == TRUE){
-# add a categ for plot legend
-tempo.df.name <- c("data1", "data1.signif.dot", "data1.incon.dot", "data2", "data2.signif.dot", "data2.unknown.dot", "data2.incon.dot")
-tempo.class.name <- c("data1", "data1", "data1", "data2", "data2", "data2", "data2")
-for(i2 in 1:length(tempo.df.name)){
-if( ! is.null(get(tempo.df.name[i2], env = sys.nframe(), inherit = FALSE))){
-assign(tempo.df.name[i2], data.frame(get(tempo.df.name[i2], env = sys.nframe(), inherit = FALSE), kind = tempo.class.name[i2]),
-stringsAsFactors = TRUE)
-}
-}
-# end add a categ for plot legend
-if(( ! is.null(x.range.split)) & ( ! is.null(y.range.split))){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, hframe, vframe), x = list(x1, "x", "x"), y = list(y1, "y", "y"), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "HORIZ FRAME" , "VERT FRAME"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_path", "geom_path"), alpha = list(0.5, 0.5, 0.5), title = "DATA1", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if( ! is.null(data1.signif.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, hframe, vframe, data1.signif.dot), x = list(x1, "x", "x", x1), y = list(y1, "y", "y", y1), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "HORIZ FRAME" , "VERT FRAME", "SIGNIF DOTS"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2), "black"), geom = list("geom_point", "geom_path", "geom_path", "geom_point"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA1 SIGNIFICANT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA1 DOTS\nOUTSIDE THE FRAMES", text.size = 8, title = "DATA1 + DATA1 SIGNIFICANT DOTS")
-}
-if( ! is.null(data1.incon.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, hframe, vframe, data1.incon.dot), x = list(x1, "x", "x", x1), y = list(y1, "y", "y", y1), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "HORIZ FRAME" , "VERT FRAME", "INCONSISTENT DOTS"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2), fun_gg_palette(7)[6]), geom = list("geom_point", "geom_path", "geom_path", "geom_point"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA1 INCONSISTENT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA1\nINCONSISTENT DOTS", text.size = 8, title = "DATA1 + DATA1 INCONSISTENT DOTS")
-}
-if( ! is.null(data2)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, hframe , vframe), x = list(x1, x2, "x", "x"), y = list(y1, y2, "y", "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "HORIZ FRAME" , "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_path", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if( ! is.null(data2.signif.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.signif.dot, hframe , vframe), x = list(x1, x2, x2, "x", "x"), y = list(y1, y2, y2, "y", "y"), categ = list("kind", "kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "SIGNIF DOTS", "HORIZ FRAME" , "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], "black", rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 SIGNIFICANT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2 DOTS\nOUTSIDE THE FRAMES", text.size = 8, title = "DATA1 + DATA2 + DATA2 SIGNIFICANT DOTS")
-}
-if( ! is.null(data2.incon.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.incon.dot, hframe , vframe), x = list(x1, x2, x2, "x", "x"), y = list(y1, y2, y2, "y", "y"), categ = list("kind", "kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "INCONSISTENT DOTS", "HORIZ FRAME" , "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], fun_gg_palette(7)[6], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 INCONSISTENT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2\nINCONSISTENT DOTS", text.size = 8, title = "DATA2 + DATA2 INCONSISTENT DOTS")
-}
-if( ! is.null(data2.unknown.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.unknown.dot, hframe , vframe), x = list(x1, x2, x2, "x", "x"), y = list(y1, y2, y2, "y", "y"), categ = list("kind", "kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "UNKNOWN DOTS", "HORIZ FRAME" , "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], fun_gg_palette(7)[5], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 UNKNOWN DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2\nUNKNOWN DOTS", text.size = 12, title = "DATA2 + DATA2 UNKNOWN DOTS")
-}
-}
-}else if(( ! is.null(x.range.split)) & is.null(y.range.split)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, hframe), x = list(x1, "x"), y = list(y1, "y"), categ = list("kind", "kind"), legend.name = list("DATASET", "HORIZ FRAME"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2)), geom = list("geom_point", "geom_path"), alpha = list(0.5, 0.5), title = "DATA1", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if( ! is.null(data1.signif.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, hframe, data1.signif.dot), x = list(x1, "x", x1), y = list(y1, "y", y1), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "HORIZ FRAME", "SIGNIF DOTS"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), "black"), geom = list("geom_point", "geom_path", "geom_point"), alpha = list(0.5, 0.5, 0.5), title = "DATA1 + DATA1 SIGNIFICANT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA1 DOTS\nOUTSIDE THE FRAMES", text.size = 8, title = "DATA1 + DATA1 SIGNIFICANT DOTS")
-}
-if( ! is.null(data1.incon.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, hframe, data1.incon.dot), x = list(x1, "x", x1), y = list(y1, "y", y1), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "HORIZ FRAME", "INCONSISTENT DOTS"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), fun_gg_palette(7)[6]), geom = list("geom_point", "geom_path", "geom_point"), alpha = list(0.5, 0.5, 0.5), title = "DATA1 + DATA1 INCONSISTENT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA1\nINCONSISTENT DOTS", text.size = 8, title = "DATA1 + DATA1 INCONSISTENT DOTS")
-}
-if( ! is.null(data2)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, hframe), x = list(x1, x2, "x"), y = list(y1, y2, "y"), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "HORIZ FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2)), geom = list("geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5), title = "DATA1 + DATA2", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if( ! is.null(data2.signif.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.signif.dot, hframe), x = list(x1, x2, x2, "x"), y = list(y1, y2, y2, "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "SIGNIF DOTS", "HORIZ FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], "black", rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 SIGNIFICANT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2 DOTS\nOUTSIDE THE FRAMES", text.size = 8, title = "DATA1 + DATA2 + DATA2 SIGNIFICANT DOTS")
-}
-if( ! is.null(data2.incon.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.incon.dot, hframe), x = list(x1, x2, x2, "x"), y = list(y1, y2, y2, "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "INCONSISTENT DOTS", "HORIZ FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], fun_gg_palette(7)[6], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 INCONSISTENT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2\nINCONSISTENT DOTS", text.size = 8, title = "DATA2 + DATA2 INCONSISTENT DOTS")
-}
-if( ! is.null(data2.unknown.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.unknown.dot, hframe), x = list(x1, x2, x2, "x"), y = list(y1, y2, y2, "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "UNKNOWN DOTS", "HORIZ FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], fun_gg_palette(7)[5], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 UNKNOWN DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2\nUNKNOWN DOTS", text.size = 8, title = "DATA2 + DATA2 UNKNOWN DOTS")
-}
-}
-}else if(is.null(x.range.split) & ( ! is.null(y.range.split))){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, vframe), x = list(x1, "x"), y = list(y1, "y"), categ = list("kind", "kind"), legend.name = list("DATASET", "VERT FRAME"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_path"), alpha = list(0.5, 0.5), title = "DATA1", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if( ! is.null(data1.signif.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, vframe, data1.signif.dot), x = list(x1, "x", x1), y = list(y1, "y", y1), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "VERT FRAME", "SIGNIF DOTS"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2), "black"), geom = list("geom_point", "geom_path", "geom_point"), alpha = list(0.5, 0.5, 0.5), title = "DATA1 + DATA1 SIGNIFICANT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA1 DOTS\nOUTSIDE THE FRAMES", text.size = 8, title = "DATA1 + DATA1 SIGNIFICANT DOTS")
-}
-if( ! is.null(data1.incon.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, vframe, data1.incon.dot), x = list(x1, "x", x1), y = list(y1, "y", y1), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "VERT FRAME", "INCONSISTENT DOTS"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2), fun_gg_palette(7)[6]), geom = list("geom_point", "geom_path", "geom_point"), alpha = list(0.5, 0.5, 0.5), title = "DATA1 + DATA1 INCONSISTENT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA1\nINCONSISTENT DOTS", text.size = 8, title = "DATA1 + DATA1 INCONSISTENT DOTS")
-}
-if( ! is.null(data2)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, vframe), x = list(x1, x2, "x"), y = list(y1, y2, "y"), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5), title = "DATA1 + DATA2", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if( ! is.null(data2.signif.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.signif.dot, vframe), x = list(x1, x2, x2, "x"), y = list(y1, y2, y2, "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "SIGNIF DOTS", "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], "black", rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 SIGNIFICANT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2 DOTS\nOUTSIDE THE FRAMES", text.size = 8, title = "DATA1 + DATA2 + DATA2 SIGNIFICANT DOTS")
-}
-if( ! is.null(data2.incon.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.incon.dot, vframe), x = list(x1, x2, x2, "x"), y = list(y1, y2, y2, "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "INCONSISTENT DOTS", "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], fun_gg_palette(7)[6], rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 INCONSISTENT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2\nINCONSISTENT DOTS", text.size = 8, title = "DATA2 + DATA2 INCONSISTENT DOTS")
-}
-if( ! is.null(data2.unknown.dot)){
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.unknown.dot, vframe), x = list(x1, x2, x2, "x"), y = list(y1, y2, y2, "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "UNKNOWN DOTS", "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], fun_gg_palette(7)[5], rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 UNKNOWN DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
-if( ! is.null(tempo.graph$warn)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(graph.in.file == FALSE){
-fun_open(pdf = FALSE)
-}
-fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2\nUNKNOWN DOTS", text.size = 8, title = "DATA2 + DATA2 UNKNOWN DOTS")
-}
-}
-}
-}
-# end plot
-if(warn.print == TRUE & ! is.null(warn)){
-options(warning.length = 8170)
-on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
-}
-on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
-tempo.list <- list(data1.removed.row.nb = data1.removed.row.nb, data1.removed.rows = data1.removed.rows, data2.removed.row.nb = data2.removed.row.nb, data2.removed.rows = data2.removed.rows, hframe = hframe, vframe = vframe, data1.signif.dot = data1.signif.dot, data1.non.signif.dot = data1.non.signif.dot, data1.inconsistent.dot = data1.incon.dot, data2.signif.dot = data2.signif.dot, data2.non.signif.dot = data2.non.signif.dot, data2.unknown.dot = data2.unknown.dot, data2.inconsistent.dot = data2.incon.dot, axes = axes, warn = warn)
-return(tempo.list)
-}
-
-
-################ Import
-
-
-######## fun_pack() #### check if R packages are present and import into the working environment
-
-
-fun_pack <- function(
-req.package, 
-load = FALSE, 
-lib.path = NULL
-){
-# AIM
-# check if the specified R packages are present in the computer and import them into the working environment
-# ARGUMENTS
-# req.package: character vector of package names to import
-# load: logical. Load the package into the environement (using library())? Interesting if packages are not in default folders or for checking the functions names of packages using search()
-# lib.path: optional character vector specifying the absolute pathways of the directories containing some of the listed packages in the req.package argument, if not in the default directories. Ignored if NULL
-# RETURN
-# nothing
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# fun_pack(req.package = "nopackage")
-# fun_pack(req.package = "ggplot2")
-# fun_pack(req.package = "ggplot2", lib.path = "blablabla")
-# DEBUGGING
-# req.package = "ggplot2" ; lib.path = "C:/Program Files/R/R-3.5.1/library"
-# req.package = "serpentine" ; lib.path = "C:/users/gael/appdata/roaming/python/python36/site-packages"
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = req.package, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = load, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(lib.path)){
-tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-if(is.null(lib.path)){
-lib.path <- .libPaths() # .libPaths(new = lib.path) # or .libPaths(new = c(.libPaths(), lib.path))
-}else{
-.libPaths(new = sub(x = lib.path, pattern = "/$|\\\\$", replacement = "")) # .libPaths(new = ) add path to default path. BEWARE: .libPaths() does not support / at the end of a submitted path. Thus check and replace last / or \\ in path
-lib.path <- .libPaths()
-}
-tempo <- NULL
-for(i1 in 1:length(req.package)){
-if( ! req.package[i1] %in% rownames(utils::installed.packages(lib.loc = lib.path))){
-tempo <- c(tempo, req.package[i1])
-}
-}
-if( ! is.null(tempo)){
-tempo.cat <- paste0(
-"ERROR IN ", 
-function.name, 
-": PACKAGE", 
-ifelse(length(tempo) == 1L, paste0("\n\n", tempo, "\n\n"), paste0("S\n", paste(tempo, collapse = "\n"), "\n")), 
-"MUST BE INSTALLED IN", 
-ifelse(length(lib.path) == 1L, "", " ONE OF THESE FOLDERS"), 
-":\n", 
-paste(lib.path, collapse = "\n")
-)
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(load == TRUE){
-for(i2 in 1:length(req.package)){
-suppressMessages(suppressWarnings(suppressPackageStartupMessages(library(req.package[i2], lib.loc = lib.path, quietly = TRUE, character.only = TRUE))))
-}
-}
-}
-
-
-######## fun_python_pack() #### check if python packages are present
-
-
-fun_python_pack <- function(
-req.package, 
-python.exec.path = NULL, 
-lib.path = NULL, 
-R.lib.path = NULL
-){
-# AIM
-# check if the specified python packages are present in the computer (no import)
-# WARNINGS
-# for python 3.7. Previous versions return an error "Error in sys$stdout$flush() : attempt to apply non-function"
-# ARGUMENTS
-# req.package: character vector of package names to import
-# python.exec.path: optional character vector specifying the absolute pathways of the executable python file to use (associated to the packages to use). If NULL, the reticulate::import_from_path() function used in fun_python_pack() seeks for an available version of python.exe, and then uses python_config(python_version, required_module, python_versions). But might not be the correct one for the lib.path parameter specified. Thus, it is recommanded to do not leave NULL, notably when using computing clusters
-# lib.path: optional character vector specifying the absolute pathways of the directories containing some of the listed packages in the req.package argument, if not in the default directories
-# R.lib.path: absolute path of the reticulate packages, if not in the default folders
-# RETURN
-# nothing
-# REQUIRED PACKAGES
-# reticulate
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# fun_pack()
-# EXAMPLES
-# example of error message
-# fun_python_pack(req.package = "nopackage")
-# example without error message (require the installation of the python serpentine package from https://github.com/koszullab/serpentine
-# fun_python_pack(req.package = "serpentine", python.exec.path = "C:/ProgramData/Anaconda3/python.exe", lib.path = "c:/programdata/anaconda3/lib/site-packages/")
-# another example of error message
-# fun_python_pack(req.package = "serpentine", lib.path = "blablabla")
-# DEBUGGING
-# req.package = "serpentine" ; python.exec.path = "C:/ProgramData/Anaconda3/python.exe" ; lib.path = "c:/programdata/anaconda3/lib/site-packages/" ; R.lib.path = NULL
-# req.package = "bad" ; lib.path = NULL ; R.lib.path = NULL
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(utils::find("fun_pack", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = req.package, class = "character", fun.name = function.name) ; eval(ee)
-if( ! is.null(python.exec.path)){
-tempo <- fun_check(data = python.exec.path, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if( ! all(file.exists(python.exec.path))){ # separation to avoid the problem of tempo$problem == FALSE and python.exec.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": FILE PATH INDICATED IN THE python.exec.path ARGUMENT DOES NOT EXISTS:\n", paste(python.exec.path, collapse = "\n"))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}
-if( ! is.null(lib.path)){
-tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}
-if( ! is.null(R.lib.path)){
-tempo <- fun_check(data = R.lib.path, class = "character", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if( ! all(dir.exists(R.lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and R.lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE R.lib.path ARGUMENT DOES NOT EXISTS:\n", paste(R.lib.path, collapse = "\n"))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# package checking
-fun_pack(req.package = "reticulate", lib.path = R.lib.path)
-# end package checking
-# main code
-if(is.null(python.exec.path)){
-python.exec.path <- reticulate::py_run_string("
-import sys ;
-path_lib = sys.path
-") # python string
-python.exec.path <- python.exec.path$path_lib
-}
-if(is.null(lib.path)){
-lib.path <- reticulate::py_run_string("
-import sys ;
-path_lib = sys.path
-") # python string
-lib.path <- lib.path$path_lib
-}
-reticulate::use_python(Sys.which(python.exec.path), required = TRUE) # required to avoid the use of erratic python exec by reticulate::import_from_path()
-for(i1 in 1:length(req.package)){
-tempo.try <- vector("list", length = length(lib.path))
-for(i2 in 1:length(lib.path)){
-tempo.try[[i2]] <- suppressWarnings(try(reticulate::import_from_path(req.package[i1], path = lib.path[i2]), silent = TRUE))
-tempo.try[[i2]] <- suppressWarnings(try(reticulate::import_from_path(req.package[i1], path = lib.path[i2]), silent = TRUE)) # done twice to avoid the error message  about flushing present the first time but not the second time. see https://stackoverflow.com/questions/57357001/reticulate-1-13-error-in-sysstdoutflush-attempt-to-apply-non-function
-}
-if(all(sapply(tempo.try, FUN = grepl, pattern = "[Ee]rror"))){
-print(tempo.try)
-tempo.cat <- paste0("ERROR IN ", function.name, ": PACKAGE ", req.package[i1], " MUST BE INSTALLED IN THE MENTIONNED DIRECTORY:\n", paste(lib.path, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-} # else{
-# suppressMessages(suppressWarnings(suppressPackageStartupMessages(assign(req.package[i1], reticulate::import(req.package[i1]))))) # not required because try() already evaluates
-# }
-}
-}
-
-
-################ Print / Exporting results (text & tables)
-
-
-######## fun_report() #### print string or data object into output file
-
-
-fun_report <- function(
-data, 
-output = "results.txt", 
-path = "C:/Users/Gael/Desktop/", 
-overwrite = FALSE, 
-rownames.kept = FALSE, 
-vector.cat = FALSE, 
-noquote = TRUE, 
-sep = 2
-){
-# AIM
-# log file function: print a character string or a data object into a same output file
-# ARGUMENTS
-# data: object to print in the output file. If NULL, nothing is done, with no warning
-# output: name of the output file
-# path: location of the output file
-# overwrite: (logical) if output file already exists, defines if the printing is appended (default FALSE) or if the output file content is erased before printing (TRUE)
-# rownames.kept: (logical) defines whether row names have to be removed or not in small tables (less than length.rows rows)
-# vector.cat (logical). If TRUE print a vector of length > 1 using cat() instead of capture.output(). Otherwise (default FALSE) the opposite
-# noquote: (logical). If TRUE no quote are present for the characters
-# sep: number of separating lines after printed data (must be integer)
-# RETURN
-# nothing
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# fun_report()
-# fun_report(data = 1:3, output = "results.txt", path = "C:/Users/Gael/Desktop", overwrite = TRUE, rownames.kept = FALSE, vector.cat = FALSE, noquote = FALSE, sep = 2)
-# DEBUGGING
-# data = 1:3 ; output = "results.txt" ; path = "C:/Users/Gael/Desktop" ; overwrite = TRUE ; rownames.kept = FALSE ; vector.cat = FALSE ; noquote = FALSE ; sep = 2 # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# argument checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = output, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & output == ""){
-tempo.cat <- paste0("ERROR IN ", function.name, ": output ARGUMENT AS \"\" DOES NOT CORRESPOND TO A VALID FILE NAME")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo <- fun_check(data = path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if( ! all(dir.exists(path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": path ARGUMENT DOES NOT CORRESPOND TO EXISTING DIRECTORY\n", paste(path, collapse = "\n"))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-tempo <- fun_check(data = overwrite, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = rownames.kept, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = vector.cat, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = noquote, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = sep, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end argument checking
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# the 4 next lines are inactivated but kept because at a time, I might have a problem with data (solved with data = NULL). These 4 lines are just to know how to detect a missing argument. Important here because if data is not provided, print the code of the data function
-# arg.user.list <- as.list(match.call(expand.dots = FALSE))[-1] # recover all the arguments provided by the function user (excluding the argument with defaults values not provided by the user. Thus, it is really the list indicated by the user)
-# default.arg.list <- formals(fun = sys.function(sys.parent())) # list of all the arguments of the function with their default values (not the values of the user !). It seems that ls() as first line of the function provide the names of the arguments (empty, called, etc., or not)
-# arg.without.default.value <- sapply(default.arg.list, is.symbol) & sapply(sapply(default.arg.list, as.character), identical, "") # logical to detect argument without default values (these are typeof "symbol" and class "name" and empty character
-# if( ! all(names(default.arg.list)[arg.without.default.value] %in% names(arg.user.list))){ # test that the arguments with no null values are provided by the user
-# tempo.cat <- paste0("ERROR IN ", function.name, ": VALUE REQUIRED FOR THESE ARGUMENTS WITH NO DEFAULTS VALUES: ", paste(names(default.arg.list)[arg.without.default.value][ ! names(default.arg.list)[arg.without.default.value] %in% names(arg.user.list)], collapse = " "))
-# stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-# }
-# end argument checking
-# main code
-if( ! is.null(data)){
-if(all(class(data) == "data.frame") | all(class(data) == "table") | all(class(data) %in% c("matrix", "array"))){ # before R4.0.0, it was  all(class(data) %in% c("matrix", "data.frame", "table"))
-if(rownames.kept == FALSE & all(class(data) == "data.frame") & nrow(data) != 0 & nrow(data) <= 4){ # for data frames with nrows <= 4
-rownames.output.tables <- ""
-length.rows <- nrow(data)
-for(i in 1:length.rows){ # replace the rownames of the first 4 rows by increasing number of spaces (because identical row names not allowed in data frames). This method cannot be extended to more rows as the printed data frame is shifted on the right because of "big empty rownames"
-rownames.output.tables <- c(rownames.output.tables, paste0(rownames.output.tables[i]," ", collapse=""))
-}
-row.names(data) <- rownames.output.tables[1:length.rows]
-}else if(rownames.kept == FALSE & (all(class(data) == "table") | all(class(data) %in% c("matrix", "array")))){ # before R4.0.0, it was  & all(class(data) %in% c("matrix", "table"))
-rownames(data) <- rep("", nrow(data)) # identical row names allowed in matrices and tables
-}
-if(noquote == TRUE){
-utils::capture.output(noquote(data), file=paste0(path, "/", output), append = ! overwrite)
-}else{
-utils::capture.output(data, file=paste0(path, "/", output), append = ! overwrite)
-}
-}else if(is.vector(data) & all(class(data) != "list") & (length(data) == 1L | vector.cat == TRUE)){
-if(noquote == TRUE){
-cat(noquote(data), file= paste0(path, "/", output), append = ! overwrite)
-}else{
-cat(data, file= paste0(path, "/", output), append = ! overwrite)
-}
-}else if(all(base::mode(data) == "character")){ # characters (array, list, factor or vector with vector.cat = FALSE)
-if(noquote == TRUE){
-utils::capture.output(noquote(data), file=paste0(path, "/", output), append = ! overwrite)
-}else{
-utils::capture.output(data, file=paste0(path, "/", output), append = ! overwrite)
-}
-}else{ # other object (S4 for instance, which do not like noquote()
-utils::capture.output(data, file=paste0(path, "/", output), append = ! overwrite)
-}
-sep.final <- paste0(rep("\n", sep), collapse = "")
-write(sep.final, file= paste0(path, "/", output), append = TRUE) # add a sep
-}
-}
-
-
-######## fun_get_message() #### return error/warning/other messages of an expression (that can be exported)
-
-
-fun_get_message <- function(
-data, 
-kind = "error", 
-header = TRUE, 
-print.no = FALSE, 
-text = NULL, 
-env = NULL
-){
-# AIM
-# evaluate an instruction written between "" and return the first of the error, or warning or standard (non error non warning) messages if ever exist
-# using argument print.no = FALSE, return NULL if no message, which is convenient in some cases
-# WARNINGS
-# Only the first message is returned
-# Always use the env argument when fun_get_message() is used inside functions
-# The function does not prevent printing if print() is used inside the instruction tested. To prevent that, use tempo <- capture.output(error <- fun_get_message(data = "fun_check(data = 'a', class = mean, neg.values = FALSE, print = TRUE)")). The return of fun_get_message() is assigned into error and the printed messages are captured by capture.output() and assigned into tempo. See the examples
-# ARGUMENTS
-# data: character string to evaluate
-# kind: character string. Either "error" to get error messages, or "warning" to get warning messages, or "message" to get non error and non warning messages
-# header: logical. Add a header in the returned message?
-# print.no: logical. Print a message saying that no message reported?
-# text: character string added to the output message (even if no message exists and print.no is TRUE). Inactivated if header is FALSE
-# env: the name of an existing environment. NULL if not required
-# RETURN
-# the message or NULL if no message and print.no is FALSE
-# REQUIRED PACKAGES
-# none
-# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-# fun_check()
-# EXAMPLES
-# fun_get_message(data = "wilcox.test(c(1,1,3), c(1, 2, 4), paired = TRUE)", kind = "error", print.no = TRUE, text = "IN A")
-# fun_get_message(data = "wilcox.test(c(1,1,3), c(1, 2, 4), paired = TRUE)", kind = "warning", print.no = TRUE, text = "IN A")
-# fun_get_message(data = "wilcox.test(c(1,1,3), c(1, 2, 4), paired = TRUE)", kind = "message", print.no = TRUE, text = "IN A")
-# fun_get_message(data = "wilcox.test()", kind = "error", print.no = TRUE, text = "IN A")
-# fun_get_message(data = "sum(1)", kind = "error", print.no = TRUE, text = "IN A")
-# fun_get_message(data = "message('ahah')", kind = "error", print.no = TRUE, text = "IN A")
-# fun_get_message(data = "message('ahah')", kind = "message", print.no = TRUE, text = "IN A")
-# fun_get_message(data = "ggplot2::ggplot(data = data.frame(X = 1:10, stringsAsFactors = TRUE), mapping = ggplot2::aes(x = X)) + ggplot2::geom_histogram()", kind = "message", print.no = TRUE, text = "IN FUNCTION 1")
-# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; fun_get_message(data = 'fun_gg_boxplot(data = obs1, y = "Time", categ = "Group1")', kind = "message", print.no = TRUE, text = "IN FUNCTION 1")
-# DEBUGGING
-# data = "wilcox.test(c(1,1,3), c(1, 2, 4), paired = TRUE)" ; kind = "warning" ; header = TRUE ; print.no = FALSE ; text = NULL ; env = NULL # for function debugging
-# data = "sum(1)" ; kind = "warning" ; header = TRUE ; print.no = FALSE ; text = NULL ; env = NULL  # for function debugging
-# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; data = 'fun_gg_boxplot(data1 = obs1, y = "Time", categ = "Group1")' ; kind = "warning" ; header = TRUE ; print.no = FALSE ; text = NULL ; env = NULL  # for function debugging
-# data = "message('ahah')" ; kind = "error" ; header = TRUE ; print.no = TRUE ; text = "IN A" ; env = NULL 
-# data = 'ggplot2::ggplot(data = data.frame(X = "a", stringsAsFactors = TRUE), mapping = ggplot2::aes(x = X)) + ggplot2::geom_histogram()' ; kind = "message" ; header = TRUE ; print.no = FALSE ; text = NULL # for function debugging
-# data = 'ggplot2::ggplot(data = data.frame(X = "a", stringsAsFactors = TRUE), mapping = ggplot2::aes(x = X)) + ggplot2::geom_histogram()' ; kind = "warning" ; header = TRUE ; print.no = FALSE ; text = NULL # for function debugging
-# data = "emmeans::emmeans(object = emm.rg, specs = contrast.var)" ; kind = "message" ; header = TRUE ; print.no = FALSE ; text = NULL ; env = NULL # for function debugging
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-# end function name
-# required function checking
-if(length(utils::find("fun_check", mode = "function")) == 0L){
-tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# no need to use reserved words to avoid bugs, because it is local, and  exists("tempo.warning", inherit = FALSE), never use the scope
-# argument checking
-# argument checking with fun_check()
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = data, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = kind, options = c("error", "warning", "message"), length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = print.no, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = header, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(text)){
-tempo <- fun_check(data = text, class = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-if( ! is.null(env)){
-tempo <- fun_check(data = env, class = "environment", fun.name = function.name) ; eval(ee) #
-}
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# end argument checking with fun_check()
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument checking
-# main code
-pdf(file = NULL) # send plots into a NULL file, no pdf file created
-window.nb <- dev.cur()
-invisible(dev.set(window.nb))
-# last warning cannot be used because suppressWarnings() does not modify last.warning present in the base evironment (created at first warning in a new R session), or warnings() # to reset the warning history : unlockBinding("last.warning", baseenv()) ; assign("last.warning", NULL, envir = baseenv())
-output <- NULL
-tempo.error <- try(suppressMessages(suppressWarnings(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env}))), silent = TRUE) # get error message, not warning or messages
-if(any(class(tempo.error) %in% c("gg", "ggplot"))){
-tempo.error <- try(suppressMessages(suppressWarnings(ggplot2::ggplot_build(tempo.error))), silent = TRUE)[1]
-}
-if(exists("tempo.error", inherit = FALSE) == TRUE){ # inherit = FALSE avoid the portee lexical and thus the declared word
-if( ! all(class(tempo.error) == "try-error")){ # deal with NULL and S4 objects. Old code:  ! (all(class(tempo.error) == "try-error") & any(grepl(x = tempo.error, pattern = "^Error|^error|^ERROR"))) but problem with S4 objects. Old code : if((length(tempo.error) > 0 & ! any(grepl(x = tempo.error, pattern = "^Error|^error|^ERROR"))) | (length(tempo.error) == 0) ){ but problem when tempo.error is a list but added this did not work: | ! all(class(tempo.error) == "character")
-tempo.error <- NULL
-}
-}else{
-tempo.error <- NULL
-}
-if(kind == "error" & ! is.null(tempo.error)){ # 
-if(header == TRUE){
-tempo.error[1] <- gsub(x = tempo.error[1], pattern = "^Error i|^error i|^ERROR I", replacement = "I")
-output <- paste0("ERROR MESSAGE REPORTED", ifelse(is.null(text), "", " "), text, ":\n", tempo.error[1]) #
-}else{
-output <- tempo.error[1] #
-}
-}else if(kind == "error" & is.null(tempo.error) & print.no == TRUE){
-output <- paste0("NO ERROR MESSAGE REPORTED", ifelse(is.null(text), "", " "), text)
-}else if(kind != "error" & ( ! is.null(tempo.error)) & print.no == TRUE){
-output <- paste0("NO ", ifelse(kind == "warning", "WARNING", "STANDARD (NON ERROR AND NON WARNING)"), " MESSAGE BECAUSE OF ERROR MESSAGE REPORTED", ifelse(is.null(text), "", " "), text)
-}else if(is.null(tempo.error)){
-fun.warning.capture <- function(expr){
-# from demo(error.catching) typed in the R console, coming from ?tryCatch
-# see also http://mazamascience.com/WorkingWithData/?p=912
-# return a character string or NULL
-# expr <- wilcox.test.default(c(1, 1, 3), c(1, 2, 4), paired = TRUE)
-W <- NULL
-w.handler <- function(w){ # warning handler
-W <<- w # send to the above env, i.e., the inside of the fun.warning.capture function
-invokeRestart("muffleWarning") # here w.handler() muffles all the warnings. See http://romainfrancois.blog.free.fr/index.php?post/2009/05/20/Disable-specific-warnings to muffle specific warnings and print others
-}
-output <- list(
-value = suppressMessages(withCallingHandlers(tryCatch(expr, error = function(e){e}), warning = w.handler)), # BEWARE: w.handler is a function written without (), like in other functions with FUN argument
-warning = W # processed by w.handler()
-)
-return(if(is.null(output$warning)){NULL}else{as.character(output$warning)})
-}
-tempo.warn <- fun.warning.capture(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env}))
-# warn.options.ini <- options()$warn ; options(warn = 1) ; tempo.warn <- utils::capture.output({tempo <- suppressMessages(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env}))}, type = "message") ; options(warn = warn.options.ini) # this recover warnings not messages and not errors but does not work in all enviroments
-tempo.message <- utils::capture.output({
-tempo <- suppressMessages(suppressWarnings(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env})))
-if(any(class(tempo) %in% c("gg", "ggplot"))){
-tempo <- ggplot2::ggplot_build(tempo)
-}else{
-tempo <- suppressWarnings(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env}))
-}
-}, type = "message") # recover messages not warnings and not errors
-if(kind == "warning" & ! is.null(tempo.warn)){
-if(length(tempo.warn) > 0){ # to avoid character(0)
-if( ! any(sapply(tempo.warn, FUN = "grepl", pattern = "() FUNCTION:$"))){
-tempo.warn <- paste(unique(tempo.warn), collapse = "\n") # if FALSE, means that the tested data is a special function. If TRUE, means that the data is a standard function. In that case, the output of capture.output() is two strings per warning messages: if several warning messages -> identical first string, which is removed in next messages by unique()
-}else{
-tempo.warn <- paste(tempo.warn, collapse = "\n")
-}
-if(header == TRUE){
-if(any(grepl(x = tempo.warn[[1]], pattern = "^simpleWarning i"))){
-tempo.warn[[1]] <- gsub(x = tempo.warn[[1]], pattern = "^Warning i", replacement = "I")
-}
-if(any(grepl(x = tempo.warn[[1]], pattern = "^Warning i"))){
-tempo.warn[[1]] <- gsub(x = tempo.warn[[1]], pattern = "^Warning i", replacement = "I")
-}
-output <- paste0("WARNING MESSAGE REPORTED", ifelse(is.null(text), "", " "), text, ":\n", tempo.warn) #
-}else{
-output <- tempo.warn #
-}
-}else{
-if(print.no == TRUE){
-output <- paste0("NO WARNING MESSAGE REPORTED", ifelse(is.null(text), "", " "), text)
-} # no need else{} here because output is already NULL at first
-}
-}else if(kind == "warning" & is.null(tempo.warn) & print.no == TRUE){
-output <- paste0("NO WARNING MESSAGE REPORTED", ifelse(is.null(text), "", " "), text)
-}else if(kind == "message" & exists("tempo.message", inherit = FALSE) == TRUE){ # inherit = FALSE avoid the portee lexical and thus the declared word
-if(length(tempo.message) > 0){ # if something is returned by capture.ouptput() (only in this env) with a length more than 1
-if(header == TRUE){
-output <- paste0("STANDARD (NON ERROR AND NON WARNING) MESSAGE REPORTED", ifelse(is.null(text), "", " "), text, ":\n", tempo.message) #
-}else{
-output <- tempo.message #
-}
-}else{
-if(print.no == TRUE){
-output <- paste0("NO STANDARD (NON ERROR AND NON WARNING) MESSAGE REPORTED", ifelse(is.null(text), "", " "), text)
-} # no need else{} here because output is already NULL at first
-}
-}else if(kind == "message" & exists("tempo.message", inherit = FALSE) == FALSE & print.no == TRUE){
-output <- paste0("NO STANDARD (NON ERROR AND NON WARNING) MESSAGE REPORTED", ifelse(is.null(text), "", " "), text)
-} # no need else{} here because output is already NULL at first
-} # no need else{} here because output is already NULL at first
-invisible(dev.off(window.nb)) # end send plots into a NULL file
-return(output) # do not use cat() because the idea is to reuse the message
-}
-
-
-
-
-
-# Error: class order not good when a class is removed due to NA
-# Error: line 136 in check 20201126 with add argument
-# Solve this: sometimes error messages can be more than the max display (8170). Thus, check every paste0("ERROR IN ", function.name, and trunck the message if to big. In addition, add at the begining of the warning message that it is too long and see the $warn output for complete message. Add also this into fun_scatter
-# add dot.shape ? See with available aesthetic layers
-# rasterise: https://cran.r-project.org/web/packages/ggrastr/vignettes/Raster_geoms.html
-# add horizontal argument and deal any conflict with vertical argument. Start with horizontal = NULL as default. If ! is.null() -> convert vertical if required
-
-fun_gg_boxplot <- function(
-data1, 
-y, 
-categ, 
-categ.class.order = NULL, 
-categ.color = NULL, 
-box.legend.name = NULL, 
-box.fill = FALSE, 
-box.width = 0.5, 
-box.space = 0.1, 
-box.line.size = 0.75, 
-box.notch = FALSE, 
-box.alpha = 1, 
-box.mean = TRUE, 
-box.whisker.kind = "std", 
-box.whisker.width = 0, 
-dot.color = grey(0.25), 
-dot.categ = NULL, 
-dot.categ.class.order = NULL, 
-dot.legend.name = NULL, 
-dot.tidy = FALSE, 
-dot.tidy.bin.nb = 50, 
-dot.jitter = 0.5, 
-dot.seed = 2, 
-dot.size = 3, 
-dot.alpha = 0.5, 
-dot.border.size = 0.5, 
-dot.border.color = NULL, 
-x.lab = NULL, 
-x.angle = 0, 
-y.lab = NULL, 
-y.lim = NULL, 
-y.log = "no", 
-y.tick.nb = NULL, 
-y.second.tick.nb = 1, 
-y.include.zero = FALSE, 
-y.top.extra.margin = 0.05, 
-y.bottom.extra.margin = 0.05, 
-stat.pos = "top", 
-stat.mean = FALSE, 
-stat.size = 4, 
-stat.dist = 5, 
-stat.angle = 0, 
-vertical = TRUE, 
-text.size = 12, 
-title = "", 
-title.text.size = 8, 
-legend.show = TRUE, 
-legend.width = 0.5, 
-article = TRUE, 
-grid = FALSE, 
-add = NULL, 
-return = FALSE, 
-return.ggplot = FALSE,
-return.gtable = TRUE,
-plot = TRUE, 
-warn.print = FALSE, 
-lib.path = NULL
-){
-# AIM
-# Plot ggplot2 boxplots + dots + means
-# For ggplot2 specifications, see: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html
-# WARNINGS
-# Rows containing NA in data1[, c(y, categ)] will be removed before processing, with a warning (see below)
-# Hinges are not computed like in the classical boxplot() function of R. See https://ggplot2.tidyverse.org/reference/geom_boxplot.html
-# To have a single box, please create a factor column with a single class and specify the name of this column in the categ argument. For a single set of grouped boxes, create a factor column with a single class and specify this column in categ argument as first element (i.e., as categ1, knowing that categ2 must also be specified in this situation). See categ argument below
-# The dot.alpha argument can alter the display of the color boxes when using pdf output
-# Size arguments (box.line.size, dot.size, dot.border.size, stat.size, text.size and title.text.size) are in mm. See Hadley comment in https://stackoverflow.com/questions/17311917/ggplot2-the-unit-of-size. See also http://sape.inf.usi.ch/quick-reference/ggplot2/size). Unit object are not accepted, but conversion can be used (e.g., grid::convertUnit(grid::unit(0.2, "inches"), "mm", valueOnly = TRUE))
-# Display seems to be done twice on Windows devices (like a blink). However, no double plots on pdf devices. Thus, the blink remains mysterious
-# To remove boxes and have only dots, use box.alpha = 0
-# ARGUMENTS
-# data1: data frame containing one column of quantitative values (see the y argument below) and one or two columns of categories (see the categ argument below). Duplicated column names are not allowed
-# y: character string of the data1 column name for y-axis (column containing numeric values). Numeric values will be split according to the classes of the column names indicated in the categ argument to generate the boxes and will also be used to plot the dots
-# categ: vector of character strings of the data1 column name for categories (column of characters or factors). Must be either one or two column names. If a single column name (further referred to as categ1), then one box per class of categ1. If two column names (further referred to as categ1 and categ2), then one box per class of categ2, which form a group of boxes in each class of categ1. WARNING: no empty classes allowed. To have a single box, create a factor column with a single class and specify the name of this column in the categ argument (here, no categ2 in categ argument). For a single set of grouped boxes, create a factor column with a single class and specify this column in categ argument as first element (i.e., as categ1), in addition to the already used category (as categ2 in this situation)
-# categ.class.order: list indicating the order of the classes of categ1 and categ2 represented on the boxplot (the first compartment for categ1 and and the second for categ2). If categ.class.order == NULL, classes are represented according to the alphabetical order. Some compartments can be NULL and others not. See the categ argument for categ1 and categ2 description
-# categ.color: vector of color character string for box frames (see the categ argument for categ1 and categ2 description)
-# If categ.color == NULL, default colors of ggplot2, whatever categ1 and categ2
-# If categ.color is non-null and only categ1 in categ argument, categ.color can be either:
-# (1) a single color string. All the boxes will have this color, whatever the number of classes of categ1
-# (2) a vector of string colors, one for each class of categ1. Each color will be associated according to categ.class.order of categ1
-# (3) a vector or factor of string colors, like if it was one of the column of data1 data frame. WARNING: a single color per class of categ1 and a single class of categ1 per color must be respected
-# Color functions, like grey(), hsv(), etc., are also accepted
-# Positive integers are also accepted instead of character strings, as long as above rules about length are respected. Integers will be processed by fun_gg_palette() using the maximal integer value among all the integers in categ.color (see fun_gg_palette())
-# If categ.color is non-null and categ1 and categ2 are specified, all the rules described above will apply to categ2 instead of categ1 (colors will be determined for boxes inside a group of boxes)
-# box.legend.name: character string of the legend title. If box.legend.name is NULL, then box.legend.name <- categ1 if only categ1 is present, and box.legend.name <- categ2 if categ1 and categ2 are present in the categ argument. Write "" if no legend required. See the categ argument for categ1 and categ2 description
-# box.fill: logical. Fill the box? If TRUE, the categ.color argument will be used to generate filled boxplots (the box frames being black) as well as filled outlier dots (the dot border being controlled by the dot.border.color argument). If all the dots are plotted (argument dot.color other than NULL), they will be over the boxes. If FALSE, the categ.color argument will be used to color the box frames and the outlier dot borders. If all the dots are plotted, they will be beneath the boxes
-# box.width: single numeric value (from 0 to 1) of width of either boxes or group of boxes
-# When categ argument has a single categ1 element (i.e., separate boxes. See the categ argument for categ1 and categ2 description), then each class of categ1 is represented by a single box. In that case, box.width argument defines each box width, from 0 (no box width) to 1 (max box width), but also the space between boxes (the code uses 1 - box.width for the box spaces). Of note, xmin and xmax of the fun_gg_boxplot() output report the box boundaries (around x-axis unit 1, 2, 3, etc., for each box)
-# When categ argument has a two categ1 and categ2 elements (i.e., grouped boxes), box.width argument defines the width allocated for each set of grouped boxes, from 0 (no group width) to 1 (max group width), but also the space between grouped boxes (the code uses 1 - box.width for the spaces). Of note, xmin and xmax of the fun_gg_boxplot() output report the box boundaries (around x-axis unit 1, 2, 3, etc., for each set of grouped box)
-# box.space: single numeric value (from 0 to 1) indicating the box separation inside grouped boxes, when categ argument has a two categ1 and categ2 elements. 0 means no space and 1 means boxes shrunk to a vertical line. Ignored if categ argument has a single categ1 element
-# box.line.size: single numeric value of line width of boxes and whiskers in mm
-# box.notch: logical. Notched boxplot? It TRUE, display notched boxplot, notches corresponding approximately to the 95% confidence interval of the median (the notch interval is exactly 1.58 x Inter Quartile Range (IQR) / sqrt(n), with n the number of values that made the box). If notch intervals between two boxes do not overlap, it can be interpreted as significant median differences
-# box.alpha: single numeric value (from 0 to 1) of box transparency (full transparent to full opaque, respectively). To remove boxplots, use box.alpha = 0
-# box.mean: logical. Add mean value? If TRUE, a diamond-shaped dot, with the horizontal diagonal corresponding to the mean value, is displayed over each boxplot
-# box.whisker.kind: range of the whiskers. Either "no" (no whiskers), or "std" (length of each whisker equal to 1.5 x Inter Quartile Range (IQR)), or "max" (length of the whiskers up or down to the most distant dot)
-# box.whisker.width: single numeric value (from 0 to 1) of the whisker width, with 0 meaning no whiskers and 1 meaning a width equal to the box width
-# dot.color: vector of color character string ruling the dot colors and the dot display. See the example section below for easier understanding of the rules described here
-# If NULL, no dots plotted
-# If "same", the dots will have the same colors as the respective boxplots
-# Otherwise, as in the rule (1), (2) or (3) described in the categ.color argument, except that in the possibility (3), the rule "a single color per class of categ and a single class of categ per color", does not have to be respected (for instance, each dot can have a different color). Colors will also depend on the dot.categ argument. If dot.categ is NULL, then colors will be applied to each class of the last column name specified in categ. If dot.categ is non-NULL, colors will be applied to each class of the column name specified in dot.categ. See examples
-# dot.categ: optional single character string of a column name (further referred to as categ3) of the data1 argument. This column of data1 will be used to generate a legend for dots, in addition to the legend for boxes. See the dot.color argument for details about the way the legend is built using the two dot.categ and dot.color arguments. If NULL, no legend created and the colors of dots will depend on dot.color and categ arguments (as explained in the dot.color argument)
-# dot.categ.class.order: optional vector of character strings indicating the order of the classes of categ3 (see the dot.categ argument). If dot.categ is non-NULL and dot.categ.class.order is NULL, classes are displayed in the legend according to the alphabetical order. Ignored if dot.categ is NULL
-# dot.legend.name: optional character string of the legend title for categ3 (see the dot.categ argument). If dot.legend.name == NULL, dot.categ value is used (name of the column in data1). Write "" if no legend required. Ignored if dot.categ is NULL
-# dot.tidy: logical. Nice dot spreading? If TRUE, use the geom_dotplot() function for a nice representation. WARNING: change the true quantitative coordinates of dots (i.e., y-axis values for vertical display) because of binning. Thus, the gain in aestheticism is associated with a loss in precision that can be very important. If FALSE, dots are randomly spread on the qualitative axis, using the dot.jitter argument (see below) keeping the true quantitative coordinates
-# dot.tidy.bin.nb: positive integer indicating the number of bins (i.e., nb of separations) of the y.lim range. Each dot will then be put in one of the bin, with a diameter of the width of the bin. In other words, increase the number of bins to have smaller dots. Not considered if dot.tidy is FALSE
-# dot.jitter: numeric value (from 0 to 1) of random dot horizontal dispersion (for vertical display), with 0 meaning no dispersion and 1 meaning dispersion in the corresponding box width interval. Not considered if dot.tidy is TRUE
-# dot.seed: integer value that set the random seed. Using the same number will generate the same dot jittering. Write NULL to have different jittering each time the same instruction is run. Ignored if dot.tidy is TRUE
-# dot.size: numeric value of dot diameter in mm. Not considered if dot.tidy is TRUE
-# dot.alpha: numeric value (from 0 to 1) of dot transparency (full transparent to full opaque, respectively)
-# dot.border.size: numeric value of border dot width in mm. Write zero for no dot border. If dot.tidy is TRUE, value 0 remove the border and other values leave the border without size control (geom_doplot() feature)
-# dot.border.color: single character color string defining the color of the dot border (same color for all the dots, whatever their categories). If dot.border.color == NULL, the border color will be the same as the dot color. A single integer is also accepted instead of a character string, that will be processed by fun_gg_palette()
-# x.lab: a character string or expression for x-axis legend. If NULL, character string of categ1 (see the categ argument for categ1 and categ2 description)
-# x.angle: integer value of the text angle for the x-axis numbers, using the same rules as in ggplot2. Positive values for counterclockwise rotation: 0 for horizontal, 90 for vertical, 180 for upside down etc. Negative values for clockwise rotation: 0 for horizontal, -90 for vertical, -180 for upside down etc.
-# y.lab: a character string or expression for y-axis legend. If NULL, character string of the y argument
-# y.lim: 2 numeric values indicating the range of the y-axis. Order matters (for inverted axis). If NULL, the range of the x column name of data1 will be used. 
-# y.log: either "no", "log2" (values in the y argument column of the data1 data frame will be log2 transformed and y-axis will be log2 scaled) or "log10" (values in the y argument column of the data1 data frame will be log10 transformed and y-axis will be log10 scaled). WARNING: not possible to have horizontal boxes with a log axis, due to a bug in ggplot2 (see https://github.com/tidyverse/ggplot2/issues/881)
-# y.tick.nb: approximate number of desired values labeling the y-axis (i.e., main ticks, see the n argument of the the cute::fun_scale() function). If NULL and if y.log is "no", then the number of labeling values is set by ggplot2. If NULL and if y.log is "log2" or "log10", then the number of labeling values corresponds to all the exposant integers in the y.lim range (e.g., 10^1, 10^2 and 10^3, meaning 3 main ticks for y.lim = c(9, 1200)). WARNING: if non-NULL and if y.log is "log2" or "log10", labeling can be difficult to read (e.g., ..., 10^2, 10^2.5, 10^3, ...)
-# y.second.tick.nb: number of desired secondary ticks between main ticks. Ignored if y.log is other than "no" (log scale plotted). Use argument return = TRUE and see $plot$y.second.tick.values to have the values associated to secondary ticks. IF NULL, no secondary ticks
-# y.include.zero: logical. Does y.lim range include 0? Ignored if y.log is "log2" or "log10"
-# y.top.extra.margin: single proportion (between 0 and 1) indicating if extra margins must be added to y.lim. If different from 0, add the range of the axis multiplied by y.top.extra.margin (e.g., abs(y.lim[2] - y.lim[1]) * y.top.extra.margin) to the top of y-axis
-# y.bottom.extra.margin: idem as y.top.extra.margin but to the bottom of y-axis
-# stat.pos: add the median number above the corresponding box. Either NULL (no number shown), "top" (at the top of the plot region) or "above" (above each box)
-# stat.mean: logical. Display mean numbers instead of median numbers? Ignored if stat.pos is NULL
-# stat.size: numeric value of the stat font size in mm. Ignored if stat.pos is NULL
-# stat.dist: numeric value of the stat distance in percentage of the y-axis range (stat.dist = 5 means move the number displayed at 5% of the y-axis range). Ignored if stat.pos is NULL or "top"
-# stat.angle: integer value of the angle of stat, using the same rules as in ggplot2. Positive values for counterclockwise rotation: 0 for horizontal, 90 for vertical, 180 for upside down etc. Negative values for clockwise rotation: 0 for horizontal, -90 for vertical, -180 for upside down etc.
-# vertical: logical. Vertical boxes? WARNING: will be automatically set to TRUE if y.log argument is other than "no". Indeed, not possible to have horizontal boxes with a log axis, due to a bug in ggplot2 (see https://github.com/tidyverse/ggplot2/issues/881)
-# text.size: numeric value of the font size of the (1) axis numbers, (2) axis labels and (3) texts in the graphic legend (in mm)
-# title: character string of the graph title
-# title.text.size: numeric value of the title font size in mm
-# legend.show: logical. Show legend? Not considered if categ argument is NULL, because this already generate no legend, excepted if legend.width argument is non-NULL. In that specific case (categ is NULL, legend.show is TRUE and legend.width is non-NULL), an empty legend space is created. This can be useful when desiring graphs of exactly the same width, whatever they have legends or not
-# legend.width: single proportion (between 0 and 1) indicating the relative width of the legend sector (on the right of the plot) relative to the width of the plot. Value 1 means that the window device width is split in 2, half for the plot and half for the legend. Value 0 means no room for the legend, which will overlay the plot region. Write NULL to inactivate the legend sector. In such case, ggplot2 will manage the room required for the legend display, meaning that the width of the plotting region can vary between graphs, depending on the text in the legend
-# article: logical. If TRUE, use an article theme (article like). If FALSE, use a classic related ggplot theme. Use the add argument (e.g., add = "+ggplot2::theme_classic()" for the exact classic ggplot theme
-# grid: logical. Draw lines in the background to better read the box values? Not considered if article == FALSE (grid systematically present)
-# add: character string allowing to add more ggplot2 features (dots, lines, themes, facet, etc.). Ignored if NULL
-# WARNING: (1) the string must start with "+", (2) the string must finish with ")" and (3) each function must be preceded by "ggplot2::". Example: "+ ggplot2::coord_flip() + ggplot2::theme_bw()"
-# If the character string contains the "ggplot2::theme" string, then the article argument of fun_gg_boxplot() (see above) is ignored with a warning. In addition, some arguments can be overwritten, like x.angle (check all the arguments)
-# Handle the add argument with caution since added functions can create conflicts with the preexisting internal ggplot2 functions
-# WARNING: the call of objects inside the quotes of add can lead to an error if the name of these objects are some of the fun_gg_boxplot() arguments. Indeed, the function will use the internal argument instead of the global environment object. Example article <- "a" in the working environment and add = '+ ggplot2::ggtitle(article)'. The risk here is to have TRUE as title. To solve this, use add = '+ ggplot2::ggtitle(get("article", envir = .GlobalEnv))'
-# return: logical. Return the graph parameters?
-# return.ggplot: logical. Return the ggplot object in the output list? Ignored if return argument is FALSE. WARNING: always assign the fun_gg_boxplot() function (e.g., a <- fun_gg_boxplot()) if return.ggplot argument is TRUE, otherwise, double plotting is performed. See $ggplot in the RETURN section below for more details
-# return.gtable: logical. Return the ggplot object as gtable of grobs in the output list? Ignored if plot argument is FALSE. Indeed, the graph must be plotted to get the grobs dispositions. See $gtable in the RETURN section below for more details
-# plot: logical. Plot the graphic? If FALSE and return argument is TRUE, graphical parameters and associated warnings are provided without plotting
-# warn.print: logical. Print warnings at the end of the execution? ? If FALSE, warning messages are never printed, but can still be recovered in the returned list. Some of the warning messages (those delivered by the internal ggplot2 functions) are not apparent when using the argument plot = FALSE
-# lib.path: character string indicating the absolute path of the required packages (see below). if NULL, the function will use the R library default folders
-# RETURN
-# A boxplot if plot argument is TRUE
-# A list of the graph info if return argument is TRUE:
-# $data: the initial data with graphic information added
-# $stat: the graphic statistics (mostly equivalent to ggplot_build()$data[[2]])
-# $removed.row.nb: which rows have been removed due to NA/Inf detection in y and categ columns (NULL if no row removed)
-# $removed.rows: removed rows (NULL if no row removed)
-# $plot: the graphic box and dot coordinates
-# $dots: dot coordinates
-# $main.box: coordinates of boxes
-# $median: median coordinates
-# $sup.whisker: coordinates of top whiskers (y for base and y.end for extremities)
-# $inf.whisker: coordinates of bottom whiskers (y for base and y.end for extremities)
-# $sup.whisker.edge: coordinates of top whisker edges (x and xend)
-# $inf.whisker.edge: coordinates of bottom whisker edges(x and xend)
-# $mean: diamond mean coordinates (only if box.mean argument is TRUE)
-# $stat.pos: coordinates of stat numbers (only if stat.pos argument is not NULL)
-# y.second.tick.positions: coordinates of secondary ticks (only if y.second.tick.nb argument is non-NULL or if y.log argument is different from "no")
-# y.second.tick.values: values of secondary ticks. NULL except if y.second.tick.nb argument is non-NULL or if y.log argument is different from "no")
-# $panel: the variable names used for the panels (NULL if no panels). WARNING: NA can be present according to ggplot2 upgrade to v3.3.0
-# $axes: the x-axis and y-axis info
-# $warn: the warning messages. Use cat() for proper display. NULL if no warning. WARNING: warning messages delivered by the internal ggplot2 functions are not apparent when using the argument plot = FALSE
-# $ggplot: ggplot object that can be used for reprint (use print(...$ggplot) or update (use ...$ggplot + ggplot2::...). NULL if return.ggplot argument is FALSE. Of note, a non-NULL $ggplot in the output list is sometimes annoying as the manipulation of this list prints the plot
-# $gtable: gtable object that can be used for reprint (use gridExtra::grid.arrange(...$ggplot) or with additionnal grobs (see the grob decomposition in the examples). NULL if return.ggplot argument is FALSE. Contrary to $ggplot, a non-NULL $gtable in the output list is not annoying as the manipulation of this list does not print the plot
-# REQUIRED PACKAGES
-# ggplot2
-# gridExtra
-# lemon (in case of use in the add argument)
-# scales
-# REQUIRED FUNCTIONS FROM THE cute PACKAGE
-# fun_check()
-# fun_comp_1d()
-# fun_comp_2d()
-# fun_gg_just()
-# fun_gg_palette()
-# fun_inter_ticks()
-# fun_name_change()
-# fun_pack()
-# fun_round()
-# fun_scale()
-# EXAMPLE
-# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(20, 100, 10), rnorm(20, 200, 50), rnorm(20, 500, 60), rnorm(20, 100, 50)), Categ1 = rep(c("CAT", "DOG"), times = 40), Categ2 = rep(c("A", "B", "C", "D"), each = 20), Color1 = rep(c("coral", "lightblue"), times = 40), Color2 = rep(c("#9F2108", "#306100", "#007479", "#8500C0"), each = 20), stringsAsFactors = TRUE) ; set.seed(NULL) ; fun_gg_boxplot(data1 = obs1, y = "Time", categ = "Categ1")
-# see http
-# DEBUGGING
-# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Categ1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; set.seed(NULL) ; obs1$Time[1:10] <- NA ; data1 = obs1 ; y = "Time" ; categ = c("Categ1") ; categ.class.order = NULL ; categ.color = NULL ; box.legend.name = NULL ; box.fill = FALSE ; box.width = 0.5 ; box.space = 0.1 ; box.line.size = 0.75 ; box.notch = FALSE ; box.alpha = 1 ; box.mean = TRUE ; box.whisker.kind = "std" ; box.whisker.width = 0 ; dot.color = grey(0.25) ; dot.categ = NULL ; dot.categ.class.order = NULL ; dot.legend.name = NULL ; dot.tidy = FALSE ; dot.tidy.bin.nb = 50 ; dot.jitter = 0.5 ; dot.seed = 2 ; dot.size = 3 ; dot.alpha = 0.5 ; dot.border.size = 0.5 ; dot.border.color = NULL ; x.lab = NULL ; x.angle = 0 ; y.lab = NULL ; y.lim = NULL ; y.log = "no" ; y.tick.nb = NULL ; y.second.tick.nb = 1 ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0.05 ; stat.pos = "top" ; stat.mean = FALSE ; stat.size = 4 ; stat.dist = 5 ; stat.angle = 0 ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; legend.show = TRUE ; legend.width = 0.5 ; article = TRUE ; grid = FALSE ; add = NULL ; return = FALSE ; return.ggplot = FALSE ; return.gtable = TRUE ; plot = TRUE ; warn.print = FALSE ; lib.path = NULL
-# function name
-function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
-arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
-# end function name
-# required function checking
-req.function <- c(
-"fun_comp_2d", 
-"fun_gg_just", 
-"fun_gg_palette", 
-"fun_name_change", 
-"fun_pack", 
-"fun_check", 
-"fun_round", 
-"fun_scale",
-"fun_inter_ticks"
-)
-tempo <- NULL
-for(i1 in req.function){
-if(length(find(i1, mode = "function")) == 0L){
-tempo <- c(tempo, i1)
-}
-}
-if( ! is.null(tempo)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# reserved words to avoid bugs (names of dataframe columns used in this function)
-reserved.words <- c("categ.check", "categ.color", "dot.color", "dot.categ", "dot.max", "dot.min", "group", "PANEL", "group.check", "MEAN", "tempo.categ1", "tempo.categ2", "text.max.pos", "text.min.pos", "x", "x.y", "y", "y.check", "y_from.dot.max", "ymax", "tidy_group", "binwidth")
-# end reserved words to avoid bugs (used in this function)
-# arg with no default values
-mandat.args <- c(
-"data1", 
-"y", 
-"categ"
-)
-tempo <- eval(parse(text = paste0("missing(", paste0(mandat.args, collapse = ") | missing("), ")")))
-if(any(tempo)){ # normally no NA for missing() output
-tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(length(mandat.args) > 1, "S HAVE", "HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end arg with no default values
-# argument primary checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo <- fun_check(data = data1, class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = categ, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-if( ! is.null(categ.class.order)){
-tempo <- fun_check(data = categ.class.order, class = "list", fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = categ.class.order, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(box.legend.name)){
-tempo <- fun_check(data = box.legend.name, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = box.legend.name, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(categ.color)){
-tempo1 <- fun_check(data = categ.color, class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name)
-tempo2 <- fun_check(data = categ.color, class = "factor", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.check.color <- fun_check(data = categ.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, neg.values = FALSE, fun.name = function.name)$problem
-if(tempo.check.color == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg.color ARGUMENT MUST BE A FACTOR OR CHARACTER VECTOR OR POSITVE INTEGER VECTOR") # integer possible because dealt above
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(any(categ.color == 0L, na.rm = TRUE)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg.color ARGUMENT MUST BE A FACTOR OR CHARACTER VECTOR OR POSITVE INTEGER VECTOR") # integer possible because dealt above
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = categ.color, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = box.fill, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = box.width, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = box.space, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = box.line.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = box.notch, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = box.alpha, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = box.mean, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = box.whisker.kind, options = c("no", "std", "max"), length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = box.whisker.width, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(dot.color)){
-tempo1 <- fun_check(data = dot.color, class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name)
-tempo2 <- fun_check(data = dot.color, class = "factor", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.check.color <- fun_check(data = dot.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, neg.values = FALSE, fun.name = function.name)$problem
-if(tempo.check.color == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.color MUST BE A FACTOR OR CHARACTER VECTOR OR POSITVE INTEGER VECTOR") # integer possible because dealt above
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(any(dot.color == 0L, na.rm = TRUE)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.color ARGUMENT MUST BE A FACTOR OR CHARACTER VECTOR OR POSITVE INTEGER VECTOR") # integer possible because dealt above
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = dot.color, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(dot.categ)){
-tempo <- fun_check(data = dot.categ, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = dot.categ, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(dot.categ.class.order)){
-tempo <- fun_check(data = dot.categ.class.order, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = dot.categ.class.order, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(dot.legend.name)){
-tempo <- fun_check(data = dot.legend.name, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = dot.legend.name, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = dot.tidy, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = dot.tidy.bin.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if(dot.tidy.bin.nb == 0L){ # length and NA checked above
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.tidy.bin.nb ARGUMENT MUST BE A NON-NULL AND POSITVE INTEGER VALUE") # integer possible because dealt above
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-tempo <- fun_check(data = dot.jitter, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(dot.seed)){
-tempo <- fun_check(data = dot.seed, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = TRUE, fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = dot.seed, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = dot.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = dot.alpha, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = dot.border.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-if( ! is.null(dot.border.color)){
-tempo1 <- fun_check(data = dot.border.color, class = "vector", mode = "character", length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = dot.border.color, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.border.color ARGUMENT MUST BE (1) A HEXADECIMAL COLOR STRING STARTING BY #, OR (2) A COLOR NAME GIVEN BY colors(), OR (3) AN INTEGER VALUE")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}else if(tempo1$problem == FALSE & tempo2$problem == TRUE){
-if( ! all(dot.border.color %in% colors() | grepl(pattern = "^#", dot.border.color), na.rm = TRUE)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.border.color ARGUMENT MUST BE (1) A HEXADECIMAL COLOR STRING STARTING BY #, OR (2) A COLOR NAME GIVEN BY colors(), OR (3) AN INTEGER VALUE")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = dot.border.color, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(x.lab)){
-tempo1 <- fun_check(data = x.lab, class = "expression", length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = x.lab,  class = "vector", mode = "character", length = 1, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nx.lab ARGUMENT MUST BE A SINGLE CHARACTER STRING OR EXPRESSION")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = x.lab, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = x.angle, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, neg.values = TRUE, fun.name = function.name) ; eval(ee)
-if( ! is.null(y.lab)){
-tempo1 <- fun_check(data = y.lab, class = "expression", length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = y.lab,  class = "vector", mode = "character", length = 1, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lab ARGUMENT MUST BE A SINGLE CHARACTER STRING OR EXPRESSION")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = y.lab, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(y.lim)){
-tempo <- fun_check(data = y.lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if(any(is.infinite(y.lim))){ # normally no NA for is.infinite() output
-tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = y.lim, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = y.log, options = c("no", "log2", "log10"), length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(y.tick.nb)){
-tempo <- fun_check(data = y.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if(y.tick.nb < 0){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ny.tick.nb ARGUMENT MUST BE A NON NULL POSITIVE INTEGER")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = y.tick.nb, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(y.second.tick.nb)){
-tempo <- fun_check(data = y.second.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if(y.second.tick.nb <= 0){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ny.second.tick.nb ARGUMENT MUST BE A NON NULL POSITIVE INTEGER")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = y.second.tick.nb, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = y.include.zero, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y.top.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y.bottom.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(stat.pos)){
-tempo <- fun_check(data = stat.pos, options = c("top", "above"), length = 1, fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = stat.pos, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = stat.mean, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = stat.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = stat.dist, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = stat.angle, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, neg.values = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = vertical, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = title, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = title.text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = legend.show, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(legend.width)){
-tempo <- fun_check(data = legend.width, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = legend.width, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = article, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = grid, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(add)){
-tempo <- fun_check(data = add, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = add, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = return, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = return.ggplot, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = return.gtable, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = plot, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(lib.path)){
-tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if( ! all(dir.exists(lib.path), na.rm = TRUE)){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, "\nDIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = lib.path, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if(any(arg.check) == TRUE){ # normally no NA
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between == #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument primary checking
-# second round of checking and data preparation
-# management of NA arguments
-tempo.arg <- names(arg.user.setting) # values provided by the user
-tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
-if(any(tempo.log) == TRUE){ # normally no NA because is.na() used here
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT JUST BE NA")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NA arguments
-# management of NULL arguments
-tempo.arg <-c(
-"data1", 
-"y", 
-"categ", 
-"box.fill", 
-"box.width", 
-"box.space", 
-"box.line.size", 
-"box.notch", 
-"box.alpha", 
-"box.mean", 
-"box.whisker.kind", 
-"box.whisker.width", 
-# "dot.color", # inactivated because can be null
-"dot.tidy", 
-"dot.tidy.bin.nb", 
-"dot.jitter", 
-# "dot.seed", # inactivated because can be null
-"dot.size", 
-"dot.alpha", 
-"dot.border.size", 
-"x.angle", 
-"y.log", 
-# "y.second.tick.nb", # inactivated because can be null
-"y.include.zero", 
-"y.top.extra.margin", 
-"y.bottom.extra.margin", 
-# "stat.pos", # inactivated because can be null
-"stat.mean", 
-"stat.size", 
-"stat.dist", 
-"stat.angle", 
-"vertical", 
-"text.size", 
-"title", 
-"title.text.size", 
-"legend.show", 
-# "legend.width", # inactivated because can be null
-"article", 
-"grid", 
-"return", 
-"return.ggplot", 
-"return.gtable", 
-"plot", 
-"warn.print"
-)
-tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
-if(any(tempo.log) == TRUE){# normally no NA with is.null()
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NULL arguments
-# code that protects set.seed() in the global environment
-# see also Protocol 100-rev0 Parallelization in R.docx
-if(exists(".Random.seed", envir = .GlobalEnv)){ # if .Random.seed does not exists, it means that no random operation has been performed yet in any R environment
-tempo.random.seed <- .Random.seed
-on.exit(assign(".Random.seed", tempo.random.seed, env = .GlobalEnv))
-}else{
-on.exit(set.seed(NULL)) # inactivate seeding -> return to complete randomness
-}
-set.seed(dot.seed)
-# end code that protects set.seed() in the global environment
-# warning initiation
-ini.warning.length <- options()$warning.length
-options(warning.length = 8170)
-warn <- NULL
-warn.count <- 0
-# end warning initiation
-# other checkings
-if(any(duplicated(names(data1)), na.rm = TRUE)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nDUPLICATED COLUMN NAMES OF data1 ARGUMENT NOT ALLOWED:\n", paste(names(data1)[duplicated(names(data1))], collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! (y %in% names(data1))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ny ARGUMENT MUST BE A COLUMN NAME OF data1")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-tempo <- fun_check(data = data1[, y], data.name = "y COLUMN OF data1", class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name)
-if(tempo$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ny ARGUMENT MUST BE NUMERIC COLUMN IN data1")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if(length(categ) > 2){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg ARGUMENT CANNOT HAVE MORE THAN 2 COLUMN NAMES OF data1")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if( ! all(categ %in% names(data1))){ # all() without na.rm -> ok because categ cannot be NA (tested above)
-tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg ARGUMENT MUST BE COLUMN NAMES OF data1. HERE IT IS:\n", paste(categ, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(length(dot.categ) > 1){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ ARGUMENT CANNOT HAVE MORE THAN 1 COLUMN NAMES OF data1")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if( ! all(dot.categ %in% names(data1))){ # all() without na.rm -> ok because dot.categ cannot be NA (tested above)
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ ARGUMENT MUST BE COLUMN NAMES OF data1. HERE IT IS:\n", paste(dot.categ, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# reserved word checking
-if(any(names(data1) %in% reserved.words, na.rm = TRUE)){
-if(any(duplicated(names(data1)), na.rm = TRUE)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nDUPLICATED COLUMN NAMES OF data1 ARGUMENT NOT ALLOWED:\n", paste(names(data1)[duplicated(names(data1))], collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! is.null(dot.categ)){
-if(dot.categ %in% categ){
-reserved.words <- c(reserved.words, paste0(dot.categ, "_DOT")) # paste0(dot.categ, "_DOT") is added to the reserved words because in such situation, a new column will be added to data1 that is named paste0(dot.categ, "_DOT")
-}
-}
-tempo.output <- fun_name_change(names(data1), reserved.words)
-for(i2 in 1:length(tempo.output$ini)){ # a loop to be sure to take the good ones
-names(data1)[names(data1) == tempo.output$ini[i2]] <- tempo.output$post[i2]
-if(any(y == tempo.output$ini[i2])){ # any() without na.rm -> ok because y cannot be NA (tested above)
-y[y == tempo.output$ini[i2]] <- tempo.output$post[i2]
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN y ARGUMENT (COLUMN NAMES OF data1 ARGUMENT),\n", tempo.output$ini[i2], " HAS BEEN REPLACED BY ", tempo.output$post[i2], "\nBECAUSE RISK OF BUG AS SOME NAMES IN y ARGUMENT ARE RESERVED WORD USED BY THE ", function.name, " FUNCTION")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# WARNING: names of y argument potentially replaced
-if(any(categ == tempo.output$ini[i2])){ # any() without na.rm -> ok because categ cannot be NA (tested above)
-categ[categ == tempo.output$ini[i2]] <- tempo.output$post[i2]
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN categ ARGUMENT (COLUMN NAMES OF data1 ARGUMENT),\n", tempo.output$ini[i2], " HAS BEEN REPLACED BY ", tempo.output$post[i2], "\nBECAUSE RISK OF BUG AS SOME NAMES IN categ ARGUMENT ARE RESERVED WORD USED BY THE ", function.name, " FUNCTION")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# WARNING: names of categ argument potentially replaced
-if( ! is.null(dot.categ)){
-if(any(dot.categ == tempo.output$ini[i2])){ # any() without na.rm -> ok because dot.categ cannot be NA (tested above)
-dot.categ[dot.categ == tempo.output$ini[i2]] <- tempo.output$post[i2]
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN dot.categ ARGUMENT (COLUMN NAMES OF data1 ARGUMENT),\n", tempo.output$ini[i2], " HAS BEEN REPLACED BY ", tempo.output$post[i2], "\nBECAUSE RISK OF BUG AS SOME NAMES IN dot.categ ARGUMENT ARE RESERVED WORD USED BY THE ", function.name, " FUNCTION")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# WARNING: names of dot.categ argument potentially replaced
-}
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") REGARDING COLUMN NAMES REPLACEMENT, THE NAMES\n", paste(tempo.output$ini, collapse = " "), "\nHAVE BEEN REPLACED BY\n", paste(tempo.output$post, collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-if( ! (is.null(add) | is.null(tempo.output$ini))){
-if(grepl(x = add, pattern = paste(tempo.output$ini, collapse = "|"))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nDETECTION OF COLUMN NAMES OF data1 IN THE add ARGUMENT STRING, THAT CORRESPOND TO RESERVED STRINGS FOR ", function.name, "\nCOLUMN NAMES HAVE TO BE CHANGED\nTHE PROBLEMATIC COLUMN NAMES ARE SOME OF THESE NAMES:\n", paste(tempo.output$ini, collapse = " "), "\nIN THE DATA FRAME OF data1 AND IN THE STRING OF add ARGUMENT, TRY TO REPLACE NAMES BY:\n", paste(tempo.output$post, collapse = " "), "\n\nFOR INFORMATION, THE RESERVED WORDS ARE:\n", paste(reserved.words, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-}
-if( ! (is.null(add))){
-if(any(sapply(X = arg.names, FUN = grepl, x = add), na.rm = TRUE)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NAMES OF ", function.name, " ARGUMENTS DETECTED IN THE add STRING:\n", paste(arg.names[sapply(X = arg.names, FUN = grepl, x = add)], collapse = "\n"), "\nRISK OF WRONG OBJECT USAGE INSIDE ", function.name)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# end reserved word checking
-# verif of add
-if( ! is.null(add)){
-if( ! grepl(pattern = "^\\s*\\+", add)){ # check that the add string start by +
-tempo.cat <- paste0("ERROR IN ", function.name, "\nadd ARGUMENT MUST START WITH \"+\": ", paste(unique(add), collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if( ! grepl(pattern = "(ggplot2|lemon)\\s*::", add)){ #
-tempo.cat <- paste0("ERROR IN ", function.name, "\nFOR EASIER FUNCTION DETECTION, add ARGUMENT MUST CONTAIN \"ggplot2::\" OR \"lemon::\" IN FRONT OF EACH GGPLOT2 FUNCTION: ", paste(unique(add), collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if( ! grepl(pattern = ")\\s*$", add)){ # check that the add string finished by )
-tempo.cat <- paste0("ERROR IN ", function.name, "\nadd ARGUMENT MUST FINISH BY \")\": ", paste(unique(add), collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end verif of add
-# management of add containing facet
-facet.categ <- NULL
-if( ! is.null(add)){
-facet.check <- TRUE
-tempo <- unlist(strsplit(x = add, split = "\\s*\\+\\s*(ggplot2|lemon)\\s*::\\s*")) #
-tempo <- sub(x = tempo, pattern = "^facet_wrap", replacement = "ggplot2::facet_wrap")
-tempo <- sub(x = tempo, pattern = "^facet_grid", replacement = "ggplot2::facet_grid")
-tempo <- sub(x = tempo, pattern = "^facet_rep", replacement = "lemon::facet_rep")
-if(any(grepl(x = tempo, pattern = "ggplot2::facet_wrap|lemon::facet_rep_wrap"), na.rm = TRUE)){
-tempo1 <- suppressWarnings(eval(parse(text = tempo[grepl(x = tempo, pattern = "ggplot2::facet_wrap|lemon::facet_rep_wrap")])))
-facet.categ <- names(tempo1$params$facets)
-tempo.text <- "facet_wrap OR facet_rep_wrap"
-facet.check <- FALSE
-}else if(grepl(x = add, pattern = "ggplot2::facet_grid|lemon::facet_rep_grid")){
-tempo1 <- suppressWarnings(eval(parse(text = tempo[grepl(x = tempo, pattern = "ggplot2::facet_grid|lemon::facet_rep_grid")])))
-facet.categ <- c(names(tempo1$params$rows), names(tempo1$params$cols))
-tempo.text <- "facet_grid OR facet_rep_grid"
-facet.check <- FALSE
-}
-if(facet.check == FALSE & ! all(facet.categ %in% names(data1))){ # WARNING: all(facet.categ %in% names(data1)) is TRUE when facet.categ is NULL # all() without na.rm -> ok because facet.categ cannot be NA (tested above)
-tempo.cat <- paste0("ERROR IN ", function.name, "\nDETECTION OF \"", tempo.text, "\" STRING IN THE add ARGUMENT BUT PROBLEM OF VARIABLE DETECTION (COLUMN NAMES OF data1)\nTHE DETECTED VARIABLES ARE:\n", paste(facet.categ, collapse = " "), "\nTHE data1 COLUMN NAMES ARE:\n", paste(names(data1), collapse = " "), "\nPLEASE REWRITE THE add STRING AND RERUN")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end management of add containing facet
-# conversion of categ columns in data1 into factors
-for(i1 in 1:length(categ)){
-tempo1 <- fun_check(data = data1[, categ[i1]], data.name = paste0("categ NUMBER ", i1, " OF data1"), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name)
-tempo2 <- fun_check(data = data1[, categ[i1]], data.name = paste0("categ NUMBER ", i1, " OF data1"), class = "factor", na.contain = TRUE, fun.name = function.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\n", paste0("categ NUMBER ", i1, " OF data1"), " MUST BE A FACTOR OR CHARACTER VECTOR")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(tempo1$problem == FALSE){ # character vector
-if(box.alpha != 0){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN categ NUMBER ", i1, " IN data1, THE CHARACTER COLUMN HAS BEEN CONVERTED TO FACTOR, WITH LEVELS ACCORDING TO THE ALPHABETICAL ORDER")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-data1[, categ[i1]] <- factor(data1[, categ[i1]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
-}
-# OK: all the categ columns of data1 are factors from here
-# end conversion of categ columns in data1 into factors
-
-
-
-# management of log scale and Inf removal
-if(any(( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])))){ # is.finite also detects NA: ( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])) detects only Inf  # normally no NA with is.finite0() and is.na()
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") PRESENCE OF -Inf OR Inf VALUES IN THE ", y, " COLUMN OF THE data1 ARGUMENT AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-data1.ini <- data1 # strictly identical to data1 except that in data1 y is log converted if and only if y.log != "no"
-if(y.log != "no"){
-tempo1 <- ! is.finite(data1[, y]) # where are initial NA and Inf
-data1[, y] <- suppressWarnings(get(y.log)(data1[, y]))# no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-if(any( ! (tempo1 | is.finite(data1[, y])))){ # normally no NA with is.finite
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") LOG CONVERSION INTRODUCED -Inf OR Inf OR NaN VALUES IN THE ", y, " COLUMN OF THE data1 ARGUMENT AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# Inf removal
-if(any(( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])))){ # is.finite also detects NA: ( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])) detects only Inf # normally no NA with is.finite
-removed.row.nb <- which(( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])))
-removed.rows <- data1.ini[removed.row.nb, ] # here data1.ini used to have the y = O rows that will be removed because of Inf creation after log transformation
-data1 <- data1[-removed.row.nb, ] #
-data1.ini <- data1.ini[-removed.row.nb, ] #
-}else{
-removed.row.nb <- NULL
-removed.rows <- data.frame(stringsAsFactors = FALSE)
-}
-# From here, data1 and data.ini have no more Inf
-# end Inf removal
-if(y.log != "no" & ! is.null(y.lim)){
-if(any(y.lim <= 0)){ # any() without na.rm -> ok because y.lim cannot be NA (tested above)
-tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT CANNOT HAVE ZERO OR NEGATIVE VALUES WITH THE y.log ARGUMENT SET TO ", y.log, ":\n", paste(y.lim, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(any( ! is.finite(if(y.log == "log10"){log10(y.lim)}else{log2(y.lim)}))){ # normally no NA with is.finite
-tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT RETURNS INF/NA WITH THE y.log ARGUMENT SET TO ", y.log, "\nAS SCALE COMPUTATION IS ", ifelse(y.log == "log10", "log10", "log2"), ":\n", paste(if(y.log == "log10"){log10(y.lim)}else{log2(y.lim)}, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if(y.log != "no" & y.include.zero == TRUE){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") y.log ARGUMENT SET TO ", y.log, " AND y.include.zero ARGUMENT SET TO TRUE -> y.include.zero ARGUMENT RESET TO FALSE BECAUSE 0 VALUE CANNOT BE REPRESENTED IN LOG SCALE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-y.include.zero <- FALSE
-}
-if(y.log != "no" & vertical == FALSE){
-vertical <- TRUE
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") BECAUSE OF A BUG IN ggplot2, CANNOT FLIP BOXES HORIZONTALLY WITH A Y.LOG SCALE -> vertical ARGUMENT RESET TO TRUE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# end management of log scale and Inf removal
-# na detection and removal (done now to be sure of the correct length of categ)
-column.check <- unique(c(y, categ, if( ! is.null(dot.color) & ! is.null(dot.categ)){dot.categ}, if( ! is.null(facet.categ)){facet.categ})) # dot.categ because can be a 3rd column of data1, categ.color and dot.color will be tested later
-if(any(is.na(data1[, column.check]))){ # data1 used here instead of data1.ini in case of new NaN created by log conversion (neg values) # normally no NA with is.na
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NA DETECTED IN COLUMNS OF data1 AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-for(i2 in 1:length(column.check)){
-if(any(is.na(data1[, column.check[i2]]))){ # normally no NA with is.na
-tempo.warn <- paste0("NA REMOVAL DUE TO COLUMN ", column.check[i2], " OF data1")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n", tempo.warn)))
-}
-}
-tempo <- unique(unlist(lapply(lapply(c(data1[column.check]), FUN = is.na), FUN = which)))
-removed.row.nb <- c(removed.row.nb, tempo) # removed.row.nb created to remove Inf
-removed.rows <- rbind(removed.rows, data1.ini[tempo, ], stringsAsFactors = FALSE) # here data1.ini used to have the non NA rows that will be removed because of NAN creation after log transformation (neg values for instance)
-column.check <- column.check[ ! column.check == y] # remove y to keep quali columns
-if(length(tempo) != 0){
-data1 <- data1[-tempo, ] # WARNING tempo here and not removed.row.nb because the latter contain more numbers thant the former
-data1.ini <- data1.ini[-tempo, ] # WARNING tempo here and not removed.row.nb because the latter contain more numbers than the former
-for(i3 in 1:length(column.check)){
-if(any( ! unique(removed.rows[, column.check[i3]]) %in% unique(data1[, column.check[i3]]), na.rm = TRUE)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN COLUMN ", column.check[i3], " OF data1, THE FOLLOWING CLASSES HAVE DISAPPEARED AFTER NA/Inf REMOVAL (IF COLUMN USED IN THE PLOT, THIS CLASS WILL NOT BE DISPLAYED):\n", paste(unique(removed.rows[, column.check[i3]])[ ! unique(removed.rows[, column.check[i3]]) %in% unique(data1[, column.check[i3]])], collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-}
-count.categ <- 0
-for(i2 in 1:length(column.check)){
-if(column.check[i2] %in% categ){
-count.categ <- count.categ + 1
-}
-if(column.check[i2] == categ[count.categ]){
-categ.class.order[count.categ] <- list(levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]])]) # remove the absent color in the character vector
-data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = unique(categ.class.order[[count.categ]]))
-}
-if( ! is.null(dot.color) & ! is.null(dot.categ)){ # reminder : dot.categ cannot be a column name of categ anymore (because in that case dot.categ name is changed into "..._DOT"
-if(column.check[i2] == dot.categ){
-dot.categ.class.order <- levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]])] # remove the absent color in the character vector
-data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = unique(dot.categ.class.order))
-}
-}
-if(column.check[i2] %in% facet.categ){ # works if facet.categ == NULL this method should keep the order of levels when removing some levels
-tempo.levels <- levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(as.character(data1[, column.check[i2]]))]
-data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = tempo.levels)
-}
-}
-}
-# end na detection and removal (done now to be sure of the correct length of categ)
-# From here, data1 and data.ini have no more NA or NaN in y, categ, dot.categ (if dot.color != NULL) and facet.categ
-
-
-
-if( ! is.null(categ.class.order)){
-if(length(categ.class.order) != length(categ)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg.class.order ARGUMENT MUST BE A LIST OF LENGTH EQUAL TO LENGTH OF categ\nHERE IT IS LENGTH: ", length(categ.class.order), " VERSUS ", length(categ))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-for(i3 in 1:length(categ.class.order)){
-if(is.null(categ.class.order[[i3]])){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE categ.class.order COMPARTMENT ", i3, " IS NULL. ALPHABETICAL ORDER WILL BE APPLIED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-data1[, categ[i3]] <- factor(as.character(data1[, categ[i3]])) # if already a factor, change nothing, if characters, levels according to alphabetical order
-categ.class.order[[i3]] <- levels(data1[, categ[i3]]) # character vector that will be used later
-}else{
-tempo <- fun_check(data = categ.class.order[[i3]], data.name = paste0("COMPARTMENT ", i3 , " OF categ.class.order ARGUMENT"), class = "vector", mode = "character", length = length(levels(data1[, categ[i3]])), fun.name = function.name) # length(data1[, categ[i1]) -> if data1[, categ[i1] was initially character vector, then conversion as factor after the NA removal, thus class number ok. If data1[, categ[i1] was initially factor, no modification after the NA removal, thus class number ok
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if(any(duplicated(categ.class.order[[i3]]), na.rm = TRUE)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nCOMPARTMENT ", i3, " OF categ.class.order ARGUMENT CANNOT HAVE DUPLICATED CLASSES: ", paste(categ.class.order[[i3]], collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if( ! (all(categ.class.order[[i3]] %in% unique(data1[, categ[i3]]), na.rm = TRUE) & all(unique(data1[, categ[i3]]) %in% categ.class.order[[i3]], na.rm = TRUE))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nCOMPARTMENT ", i3, " OF categ.class.order ARGUMENT MUST BE CLASSES OF ELEMENT ", i3, " OF categ ARGUMENT\nHERE IT IS:\n", paste(categ.class.order[[i3]], collapse = " "), "\nFOR COMPARTMENT ", i3, " OF categ.class.order AND IT IS:\n", paste(unique(data1[, categ[i3]]), collapse = " "), "\nFOR COLUMN ", categ[i3], " OF data1")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-data1[, categ[i3]] <- factor(data1[, categ[i3]], levels = categ.class.order[[i3]]) # reorder the factor
-
-}
-names(categ.class.order)[i3] <- categ[i3]
-}
-}
-}else{
-categ.class.order <- vector("list", length = length(categ))
-tempo.categ.class.order <- NULL
-for(i2 in 1:length(categ.class.order)){
-categ.class.order[[i2]] <- levels(data1[, categ[i2]])
-names(categ.class.order)[i2] <- categ[i2]
-tempo.categ.class.order <- c(tempo.categ.class.order, ifelse(i2 != 1, "\n", ""), categ.class.order[[i2]])
-}
-if(box.alpha != 0){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE categ.class.order SETTING IS NULL. ALPHABETICAL ORDER WILL BE APPLIED FOR BOX ORDERING:\n", paste(tempo.categ.class.order, collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# categ.class.order not NULL anymore (list)
-if(is.null(box.legend.name) & box.alpha != 0){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE box.legend.name SETTING IS NULL. NAMES OF categ WILL BE USED: ", paste(categ, collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-box.legend.name <- categ[length(categ)] # if only categ1, then legend name of categ1, if length(categ) == 2L, then legend name of categ2
-}
-# box.legend.name not NULL anymore (character string)
-# management of categ.color
-if( ! is.null(categ.color)){
-# check the nature of color
-# integer colors into gg_palette
-tempo.check.color <- fun_check(data = categ.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name)$problem
-if(tempo.check.color == FALSE){
-# convert integers into colors
-categ.color <- fun_gg_palette(max(categ.color, na.rm = TRUE))[categ.color]
-}
-# end integer colors into gg_palette
-if( ! (all(categ.color %in% colors() | grepl(pattern = "^#", categ.color)))){ # check that all strings of low.color start by #, # all() without na.rm -> ok because categ.color cannot be NA (tested above)
-tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg.color ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors(): ", paste(unique(categ.color), collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(is.na(categ.color)) & box.alpha != 0){ # normally no NA with is.na
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") categ.color ARGUMENT CONTAINS NA")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# end check the nature of color
-# check the length of color
-categ.len <- length(categ) # if only categ1, then colors for classes of categ1, if length(categ) == 2L, then colors for classes of categ2
-if(length(data1[, categ[categ.len]]) == length(levels(data1[, categ[categ.len]])) & length(categ.color) == length(data1[, categ[categ.len]])){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE NUMBER OF CLASSES OF THE COLUMN ", categ[categ.len], " THE NUMBER OF ROWS OF THIS COLUMN AND THE NUMBER OF COLORS OF THE categ.color ARGUMENT ARE ALL EQUAL. BOX COLORS WILL BE ATTRIBUTED ACCORDING THE LEVELS OF ", categ[categ.len], ", NOT ACCORDING TO THE ROWS OF ", categ[categ.len])
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if(length(categ.color) == length(levels(data1[, categ[categ.len]]))){ # here length(categ.color) is equal to the different number of categ
-# data1[, categ[categ.len]] <- factor(data1[, categ[categ.len]]) # not required because sure that is is a factor
-data1 <- data.frame(data1, categ.color = data1[, categ[categ.len]], stringsAsFactors = TRUE)  # no need stringsAsFactors here for stat.nolog as factors remain factors
-data1$categ.color <- factor(data1$categ.color, labels = categ.color) # replace the characters of data1[, categ[categ.len]] put in the categ.color column by the categ.color (can be write like this because categ.color is length of levels of data1[, categ[categ.len]])
-if(box.alpha != 0){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN ", categ[categ.len], " OF categ ARGUMENT, THE FOLLOWING COLORS:\n", paste(categ.color, collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(factor(data1[, categ[categ.len]])), collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else if(length(categ.color) == length(data1[, categ[categ.len]])){# here length(categ.color) is equal to nrow(data1) -> Modif to have length(categ.color) equal to the different number of categ (length(categ.color) == length(levels(data1[, categ[categ.len]])))
-data1 <- data.frame(data1, categ.color = categ.color, stringsAsFactors = TRUE)
-tempo.check <- unique(data1[ , c(categ[categ.len], "categ.color")])
-if( ! (nrow(tempo.check) == length(unique(categ.color)) & nrow(tempo.check) == length(unique(data1[ , categ[categ.len]])))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg.color ARGUMENT HAS THE LENGTH OF data1 ROW NUMBER\nBUT IS INCORRECTLY ASSOCIATED TO EACH CLASS OF categ ", categ[categ.len], ":\n", paste(unique(mapply(FUN = "paste", data1[ ,categ[categ.len]], data1[ ,"categ.color"])), collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-# data1[, categ[categ.len]] <- factor(data1[, categ[categ.len]]) # not required because sure that is is a factor
-categ.color <- unique(data1$categ.color[order(data1[, categ[categ.len]])]) # Modif to have length(categ.color) equal to the different number of categ (length(categ.color) == length(levels(data1[, categ[categ.len]])))
-if(box.alpha != 0){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") categ.color ARGUMENT HAS THE LENGTH OF data1 ROW NUMBER\nCOLORS HAVE BEEN RESPECTIVELY ASSOCIATED TO EACH CLASS OF categ ", categ[categ.len], " AS:\n", paste(levels(factor(data1[, categ[categ.len]])), collapse = " "), "\n", paste(categ.color, collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-}else if(length(categ.color) == 1L){
-# data1[, categ[categ.len]] <- factor(data1[, categ[categ.len]]) # not required because sure that is is a factor
-data1 <- data.frame(data1, categ.color = categ.color, stringsAsFactors = TRUE)
-categ.color <- rep(categ.color, length(levels(data1[, categ[categ.len]])))
-if(box.alpha != 0){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") categ.color ARGUMENT HAS LENGTH 1, MEANING THAT ALL THE DIFFERENT CLASSES OF ", categ[categ.len], "\n", paste(levels(factor(data1[, categ[categ.len]])), collapse = " "), "\nWILL HAVE THE SAME COLOR\n", paste(categ.color, collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg.color ARGUMENT MUST BE (1) LENGTH 1, OR (2) THE LENGTH OF data1 NROWS AFTER NA/Inf REMOVAL, OR (3) THE LENGTH OF THE CLASSES IN THE categ ", categ[categ.len], " COLUMN. HERE IT IS COLOR LENGTH ", length(categ.color), " VERSUS CATEG LENGTH ", length(data1[, categ[categ.len]]), " AND CATEG CLASS LENGTH ", length(unique(data1[, categ[categ.len]])), "\nPRESENCE OF NA/Inf COULD BE THE PROBLEM")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}else{
-categ.len <- length(categ) # if only categ1, then colors for classes of categ1, if length(categ) == 2L, then colors for classes of categ2
-# data1[, categ[categ.len]] <- factor(data1[, categ[categ.len]]) # not required because sure that is is a factor
-categ.color <- fun_gg_palette(length(levels(data1[, categ[categ.len]])))
-data1 <- data.frame(data1, categ.color = data1[, categ[categ.len]], stringsAsFactors = TRUE)
-data1$categ.color <- factor(data1$categ.color, labels = categ.color)  # replace the characters of data1[, categ[categ.len]] put in the categ.color column by the categ.color (can be write like this because categ.color is length of levels of data1[, categ[categ.len]])
-if(box.alpha != 0){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NULL categ.color ARGUMENT -> COLORS RESPECTIVELY ATTRIBUTED TO EACH CLASS OF ", categ[categ.len], " IN data1:\n", paste(categ.color, collapse = " "), "\n", paste(levels(data1[, categ[categ.len]]), collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# categ.color not NULL anymore
-categ.color <- as.character(categ.color)
-# categ.color is a character string representing the diff classes
-data1$categ.color <- factor(data1$categ.color, levels = unique(categ.color)) # ok because if categ.color is a character string, the order make class 1, class 2, etc. unique() because no duplicates allowed
-# data1$categ.color is a factor with order of levels -> categ.color
-# end management of categ.color
-# management of dot.color
-if( ! is.null(dot.color)){
-# optional legend of dot colors
-if( ! is.null(dot.categ)){
-ini.dot.categ <- dot.categ
-if( ! dot.categ %in% names(data1)){ # no need to use all() because length(dot.categ) = 1
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ ARGUMENT MUST BE A COLUMN NAME OF data1. HERE IT IS:\n", dot.categ)
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(dot.categ %in% categ){ # no need to use all() because length(dot.categ) = 1. Do not use dot.categ %in% categ[length(categ)] -> error
-# management of dot legend if dot.categ %in% categ (because legends with the same name are joined in ggplot2) 
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE COLUMN NAME OF data1 INDICATED IN THE dot.categ ARGUMENT (", dot.categ, ") HAS BEEN REPLACED BY ", paste0(dot.categ, "_DOT"), " TO AVOID MERGED LEGEND BY GGPLOT2")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-data1 <- data.frame(data1, dot.categ = data1[, dot.categ], stringsAsFactors = TRUE) # dot.categ is not a column name of data1 (checked above with reserved words)
-dot.categ <- paste0(dot.categ, "_DOT")
-names(data1)[names(data1) == "dot.categ"] <- dot.categ # paste0(dot.categ, "_DOT") is not a column name of data1 (checked above with reserved words)
-# tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ ARGUMENT CANNOT BE A COLUMN NAME OF data1 ALREADY SPECIFIED IN THE categ ARGUMENT:\n", dot.categ, "\nINDEED, dot.categ ARGUMENT IS MADE TO HAVE MULTIPLE DOT COLORS NOT RELATED TO THE BOXPLOT CATEGORIES")
-# stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-tempo1 <- fun_check(data = data1[, dot.categ], data.name = paste0(dot.categ, " COLUMN OF data1"), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name)
-tempo2 <- fun_check(data = data1[, dot.categ], data.name = paste0(dot.categ, " COLUMN OF data1"), class = "factor", na.contain = TRUE, fun.name = function.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ COLUMN MUST BE A FACTOR OR CHARACTER VECTOR") #
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-data1[, dot.categ] <- factor(data1[, dot.categ]) # if already a factor, change nothing, if characters, levels according to alphabetical order
-# dot.categ column of data1 is factor from here
-if( ! is.null(dot.categ.class.order)){
-if(any(duplicated(dot.categ.class.order), na.rm = TRUE)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ.class.order ARGUMENT CANNOT HAVE DUPLICATED CLASSES: ", paste(dot.categ.class.order, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if( ! (all(dot.categ.class.order %in% levels(data1[, dot.categ])) & all(levels(data1[, dot.categ]) %in% dot.categ.class.order, na.rm = TRUE))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ.class.order ARGUMENT MUST BE CLASSES OF dot.categ ARGUMENT\nHERE IT IS:\n", paste(dot.categ.class.order, collapse = " "), "\nFOR dot.categ.class.order AND IT IS:\n", paste(levels(data1[, dot.categ]), collapse = " "), "\nFOR dot.categ COLUMN (", ini.dot.categ, ") OF data1")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-data1[, dot.categ] <- factor(data1[, dot.categ], levels = dot.categ.class.order) # reorder the factor
-}
-}else{
-if(all(dot.color == "same") & length(dot.color)== 1L){ # all() without na.rm -> ok because dot.color cannot be NA (tested above)
-dot.categ.class.order <- unlist(categ.class.order[length(categ)])
-data1[, dot.categ] <- factor(data1[, dot.categ], levels = dot.categ.class.order) # reorder the factor
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE dot.categ.class.order SETTING IS NULL AND dot.color IS \"same\". ORDER OF categ.class.order WILL BE APPLIED FOR LEGEND DISPLAY: ", paste(dot.categ.class.order, collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else{
-dot.categ.class.order <- sort(levels(data1[, dot.categ]))
-data1[, dot.categ] <- factor(data1[, dot.categ], levels = dot.categ.class.order) # reorder the factor
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE dot.categ.class.order SETTING IS NULL. ALPHABETICAL ORDER WILL BE APPLIED FOR LEGEND DISPLAY: ", paste(dot.categ.class.order, collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# dot.categ.class.order not NULL anymore (character string) if dot.categ is not NULL
-if(all(dot.color == "same") & length(dot.color)== 1L){ # all() without na.rm -> ok because dot.color cannot be NA (tested above)
-if( ! identical(ini.dot.categ, categ[length(categ)])){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nWHEN dot.color ARGUMENT IS \"same\", THE COLUMN NAME IN dot.categ ARGUMENT MUST BE IDENTICAL TO THE LAST COLUMN NAME IN categ ARGUMENT. HERE IT IS:\ndot.categ: ", paste(ini.dot.categ, collapse = " "), "\ncateg: ", paste(categ, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if( ! fun_comp_1d(unlist(categ.class.order[length(categ)]), dot.categ.class.order)$identical.content){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nWHEN dot.color ARGUMENT IS \"same\",\nLAST COMPARTMENT OF categ.class.order ARGUMENT AND dot.categ.class.order ARGUMENT CANNOT BE DIFFERENT:\nLAST COMPARTMENT OF categ.class.order: ", paste(unlist(categ.class.order[length(categ)]), collapse = " "), "\ndot.categ.class.order: ", paste(dot.categ.class.order, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-for(i3 in 1:length(categ)){
-if(identical(categ[i3], ini.dot.categ) & ! identical(unlist(categ.class.order[i3]), dot.categ.class.order) & identical(sort(unlist(categ.class.order[i3])), sort(dot.categ.class.order))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE dot.categ ARGUMENT SETTING IS PRESENT IN THE categ ARGUMENT SETTING, BUT ORDER OF THE CLASSES IS NOT THE SAME:\ncateg.class.order: ", paste(unlist(categ.class.order[i3]), collapse = " "), "\ndot.categ.class.order: ", paste(dot.categ.class.order, collapse = " "), "\nNOTE THAT ORDER OF categ.class.order IS THE ONE USED FOR THE AXIS REPRESENTATION")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-if(is.null(dot.legend.name)){
-dot.legend.name <- if(ini.dot.categ %in% categ[length(categ)]){dot.categ}else{ini.dot.categ} #
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE dot.legend.name SETTING IS NULL -> ", dot.legend.name, " WILL BE USED AS LEGEND TITLE OF DOTS")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# dot.legend.name not NULL anymore (character string)
-}else{
-if( ! is.null(dot.categ.class.order)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE dot.categ.class.order ARGUMENT IS NOT NULL, BUT IS THE dot.categ ARGUMENT\n-> dot.categ.class.order NOT CONSIDERED AS NO LEGEND WILL BE DRAWN")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# But dot.categ.class.order will be converted to NULL below (not now)
-}
-# end optional legend of dot colors
-# check the nature of color
-# integer colors into gg_palette
-tempo.check.color <- fun_check(data = dot.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name)$problem
-if(tempo.check.color == FALSE){
-# convert integers into colors
-dot.color <- fun_gg_palette(max(dot.color, na.rm = TRUE))[dot.color]
-}
-# end integer colors into gg_palette
-if(all(dot.color == "same") & length(dot.color)== 1L){# all() without na.rm -> ok because dot.color cannot be NA (tested above)
-dot.color <- categ.color # same color of the dots as the corresponding box color
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") dot.color ARGUMENT HAS BEEN SET TO \"same\"\nTHUS, DOTS WILL HAVE THE SAME COLORS AS THE CORRESPONDING BOXPLOT")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else if( ! (all(dot.color %in% colors() | grepl(pattern = "^#", dot.color)))){ # check that all strings of low.color start by #, # all() without na.rm -> ok because dot.color cannot be NA (tested above)
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.color ARGUMENT MUST BE (1) A HEXADECIMAL COLOR VECTOR STARTING BY #, OR (2) COLOR NAMES GIVEN BY colors(), OR (3) INTEGERS, OR THE STRING \"same\"\nHERE IT IS: ", paste(unique(dot.color), collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(any(is.na(dot.color))){ # normally no NA with is.finite
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") dot.color ARGUMENT CONTAINS NA")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# end check the nature of color
-# check the length of color
-if( ! is.null(dot.categ)){
-# optional legend of dot colors
-if(length(data1[, dot.categ]) == length(levels(data1[, dot.categ])) & length(dot.color) == length(data1[, dot.categ])){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE NUMBER OF CLASSES OF THE COLUMN ", dot.categ, " THE NUMBER OF ROWS OF THIS COLUMN AND THE NUMBER OF COLORS OF THE dot.color ARGUMENT ARE ALL EQUAL. DOT COLORS WILL BE ATTRIBUTED ACCORDING THE LEVELS OF ", dot.categ, ", NOT ACCORDING TO THE ROWS OF ", dot.categ)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if(length(dot.color) > 1 & ! (length(dot.color) == length(unique(data1[, dot.categ])) | length(dot.color) == length(data1[, dot.categ]))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nWHEN LENGTH OF THE dot.color ARGUMENT IS MORE THAN 1, IT MUST BE EQUAL TO THE NUMBER OF 1) ROWS OR 2) LEVELS OF dot.categ COLUMN (", dot.categ, "):\ndot.color: ", paste(dot.color, collapse = " "), "\ndot.categ LEVELS: ", paste(levels(data1[, dot.categ]), collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else if(length(dot.color) > 1 & length(dot.color) == length(unique(data1[, dot.categ]))){
-data1 <- data.frame(data1, dot.color = data1[, dot.categ], stringsAsFactors = TRUE)
-data1$dot.color <- factor(data1$dot.color, labels = dot.color) # do not use labels = unique(dot.color). Otherwise, we can have green1 green2 when dot.color is c("green", "green")
-}else if(length(dot.color) > 1 & length(dot.color) == length(data1[, dot.categ])){
-data1 <- data.frame(data1, dot.color = dot.color, stringsAsFactors = TRUE)
-}else if(length(dot.color)== 1L){ # to deal with single color. Warning: & length(dot.categ.class.order) > 1 removed because otherwise, the data1 is not with dot.color column when length(dot.categ.class.order) == 1
-data1 <- data.frame(data1, dot.color = dot.color, stringsAsFactors = TRUE)
-}
-dot.color <- as.character(unique(data1$dot.color[order(data1[, dot.categ])])) # reorder the dot.color character vector
-if(length(dot.color)== 1L & length(dot.categ.class.order) > 1){ # to deal with single color
-dot.color <- rep(dot.color, length(dot.categ.class.order))
-}
-tempo.check <- unique(data1[ , c(dot.categ, "dot.color")])
-if(length(unique(data1[ , "dot.color"])) > 1 & ( ! (nrow(tempo.check) == length(unique(data1[ , "dot.color"])) & nrow(tempo.check) == length(unique(data1[ , dot.categ]))))){ # length(unique(data1[ , "dot.color"])) > 1 because if only one color, can be attributed to each class of dot.categ
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.color ARGUMENT IS INCORRECTLY ASSOCIATED TO EACH CLASS OF dot.categ (", dot.categ, ") COLUMN:\n", paste(unique(mapply(FUN = "paste", data1[ , dot.categ], data1[ ,"dot.color"])), collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN dot.categ ARGUMENT (", ini.dot.categ, "), THE FOLLOWING COLORS OF DOTS:\n", paste(dot.color, collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(data1[, dot.categ]), collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# dot.color is a character string representing the diff classes of dot.categ
-# data1$dot.color is a factor with order of levels -> dot.categ
-# end optional legend of dot colors
-}else{
-categ.len <- length(categ) # if only categ1, then colors for classes of categ1, if length(categ) == 2L, then colors for classes of categ2
-if(length(dot.color) == length(levels(data1[, categ[categ.len]]))){ # here length(dot.color) is equal to the different number of categ
-# data1[, categ[categ.len]] <- factor(data1[, categ[categ.len]]) # not required because sure that is is a factor
-data1 <- data.frame(data1, dot.color = data1[, categ[categ.len]], stringsAsFactors = TRUE)
-data1$dot.color <- factor(data1$dot.color, labels = dot.color)
-if(box.alpha != 0){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN ", categ[categ.len], " OF categ ARGUMENT, THE FOLLOWING COLORS:\n", paste(dot.color, collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(factor(data1[, categ[categ.len]])), collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else if(length(dot.color) == length(data1[, categ[categ.len]])){# here length(dot.color) is equal to nrow(data1) -> Modif to have length(dot.color) equal to the different number of categ (length(dot.color) == length(levels(data1[, categ[categ.len]])))
-data1 <- data.frame(data1, dot.color = dot.color, stringsAsFactors = TRUE)
-}else if(length(dot.color)== 1L & ! all(dot.color == "same")){ # all() without na.rm -> ok because dot.color cannot be NA (tested above)
-# data1[, categ[categ.len]] <- factor(data1[, categ[categ.len]]) # not required because sure that is is a factor
-data1 <- data.frame(data1, dot.color = dot.color, stringsAsFactors = TRUE)
-dot.color <- rep(dot.color, length(levels(data1[, categ[categ.len]])))
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") dot.color ARGUMENT HAS LENGTH 1, MEANING THAT ALL THE DIFFERENT CLASSES OF ", categ[categ.len], "\n", paste(levels(factor(data1[, categ[categ.len]])), collapse = " "), "\nWILL HAVE THE SAME COLOR\n", paste(dot.color, collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.color ARGUMENT MUST BE (1) LENGTH 1, OR (2) THE LENGTH OF data1 NROWS AFTER NA/Inf REMOVAL, OR (3) THE LENGTH OF THE CLASSES IN THE categ ", categ[categ.len], " COLUMN. HERE IT IS COLOR LENGTH ", length(dot.color), " VERSUS CATEG LENGTH ", length(data1[, categ[categ.len]]), " AND CATEG CLASS LENGTH ", length(unique(data1[, categ[categ.len]])), "\nPRESENCE OF NA/Inf COULD BE THE PROBLEM")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end check the length of color
-dot.color <- as.character(dot.color)
-# dot.color is a character string representing the diff classes
-data1$dot.color <- factor(data1$dot.color, levels = unique(dot.color)) # ok because if dot.color is a character string, the order make class 1, class 2, etc. If dot.color is a column of data1, then levels will be created, without incidence, except if dot.categ specified (see below). unique() because no duplicates allowed
-# data1$dot.color is a factor with order of levels -> dot.color
-}
-# end optional legend of dot colors
-}else if(is.null(dot.color) & ! (is.null(dot.categ) & is.null(dot.categ.class.order) & is.null(dot.legend.name))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") dot.categ OR dot.categ.class.order OR dot.legend.name ARGUMENT HAS BEEN SPECIFIED BUT dot.color ARGUMENT IS NULL (NO DOT PLOTTED)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# dot.color either NULL (no dot plotted) or character string (potentially representing the diff classes of dot.categ)
-# data1$dot.color is either NA or a factor (with order of levels -> depending on dot.categ or categ[length(categ)], or other
-if(is.null(dot.categ)){
-dot.categ.class.order <- NULL # because not used anyway
-}
-# dot.categ.class.order either NULL if dot.categ is NULL (no legend displayed) or character string (potentially representing the diff classes of dot.categ)
-# end management of dot.color
-if(is.null(dot.color) & box.fill == FALSE & dot.alpha <= 0.025){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE FOLLOWING ARGUMENTS WERE SET AS:\ndot.color = NULL (NOT ALL DOTS BUT ONLY POTENTIAL OUTLIER DOTS DISPLAYED)\nbox.fill = FALSE (NO FILLING COLOR FOR BOTH BOXES AND POTENTIAL OUTLIER DOTS)\ndot.alpha = ", fun_round(dot.alpha, 4), "\n-> POTENTIAL OUTLIER DOTS MIGHT NOT BE VISIBLE BECAUSE ALMOST TRANSPARENT")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if(is.null(dot.color) & box.fill == FALSE & dot.border.size == 0){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nTHE FOLLOWING ARGUMENTS WERE SET AS:\ndot.color = NULL (NOT ALL DOTS BUT ONLY POTENTIAL OUTLIER DOTS DISPLAYED)\nbox.fill = FALSE (NO FILLING COLOR FOR BOTH BOXES AND POTENTIAL OUTLIER DOTS)\ndot.border.size = 0 (NO BORDER FOR POTENTIAL OUTLIER DOTS)\n-> THESE SETTINGS ARE NOT ALLOWED BECAUSE THE POTENTIAL OUTLIER DOTS WILL NOT BE VISIBLE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# integer dot.border.color into gg_palette
-if( ! is.null(dot.border.color)){
-tempo <- fun_check(data = dot.border.color, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name)
-if(tempo$problem == FALSE){ # convert integers into colors
-dot.border.color <- fun_gg_palette(max(dot.border.color, na.rm = TRUE))[dot.border.color]
-}
-}
-# end integer dot.border.color into gg_palette
-# na detection and removal (done now to be sure of the correct length of categ)
-column.check <- c("categ.color", if( ! is.null(dot.color)){"dot.color"}) # 
-if(any(is.na(data1[, column.check]))){ # data1 used here instead of data1.ini in case of new NaN created by log conversion (neg values) # normally no NA with is.na
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NA DETECTED IN COLUMNS ", paste(column.check, collapse = " "), " OF data1 AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-for(i2 in 1:length(column.check)){
-if(any(is.na(data1[, column.check[i2]]))){ # normally no NA with is.na
-tempo.warn <- paste0("NA REMOVAL DUE TO COLUMN ", column.check[i2], " OF data1")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n", tempo.warn)))
-}
-}
-tempo <- unique(unlist(lapply(lapply(c(data1[column.check]), FUN = is.na), FUN = which)))
-removed.row.nb <- c(removed.row.nb, tempo)
-removed.rows <- rbind(removed.rows, data1[tempo, ], stringsAsFactors = FALSE) # here data1 used because categorical columns tested
-if(length(tempo) != 0){
-data1 <- data1[-tempo, ] # WARNING tempo here and not removed.row.nb because the latter contain more numbers thant the former
-data1.ini <- data1.ini[-tempo, ] # WARNING tempo here and not removed.row.nb because the latter contain more numbers thant the former
-for(i3 in 1:length(column.check)){
-if(any( ! unique(removed.rows[, column.check[i3]]) %in% unique(data1[, column.check[i3]]), na.rm = TRUE)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN COLUMN ", column.check[i3], " OF data1, THE FOLLOWING CLASSES HAVE DISAPPEARED AFTER NA/Inf REMOVAL (IF COLUMN USED IN THE PLOT, THIS CLASS WILL NOT BE DISPLAYED):\n", paste(unique(removed.rows[, column.check[i3]])[ ! unique(removed.rows[, column.check[i3]]) %in% unique(data1[, column.check[i3]])], collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-}
-for(i2 in 1:length(column.check)){
-if(column.check[i2] == "categ.color"){
-categ.color <- levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]])] # remove the absent color in the character vector
-if(length(categ.color)== 1L & length(unlist(categ.class.order[length(categ)])) > 1){ # to deal with single color
-categ.color <- rep(categ.color, length(unlist(categ.class.order[length(categ)])))
-}
-data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = unique(categ.color))
-}
-if(column.check[i2] == "dot.color"){
-dot.color <- levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]])] # remove the absent color in the character vector
-if(length(dot.color)== 1L & length(dot.categ.class.order) > 1){ # to deal with single color. If dot.categ.class.order == NULL (which is systematically the case if dot.categ == NULL), no rep(dot.color, length(dot.categ.class.order)
-dot.color <- rep(dot.color, length(dot.categ.class.order))
-}
-data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = unique(dot.color))
-}
-}
-}
-# end na detection and removal (done now to be sure of the correct length of categ)
-# From here, data1 and data.ini have no more NA or NaN
-# end other checkings
-# reserved word checking
-#already done above
-# end reserved word checking
-# end second round of checking and data preparation
-
-
-# package checking
-fun_pack(req.package = c(
-"ggplot2", 
-"gridExtra", 
-"lemon", 
-"scales"
-), lib.path = lib.path)
-# end package checking
-
-
-
-
-
-# main code
-# y coordinates recovery (create ini.box.coord, dot.coord and modify data1)
-if(length(categ)== 1L){
-# width commputations
-box.width2 <- box.width
-box.space <- 0 # to inactivate the shrink that add space between grouped boxes, because no grouped boxes here
-# end width commputations
-# data1 check categ order for dots coordinates recovery
-data1 <- data.frame(data1, categ.check = data1[, categ[1]], stringsAsFactors = TRUE)
-data1$categ.check <- as.integer(data1$categ.check) # to check that data1[, categ[1]] and dot.coord$group are similar, during merging
-# end data1 check categ order for dots coordinates recovery
-# per box dots coordinates recovery
-tempo.gg.name <- "gg.indiv.plot."
-tempo.gg.count <- 0
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::ggplot()", if(is.null(add)){""}else{add})))) # add added here to have the facets
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, color = categ[1]), stroke = dot.border.size, size = dot.size, alpha = dot.alpha, shape = 21))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "color", name = box.legend.name, values = if(is.null(categ.color)){rep(NA, length(unique(data1[, categ[1]])))}else if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[1]])))}else{categ.color})) # categ.color used for dot colors because at that stage, we do not care about colors
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, fill = categ[1]), coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf})) # fill because this is what is used with geom_box # to easily have the equivalent of the grouped boxes
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "fill", name = box.legend.name, values = if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[1]])))}else{categ.color}))
-# end per box dots coordinates recovery
-}else if(length(categ) == 2L){
-# width commputations
-box.width2 <- box.width / length(unique(data1[, categ[length(categ)]])) # real width of each box in x-axis unit, among the set of grouped box. Not relevant if no grouped boxes length(categ)== 1L
-# end width commputations
-# data1 check categ order for dots coordinates recovery
-tempo.factor <- paste0(data1[order(data1[, categ[2]], data1[, categ[1]]), categ[2]], "_", data1[order(data1[, categ[2]], data1[, categ[1]]), categ[1]])
-data1 <- data.frame(data1[order(data1[, categ[2]], data1[, categ[1]]), ], categ.check = factor(tempo.factor, levels = unique(tempo.factor)), stringsAsFactors = TRUE)
-data1$categ.check <- as.integer(data1$categ.check)
-# end data1 check categ order for dots coordinates recovery
-# per box dots coordinates recovery
-tempo.gg.name <- "gg.indiv.plot."
-tempo.gg.count <- 0
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::ggplot()", if(is.null(add)){""}else{add})))) # add added here to have the facets
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, color = categ[2]), stroke = dot.border.size, size = dot.size, alpha = dot.alpha, shape = 21))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "color", name = box.legend.name, values = if(is.null(categ.color)){rep(NA, length(unique(data1[, categ[2]])))}else if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[2]])))}else{categ.color})) # categ.color used for dot colors because at that stage, we do not care about colors
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, fill = categ[2]), coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf})) # fill because this is what is used with geom_box # to easily have the equivalent of the grouped boxes
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "fill", name = box.legend.name, values = if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[2]])))}else{categ.color}))
-# end per box dots coordinates recovery
-}else{
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 1")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if( ! is.null(stat.pos)){
-stat.just <- fun_gg_just(
-angle = stat.angle, 
-pos = ifelse(
-vertical == TRUE, 
-ifelse(stat.pos == "top", "bottom", "top"), # "bottom" because we want justification for text that are below the ref point which is the top of the graph. The opposite for "above"
-ifelse(stat.pos == "top", "left", "right") # "left" because we want justification for text that are on the left of the ref point which is the right border of the graph. The opposite for "above"
-), 
-kind = "text"
-)
-}
-# has in fact no interest because ggplot2 does not create room for geom_text()
-tempo.data.max <- data1[which.max(data1[, y]), ]
-tempo.data.max <- data.frame(tempo.data.max, label = formatC(tempo.data.max[, y], digit = 2, drop0trailing = TRUE, format = "f"), stringsAsFactors = TRUE)
-# end has in fact no interest because ggplot2 does not create room for geom_text()
-tempo.graph.info.ini <- ggplot2::ggplot_build(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if( ! is.null(stat.pos)){' + ggplot2::geom_text(data = tempo.data.max, mapping = ggplot2::aes_string(x = 1, y = y, label = "label"), size = stat.size, color = "black", angle = stat.angle, hjust = stat.just$hjust, vjust = stat.just$vjust)'})))) # added here to have room for annotation
-dot.coord <- tempo.graph.info.ini$data[[1]]
-dot.coord$x <- as.numeric(dot.coord$x) # because weird class
-dot.coord$PANEL <- as.numeric(dot.coord$PANEL) # because numbers as levels. But may be a problem is facet are reordered ?
-tempo.mean <- aggregate(x = dot.coord$y, by = list(dot.coord$group, dot.coord$PANEL), FUN = mean, na.rm = TRUE)
-names(tempo.mean)[names(tempo.mean) == "x"] <- "MEAN"
-names(tempo.mean)[names(tempo.mean) == "Group.1"] <- "BOX"
-names(tempo.mean)[names(tempo.mean) == "Group.2"] <- "PANEL"
-dot.coord <- data.frame(
-dot.coord[order(dot.coord$group, dot.coord$y), ], # dot.coord$PANEL deals below
-y.check = as.double(data1[order(data1$categ.check, data1[, y]), y]), 
-categ.check = data1[order(data1$categ.check, data1[, y]), "categ.check"], 
-dot.color = if(is.null(dot.color)){NA}else{data1[order(data1$categ.check, data1[, y]), "dot.color"]}, 
-data1[order(data1$categ.check, data1[, y]), ][categ], # avoid the renaming below
-stringsAsFactors = TRUE
-) # y.check to be sure that the order is the same between the y of data1 and the y of dot.coord
-# names(dot.coord)[names(dot.coord) == "tempo.categ1"] <- categ[1]
-if( ! is.null(dot.categ)){
-dot.coord <- data.frame(dot.coord, data1[order(data1$categ.check, data1[, y]), ][dot.categ], stringsAsFactors = TRUE) # avoid the renaming
-}
-if( ! is.null(facet.categ)){
-dot.coord <- data.frame(dot.coord, data1[order(data1$categ.check, data1[, y]), ][facet.categ], stringsAsFactors = TRUE) # for facet panels
-tempo.test <- NULL
-for(i2 in 1:length(facet.categ)){
-tempo.test <- paste0(tempo.test, ".", formatC(as.numeric(dot.coord[, facet.categ[i2]]), width = nchar(max(as.numeric(dot.coord[, facet.categ[i2]]), na.rm = TRUE)), flag = "0")) # convert factor into numeric with leading zero for proper ranking # merge the formatC() to create a new factor. The convertion to integer should recreate the correct group number. Here as.numeric is used and not as.integer in case of numeric in facet.categ (because comes from add and not checked by fun_check, contrary to categ)
-}
-tempo.test <- as.integer(factor(tempo.test))
-if( ! identical(as.integer(dot.coord$PANEL), tempo.test)){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nas.integer(dot.coord$PANEL) AND tempo.test MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if(dot.tidy == TRUE){
-if( ! is.null(dot.categ)){
-dot.coord <- data.frame(dot.coord, tidy_group = data1[order(data1$categ.check, data1[, y]), ][, dot.categ], stringsAsFactors = TRUE) # avoid the renaming
-# tidy_group_coord is to be able to fuse table when creating the table for dot coordinates
-if(dot.categ %in% categ){
-dot.coord <- data.frame(dot.coord, tidy_group_coord = dot.coord$group, stringsAsFactors = TRUE)
-}else{
-dot.coord <- data.frame(dot.coord, tidy_group_coord = as.integer(factor(paste0(
-formatC(as.integer(dot.coord[, categ[1]]), width = nchar(max(as.integer(dot.coord[, categ[1]]), na.rm = TRUE)), flag = "0"), # convert factor into numeric with leading zero for proper ranking
-".", 
-if(length(categ) == 2L){formatC(as.integer(dot.coord[, categ[2]]), width = nchar(max(as.integer(dot.coord[, categ[2]]), na.rm = TRUE)), flag = "0")}, # convert factor into numeric with leading zero for proper ranking
-if(length(categ) == 2L){"."}, 
-formatC(as.integer(dot.coord[, dot.categ]), width = nchar(max(as.integer(dot.coord[, dot.categ]), na.rm = TRUE)), flag = "0") # convert factor into numeric with leading zero for proper ranking
-)), stringsAsFactors = TRUE) # merge the 2 or 3 formatC() to create a new factor. The convertion to integer should recreate the correct group number
-) # for tidy dot plots
-}
-}else{
-dot.coord <- data.frame(dot.coord, tidy_group = if(length(categ)== 1L){
-dot.coord[, categ]}else{as.integer(factor(paste0(
-formatC(as.integer(dot.coord[, categ[1]]), width = nchar(max(as.integer(dot.coord[, categ[1]]), na.rm = TRUE)), flag = "0"), # convert factor into numeric with leading zero for proper ranking
-".", 
-formatC(as.integer(dot.coord[, categ[2]]), width = nchar(max(as.integer(dot.coord[, categ[2]]), na.rm = TRUE)), flag = "0")# convert factor into numeric with leading zero for proper ranking
-)), stringsAsFactors = TRUE) # merge the 2 formatC() to create a new factor. The convertion to integer should recreate the correct group number
-}) # for tidy dot plots
-# tidy_group_coord is to be able to fuse table when creating the table for dot coordinates
-dot.coord <- data.frame(dot.coord, tidy_group_coord = dot.coord$group, stringsAsFactors = TRUE)
-}
-}
-if( ! (identical(dot.coord$y, dot.coord$y.check) & identical(dot.coord$group, dot.coord$categ.check))){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\n(dot.coord$y AND dot.coord$y.check) AS WELL AS (dot.coord$group AND dot.coord$categ.check) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-if( ! identical(tempo.mean[order(tempo.mean$BOX, tempo.mean$PANEL), ]$BOX, unique(dot.coord[order(dot.coord$group, dot.coord$PANEL), c("group", "PANEL")])$group)){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\n(tempo.mean$BOX, tempo.mean$PANEL) AND (dot.coord$group, dot.coord$PANEL) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-tempo <- unique(dot.coord[order(dot.coord$group, dot.coord$PANEL), c(categ, if( ! is.null(dot.color) & ! is.null(dot.categ)){if(dot.categ != ini.dot.categ){dot.categ}}, if( ! is.null(facet.categ)){facet.categ}), drop = FALSE])
-# names(tempo) <- paste0(names(tempo), ".mean")
-tempo.mean <- data.frame(tempo.mean[order(tempo.mean$BOX, tempo.mean$PANEL), ], tempo, stringsAsFactors = TRUE)
-}
-}
-# at that stage, categ color and dot color are correctly attributed in data1, box.coord and dot.coord
-# end y dot coordinates recovery (create ini.box.coord, dot.coord and modify data1)
-# ylim range
-if(is.null(y.lim)){
-y.lim <- tempo.graph.info.ini$layout$panel_params[[1]]$y.range # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
-if(any(( ! is.finite(y.lim)) | is.na(y.lim)) | length(y.lim) != 2){ # kept but normally no more Inf in data1 # normally no NA with is.finite, etc.
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\ntempo.graph.info.ini$layout$panel_params[[1]]$y.range[1] CONTAINS NA OR Inf OR HAS LENGTH 1")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}else if(y.log != "no"){
-y.lim <- get(y.log)(y.lim) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-}
-if(y.log != "no"){
-# normally this control is not necessary anymore
-if(any( ! is.finite(y.lim))){ # normally no NA with is.finite
-tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT CANNOT HAVE ZERO OR NEGATIVE VALUES WITH THE y.log ARGUMENT SET TO ", y.log, ":\n", paste(y.lim, collapse = " "), "\nPLEASE, CHECK DATA VALUES (PRESENCE OF ZERO OR INF VALUES)")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-if(suppressWarnings(all(y.lim %in% c(Inf, -Inf)))){ # all() without na.rm -> ok because y.lim cannot be NA (tested above)
-# normally this control is not necessary anymore
-tempo.cat <- paste0("ERROR IN ", function.name, " y.lim CONTAINS Inf VALUES, MAYBE BECAUSE VALUES FROM data1 ARGUMENTS ARE NA OR Inf ONLY OR BECAUSE OF LOG SCALE REQUIREMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-if(suppressWarnings(any(is.na(y.lim)))){ # normally no NA with is.na
-# normally this control is not necessary anymore
-tempo.cat <- paste0("ERROR IN ", function.name, " y.lim CONTAINS NA OR NaN VALUES, MAYBE BECAUSE VALUES FROM data1 ARGUMENTS ARE NA OR Inf ONLY OR BECAUSE OF LOG SCALE REQUIREMENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-y.lim.order <- order(y.lim) # to deal with inverse axis
-y.lim <- sort(y.lim)
-y.lim[1] <- y.lim[1] - abs(y.lim[2] - y.lim[1]) * ifelse(diff(y.lim.order) > 0, y.bottom.extra.margin, y.top.extra.margin) # diff(y.lim.order) > 0 medians not inversed axis
-y.lim[2] <- y.lim[2] + abs(y.lim[2] - y.lim[1]) * ifelse(diff(y.lim.order) > 0, y.top.extra.margin, y.bottom.extra.margin) # diff(y.lim.order) > 0 medians not inversed axis
-if(y.include.zero == TRUE){ # no need to check y.log != "no" because done before
-y.lim <- range(c(y.lim, 0), na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
-}
-y.lim <- y.lim[y.lim.order]
-if(any(is.na(y.lim))){ # normally no NA with is.na
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 2")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end ylim range
-
-
-
-
-
-
-# drawing
-# constant part
-tempo.gg.name <- "gg.indiv.plot."
-tempo.gg.count <- 0
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::ggplot()", if(is.null(add)){""}else{add})))) # add is directly put here to deal with additional variable of data, like when using facet_grid. No problem if add is a theme, will be dealt below
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::xlab(if(is.null(x.lab)){categ[1]}else{x.lab}))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ylab(if(is.null(y.lab)){y}else{y.lab}))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggtitle(title))
-# text angle management
-axis.just <- fun_gg_just(angle = x.angle, pos = ifelse(vertical == TRUE, "bottom", "left"), kind = "axis")
-# end text angle management
-add.check <- TRUE
-if( ! is.null(add)){ # if add is NULL, then = 0
-if(grepl(pattern = "ggplot2\\s*::\\s*theme", add) == TRUE){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") \"ggplot2::theme\" STRING DETECTED IN THE add ARGUMENT\n-> INTERNAL GGPLOT2 THEME FUNCTIONS theme() AND theme_classic() HAVE BEEN INACTIVATED, TO BE USED BY THE USER\n-> article ARGUMENT WILL BE IGNORED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-add.check <- FALSE
-}
-}
-if(add.check == TRUE & article == TRUE){
-# WARNING: not possible to add theme()several times. NO message but the last one overwrites the others
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::theme_classic(base_size = text.size))
-if(grid == TRUE){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
-text = ggplot2::element_text(size = text.size), 
-plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
-line = ggplot2::element_line(size = 0.5), 
-legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
-axis.line.y.left = ggplot2::element_line(colour = "black"), # draw lines for the y axis
-axis.line.x.bottom = ggplot2::element_line(colour = "black"), # draw lines for the x axis
-panel.grid.major.x = if(vertical == TRUE){NULL}else{ggplot2::element_line(colour = "grey85", size = 0.75)},
-panel.grid.major.y = if(vertical == TRUE){ggplot2::element_line(colour = "grey85", size = 0.75)}else{NULL},
-panel.grid.minor.y = if(vertical == TRUE){ggplot2::element_line(colour = "grey90", size = 0.25)}else{NULL},
-axis.text.x = if(vertical == TRUE){ggplot2::element_text(angle = axis.just$angle, hjust = axis.just$hjust, vjust = axis.just$vjust)}else{NULL},
-axis.text.y = if(vertical == TRUE){NULL}else{ggplot2::element_text(angle = axis.just$angle, hjust = axis.just$hjust, vjust = axis.just$vjust)},
-strip.background = ggplot2::element_rect(fill = NA, colour = NA) # for facet background
-))
-}else{
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
-text = ggplot2::element_text(size = text.size), 
-plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
-line = ggplot2::element_line(size = 0.5), 
-legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
-axis.line.y.left = ggplot2::element_line(colour = "black"), 
-axis.line.x.bottom = ggplot2::element_line(colour = "black"),
-axis.text.x = if(vertical == TRUE){ggplot2::element_text(angle = axis.just$angle, hjust = axis.just$hjust, vjust = axis.just$vjust)}else{NULL},
-axis.text.y = if(vertical == TRUE){NULL}else{ggplot2::element_text(angle = axis.just$angle, hjust = axis.just$hjust, vjust = axis.just$vjust)},
-strip.background = ggplot2::element_rect(fill = NA, colour = NA)
-))
-}
-}else if(add.check == TRUE & article == FALSE){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
-text = ggplot2::element_text(size = text.size), 
-plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
-line = ggplot2::element_line(size = 0.5), 
-legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
-panel.background = ggplot2::element_rect(fill = "grey95"), 
-axis.line.y.left = ggplot2::element_line(colour = "black"), 
-axis.line.x.bottom = ggplot2::element_line(colour = "black"), 
-panel.grid.major.x = ggplot2::element_line(colour = "grey85", size = 0.75), 
-panel.grid.major.y = ggplot2::element_line(colour = "grey85", size = 0.75), 
-panel.grid.minor.x = ggplot2::element_blank(), 
-panel.grid.minor.y = ggplot2::element_line(colour = "grey90", size = 0.25), 
-strip.background = ggplot2::element_rect(fill = NA, colour = NA),
-axis.text.x = if(vertical == TRUE){ggplot2::element_text(angle = axis.just$angle, hjust = axis.just$hjust, vjust = axis.just$vjust)}else{NULL},
-axis.text.y = if(vertical == TRUE){NULL}else{ggplot2::element_text(angle = axis.just$angle, hjust = axis.just$hjust, vjust = axis.just$vjust)}
-))
-}
-# Contrary to fun_gg_bar(), cannot plot the boxplot right now, because I need the dots plotted first
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, group = categ[length(categ)]), position = ggplot2::position_dodge(width = NULL), color = NA, width = box.width, fill = NA)) # this is to set the graph (i.e., a blanck boxplot to be able to use x coordinates to plot dots before boxes)
-# end constant part
-
-
-
-
-# graphic info recovery (including means)
-tempo.graph.info <- ggplot2::ggplot_build(eval(parse(text = paste0(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), ' + ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, fill = categ[length(categ)]), position = ggplot2::position_dodge(width = NULL), width = box.width, notch = box.notch, coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf}) + ggplot2::scale_discrete_manual(aesthetics = "fill", name = box.legend.name, values = if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[length(categ)]])))}else{categ.color})')))) # will be recovered later again, when ylim will be considered
-tempo.yx.ratio <- (tempo.graph.info$layout$panel_params[[1]]$y.range[2] - tempo.graph.info$layout$panel_params[[1]]$y.range[1]) / (tempo.graph.info$layout$panel_params[[1]]$x.range[2] - tempo.graph.info$layout$panel_params[[1]]$x.range[1])
-box.coord <- tempo.graph.info$data[[2]] # to have the summary statistics of the plot. Contrary to ini.box.plot, now integrates ylim Here because can be required for stat.pos when just box are plotted
-box.coord$x <- as.numeric(box.coord$x) # because x is of special class that block comparison of values using identical
-box.coord$PANEL <- as.numeric(box.coord$PANEL) # because numbers as levels. But may be a problem is facet are reordered ?
-box.coord <- box.coord[order(box.coord$group, box.coord$PANEL), ]
-if( ! (identical(tempo.mean$BOX, box.coord$group) & identical(tempo.mean$PANEL, box.coord$PANEL))){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nidentical(tempo.mean$BOX, box.coord$group) & identical(tempo.mean$PANEL, box.coord$PANEL) DO NOT HAVE THE SAME VALUE ORDER")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-# tempo <- c(categ, if( ! is.null(dot.color) & ! is.null(dot.categ)){if(dot.categ != ini.dot.categ){dot.categ}}, if( ! is.null(facet.categ)){facet.categ})
-if(any(names(tempo.mean) %in% names(box.coord), na.rm = TRUE)){
-names(tempo.mean)[names(tempo.mean) %in% names(box.coord)] <- paste0(names(tempo.mean)[names(tempo.mean) %in% names(box.coord)], ".mean")
-}
-box.coord <- data.frame(box.coord, tempo.mean, stringsAsFactors = TRUE)
-}
-# end graphic info recovery (including means)
-
-
-
-# stat output (will also serve for boxplot and mean display)
-# x not added know to do not have them in stat.nolog
-stat <- data.frame(
-MIN = box.coord$ymin_final, 
-QUART1 = box.coord$lower, 
-MEDIAN = box.coord$middle, 
-MEAN = box.coord$MEAN, 
-QUART3 = box.coord$upper, 
-MAX = box.coord$ymax_final, 
-WHISK_INF = box.coord$ymin, 
-BOX_INF = box.coord$lower, 
-NOTCH_INF = box.coord$notchlower, 
-NOTCH_SUP = box.coord$notchupper, 
-BOX_SUP = box.coord$upper, 
-WHISK_SUP = box.coord$ymax, 
-OUTLIERS = box.coord["outliers"], 
-tempo.mean[colnames(tempo.mean) != "MEAN"], 
-COLOR = box.coord$fill, 
-stringsAsFactors = TRUE
-) # box.coord["outliers"] written like this because it is a list. X coordinates not put now because several features to set
-names(stat)[names(stat) == "outliers"] <- "OUTLIERS"
-stat.nolog <- stat # stat.nolog ini will serve for outputs
-if(y.log != "no"){
-stat.nolog[c("MIN", "QUART1", "MEDIAN", "MEAN", "QUART3", "MAX", "WHISK_INF", "BOX_INF", "NOTCH_INF", "NOTCH_SUP", "BOX_SUP", "WHISK_SUP")] <- ifelse(y.log == "log2", 2, 10)^(stat.nolog[c("MIN", "QUART1", "MEDIAN", "MEAN", "QUART3", "MAX", "WHISK_INF", "BOX_INF", "NOTCH_INF", "NOTCH_SUP", "BOX_SUP", "WHISK_SUP")])
-stat.nolog$OUTLIERS <- lapply(stat.nolog$OUTLIERS, FUN = function(X){ifelse(y.log == "log2", 2, 10)^X})
-}
-# end stat output (will also serve for boxplot and mean display)
-
-
-
-
-
-
-# x coordinates management (for random plotting and for stat display)
-# width commputations
-width.ini <- c(box.coord$xmax - box.coord$xmin)[1] # all the box widths are equal here. Only the first one taken
-width.correct <- width.ini * box.space / 2
-if( ! (identical(stat$BOX, box.coord$group) & identical(stat$PANEL, box.coord$PANEL))){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nidentical(stat$BOX, box.coord$group) & identical(stat$PANEL, box.coord$PANEL) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-stat <- data.frame(
-stat, 
-X = box.coord$x, 
-X_BOX_INF = box.coord$xmin + width.correct, 
-X_BOX_SUP = box.coord$xmax - width.correct, 
-X_NOTCH_INF = box.coord$x - (box.coord$x - (box.coord$xmin + width.correct)) / 2, 
-X_NOTCH_SUP = box.coord$x + (box.coord$x - (box.coord$xmin + width.correct)) / 2, 
-X_WHISK_INF = box.coord$x - (box.coord$x - (box.coord$xmin + width.correct)) * box.whisker.width, 
-X_WHISK_SUP = box.coord$x + (box.coord$x - (box.coord$xmin + width.correct)) * box.whisker.width, 
-# tempo.mean[colnames(tempo.mean) != "MEAN"], # already added above
-stringsAsFactors = TRUE
-)
-stat$COLOR <- factor(stat$COLOR, levels = unique(categ.color))
-if( ! all(stat$NOTCH_SUP < stat$BOX_SUP & stat$NOTCH_INF > stat$BOX_INF, na.rm = TRUE) & box.notch == TRUE){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") SOME NOTCHES ARE BEYOND BOX HINGES. TRY ARGUMENT box.notch = FALSE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-dot.jitter <- c((box.coord$xmax - width.correct) - (box.coord$xmin + width.correct))[1] * dot.jitter # real dot.jitter. (box.coord$xmin + width.correct) - (box.coord$xmax - width.correct))[1] is the width of the box. Is equivalent to (box.coord$x - (box.coord$xmin + width.correct))[1] * 2
-# end width commputations
-if( ! is.null(dot.color)){
-# random dots
-if(dot.tidy == FALSE){
-dot.coord.rd1 <- merge(dot.coord, box.coord[c("fill", "PANEL", "group", "x")], by = c("PANEL", "group"), sort = FALSE) # rd for random. Send the coord of the boxes into the coord data.frame of the dots (in the column x.y). WARNING: by = c("PANEL", "group") without fill column because PANEL & group columns are enough as only one value of x column per group number in box.coord. Thus, no need to consider fill column
-if(nrow(dot.coord.rd1) != nrow(dot.coord)){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nTHE merge() FUNCTION DID NOT RETURN A CORRECT dot.coord.rd1 DATA FRAME. CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-sampled.dot.jitter <- if(nrow(dot.coord.rd1)== 1L){runif(n = nrow(dot.coord.rd1), min = - dot.jitter / 2, max = dot.jitter / 2)}else{sample(x = runif(n = nrow(dot.coord.rd1), min = - dot.jitter / 2, max = dot.jitter / 2), size = nrow(dot.coord.rd1), replace = FALSE)}
-dot.coord.rd2 <- data.frame(dot.coord.rd1, dot.x = dot.coord.rd1$x.y + sampled.dot.jitter, stringsAsFactors = TRUE) # set the dot.jitter thanks to runif and dot.jitter range. Then, send the coord of the boxes into the coord data.frame of the dots (in the column x.y)
-if(length(categ)== 1L){
-tempo.data1 <- unique(data.frame(data1[categ[1]], group = as.integer(data1[, categ[1]]), stringsAsFactors = TRUE)) # categ[1] is factor
-names(tempo.data1)[names(tempo.data1) == categ[1]] <- paste0(categ[1], ".check")
-verif <- paste0(categ[1], ".check")
-}else if(length(categ) == 2L){
-tempo.data1 <- unique(
-data.frame(
-data1[c(categ[1], categ[2])], 
-group = as.integer(factor(paste0(
-formatC(as.integer(data1[, categ[2]]), width = nchar(max(as.integer(data1[, categ[2]]), na.rm = TRUE)), flag = "0"), # convert factor into numeric with leading zero for proper ranking
-".", 
-formatC(as.integer(data1[, categ[1]]), width = nchar(max(as.integer(data1[, categ[1]]), na.rm = TRUE)), flag = "0")# convert factor into numeric with leading zero for proper ranking
-)), stringsAsFactors = TRUE) # merge the 2 formatC() to create a new factor. The convertion to integer should recreate the correct group number
-)
-) # categ[2] first if categ[2] is used to make the categories in ggplot and categ[1] is used to make the x-axis
-names(tempo.data1)[names(tempo.data1) == categ[1]] <- paste0(categ[1], ".check")
-names(tempo.data1)[names(tempo.data1) == categ[2]] <- paste0(categ[2], ".check")
-verif <- c(paste0(categ[1], ".check"), paste0(categ[2], ".check"))
-}else{
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 3")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-dot.coord.rd3 <- merge(dot.coord.rd2, tempo.data1, by = intersect("group", "group"), sort = FALSE) # send the factors of data1 into coord. WARNING: I have replaced by = "group" by intersect("group", "group") because of an error due to wrong group group merging in dot.coord.rd3
-if(nrow(dot.coord.rd3) != nrow(dot.coord) | ( ! fun_comp_2d(dot.coord.rd3[categ], dot.coord.rd3[verif])$identical.content)){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nTHE merge() FUNCTION DID NOT RETURN A CORRECT dot.coord.rd3 DATA FRAME. CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end random dots
-}
-# tidy dots
-# coordinates are recovered during plotting (see dot.coord.tidy1 below)
-# end tidy dots
-}
-# end x coordinates management (for random plotting and for stat display)
-
-
-
-
-
-# boxplot display before dot display if box.fill = TRUE
-coord.names <- NULL
-# creation of the data frame for (main box + legend) and data frame for means
-if(box.notch == FALSE){
-for(i3 in 1:length(categ)){
-if(i3== 1L){
-tempo.polygon <- data.frame(GROUPX = c(t(stat[, rep(categ[i3], 5)])), stringsAsFactors = TRUE)
-}else{
-tempo.polygon <- cbind(tempo.polygon, c(t(stat[, rep(categ[i3], 5)])), stringsAsFactors = TRUE)
-}
-}
-names(tempo.polygon) <- categ
-tempo.polygon <- data.frame(X = c(t(stat[, c("X_BOX_INF", "X_BOX_SUP", "X_BOX_SUP", "X_BOX_INF", "X_BOX_INF")])), Y = c(t(stat[, c("BOX_INF", "BOX_INF", "BOX_SUP", "BOX_SUP", "BOX_INF")])), COLOR = c(t(stat[, c("COLOR", "COLOR", "COLOR", "COLOR", "COLOR")])), BOX = as.character(c(t(stat[, c("BOX", "BOX", "BOX", "BOX", "BOX")]))), tempo.polygon, stringsAsFactors = TRUE)
-if( ! is.null(facet.categ)){
-for(i4 in 1:length(facet.categ)){
-tempo.polygon <- data.frame(tempo.polygon, c(t(stat[, c(facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4])])), stringsAsFactors = TRUE)
-names(tempo.polygon)[length(names(tempo.polygon))] <- facet.categ[i4]
-}
-}
-}else{
-for(i3 in 1:length(categ)){
-if(i3== 1L){
-tempo.polygon <- data.frame(GROUPX = c(t(stat[, rep(categ[i3], 11)])), stringsAsFactors = TRUE)
-}else{
-tempo.polygon <- cbind(tempo.polygon, c(t(stat[, rep(categ[i3], 11)])), stringsAsFactors = TRUE)
-}
-}
-names(tempo.polygon) <- categ
-tempo.polygon <- data.frame(X = c(t(stat[, c("X_BOX_INF", "X_BOX_SUP", "X_BOX_SUP", "X_NOTCH_SUP", "X_BOX_SUP", "X_BOX_SUP", "X_BOX_INF", "X_BOX_INF", "X_NOTCH_INF", "X_BOX_INF", "X_BOX_INF")])), Y = c(t(stat[, c("BOX_INF", "BOX_INF", "NOTCH_INF", "MEDIAN", "NOTCH_SUP", "BOX_SUP", "BOX_SUP", "NOTCH_SUP", "MEDIAN", "NOTCH_INF", "BOX_INF")])), COLOR = c(t(stat[, c("COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR")])), BOX = as.character(c(t(stat[, c("BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX")]))), tempo.polygon, stringsAsFactors = TRUE)
-if( ! is.null(facet.categ)){
-for(i4 in 1:length(facet.categ)){
-tempo.polygon <- data.frame(tempo.polygon, c(t(stat[, c(facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4])])), stringsAsFactors = TRUE)
-names(tempo.polygon)[length(names(tempo.polygon))] <- facet.categ[i4]
-}
-}
-}
-tempo.polygon$COLOR <- factor(tempo.polygon$COLOR, levels = unique(categ.color))
-if( ! is.null(categ.class.order)){
-for(i3 in 1:length(categ)){
-tempo.polygon[, categ[i3]] <- factor(tempo.polygon[, categ[i3]], levels = categ.class.order[[i3]])
-}
-}
-# modified name of dot.categ column (e.g., "Categ1_DOT") must be included for boxplot using ridy dots
-if( ! is.null(dot.color) & ! is.null(dot.categ)){
-if(dot.categ != ini.dot.categ){
-tempo.polygon <- data.frame(tempo.polygon, GROUPX = tempo.polygon[, ini.dot.categ], stringsAsFactors = TRUE)
-names(tempo.polygon)[names(tempo.polygon) == "GROUPX"] <- dot.categ
-
-}
-}
-tempo.diamon.mean <- data.frame(X = c(t(stat[, c("X", "X_NOTCH_INF", "X", "X_NOTCH_SUP", "X")])), Y = c(t(cbind(stat["MEAN"] - (stat[, "X"] - stat[, "X_NOTCH_INF"]) * tempo.yx.ratio, stat["MEAN"], stat["MEAN"] + (stat[, "X"] - stat[, "X_NOTCH_INF"]) * tempo.yx.ratio, stat["MEAN"], stat["MEAN"] - (stat[, "X"] - stat[, "X_NOTCH_INF"]) * tempo.yx.ratio, stringsAsFactors = TRUE))), COLOR = c(t(stat[, c("COLOR", "COLOR", "COLOR", "COLOR", "COLOR")])), GROUP = c(t(stat[, c("BOX", "BOX", "BOX", "BOX", "BOX")])), stringsAsFactors = TRUE) # stringsAsFactors = TRUE for cbind() because stat["MEAN"] is a data frame. Otherwise, stringsAsFactors is not an argument for cbind() on vectors
-if( ! is.null(facet.categ)){
-for(i3 in 1:length(facet.categ)){
-tempo.diamon.mean <- data.frame(tempo.diamon.mean, c(t(stat[, c(facet.categ[i3], facet.categ[i3], facet.categ[i3], facet.categ[i3], facet.categ[i3])])), stringsAsFactors = TRUE)
-names(tempo.diamon.mean)[length(names(tempo.diamon.mean))] <- facet.categ[i3]
-}
-}
-tempo.diamon.mean$COLOR <- factor(tempo.diamon.mean$COLOR, levels = unique(categ.color))
-# end creation of the data frame for (main box + legend) and data frame for means
-if(box.fill == TRUE){
-# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, color = categ[length(categ)], fill = categ[length(categ)]), position = ggplot2::position_dodge(width = NULL), width = box.width, size = box.line.size, notch = box.notch, coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf}, alpha = box.alpha, outlier.shape = if( ! is.null(dot.color)){NA}else{21}, outlier.color = if( ! is.null(dot.color)){NA}else{dot.border.color}, outlier.fill = if( ! is.null(dot.color)){NA}else{NULL}, outlier.size = if( ! is.null(dot.color)){NA}else{dot.size}, outlier.stroke = if( ! is.null(dot.color)){NA}else{dot.border.size}, outlier.alpha = if( ! is.null(dot.color)){NA}else{dot.alpha})) # the color, size, etc. of the outliers are dealt here. outlier.color = NA to do not plot outliers when dots are already plotted. Finally, boxplot redrawn (see below)
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_polygon(
-data = tempo.polygon, 
-mapping = ggplot2::aes_string(x = "X", y = "Y", group = "BOX", fill = categ[length(categ)], color = categ[length(categ)]), 
-size = box.line.size, 
-alpha = box.alpha # works only for fill, not for color
-))
-coord.names <- c(coord.names, "main.box")
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X, xend = X, y = BOX_SUP, yend = WHISK_SUP, group = categ[length(categ)]), color = "black", size = box.line.size, alpha = box.alpha)) # 
-coord.names <- c(coord.names, "sup.whisker")
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X, xend = X, y = BOX_INF, yend = WHISK_INF, group = categ[length(categ)]), color = "black", size = box.line.size, alpha = box.alpha)) # 
-coord.names <- c(coord.names, "inf.whisker")
-if(box.whisker.width > 0){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X_WHISK_INF, xend = X_WHISK_SUP, y = WHISK_SUP, yend = WHISK_SUP, group = categ[length(categ)]), color = "black", size = box.line.size, alpha = box.alpha, lineend = "round")) # 
-coord.names <- c(coord.names, "sup.whisker.edge")
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X_WHISK_INF, xend = X_WHISK_SUP, y = WHISK_INF, yend = WHISK_INF, group = categ[length(categ)]), color = "black", size = box.line.size, alpha = box.alpha, lineend = "round")) # 
-coord.names <- c(coord.names, "inf.whisker.edge")
-}
-if(box.mean == TRUE){
-# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(data = stat, mapping = ggplot2::aes_string(x = "X", y = "MEAN", group = categ[length(categ)]), shape = 23, stroke = box.line.size * 2, fill = stat$COLOR, size = box.mean.size, color = "black", alpha = box.alpha)) # group used in aesthetic to do not have it in the legend
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_polygon(
-data = tempo.diamon.mean, 
-mapping = ggplot2::aes(x = X, y = Y, group = GROUP), 
-fill = tempo.diamon.mean[, "COLOR"], 
-color = hsv(0, 0, 0, alpha = box.alpha), # outline of the polygon in black but with alpha
-size = box.line.size, 
-alpha = box.alpha
-))
-coord.names <- c(coord.names, "mean")
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = if(box.notch == FALSE){X_BOX_INF}else{X_NOTCH_INF}, xend = if(box.notch == FALSE){X_BOX_SUP}else{X_NOTCH_SUP}, y = MEDIAN, yend = MEDIAN, group = categ[length(categ)]), color = "black", size = box.line.size * 2, alpha = box.alpha)) # 
-coord.names <- c(coord.names, "median")
-}
-# end boxplot display before dot display if box.fill = TRUE
-
-
-
-
-
-
-# dot display
-if( ! is.null(dot.color)){
-if(dot.tidy == FALSE){
-if(is.null(dot.categ)){
-if(dot.border.size == 0){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(
-data = dot.coord.rd3, 
-mapping = ggplot2::aes_string(x = "dot.x", y = "y", group = categ[length(categ)]), 
-size = dot.size, 
-shape = 19, 
-color = dot.coord.rd3$dot.color, 
-alpha = dot.alpha
-)) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
-}else{
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(
-data = dot.coord.rd3, 
-mapping = ggplot2::aes_string(x = "dot.x", y = "y", group = categ[length(categ)]), 
-shape = 21, 
-stroke = dot.border.size, 
-color = if(is.null(dot.border.color)){dot.coord.rd3$dot.color}else{rep(dot.border.color, nrow(dot.coord.rd3))}, 
-size = dot.size, 
-fill = dot.coord.rd3$dot.color, 
-alpha = dot.alpha
-)) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
-}
-}else{
-if(dot.border.size == 0){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(
-data = dot.coord.rd3, 
-mapping = ggplot2::aes_string(x = "dot.x", y = "y", alpha = dot.categ), 
-size = dot.size, 
-shape = 19, 
-color = dot.coord.rd3$dot.color
-)) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
-}else{
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(
-data = dot.coord.rd3, 
-mapping = ggplot2::aes_string(x = "dot.x", y = "y", alpha = dot.categ), 
-size = dot.size, 
-shape = 21, 
-stroke = dot.border.size, 
-color = if(is.null(dot.border.color)){dot.coord.rd3$dot.color}else{rep(dot.border.color, nrow(dot.coord.rd3))}, 
-fill = dot.coord.rd3$dot.color
-)) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "alpha", name = dot.legend.name, values = rep(dot.alpha, length(dot.categ.class.order)), guide = ggplot2::guide_legend(override.aes = list(fill = dot.color, color = if(is.null(dot.border.color)){dot.color}else{dot.border.color}, stroke = dot.border.size, alpha = dot.alpha)))) # values are the values of color (which is the border color in geom_box. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor
-}
-coord.names <- c(coord.names, "dots")
-}else if(dot.tidy == TRUE){
-# here plot using group -> no scale
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_dotplot(
-data = dot.coord, 
-mapping = ggplot2::aes_string(x = categ[1], y = "y", group = "group"), # not dot.categ here because the classes of dot.categ create new separations
-position = ggplot2::position_dodge(width = box.width), 
-binpositions = "all", 
-binaxis = "y", 
-stackdir = "center", 
-alpha = dot.alpha, 
-fill = dot.coord$dot.color, 
-stroke = dot.border.size, 
-color = if(is.null(dot.border.color)){dot.coord$dot.color}else{rep(dot.border.color, nrow(dot.coord))}, 
-show.legend = FALSE, # WARNING: do not use show.legend = TRUE because it uses the arguments outside aes() as aesthetics (here color and fill). Thus I must find a way using ggplot2::scale_discrete_manual()
-binwidth = (y.lim[2] - y.lim[1]) / dot.tidy.bin.nb
-)) # geom_dotplot ggplot2 v3.3.0: I had to remove rev() in fill and color # very weird behavior of geom_dotplot ggplot2 v3.2.1, (1) because with aes group = (to avoid legend), the dot plotting is not good in term of coordinates, and (2) because data1 seems reorderer according to x = categ[1] before plotting. Thus, I have to use fill = dot.coord[rev(order(dot.coord[, categ[1]], decreasing = TRUE)), "dot.color"] to have the good corresponding colors # show.legend option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
-coord.names <- c(coord.names, "dots")
-if( ! is.null(dot.categ)){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_dotplot(
-data = dot.coord, 
-mapping = ggplot2::aes_string(x = categ[1], y = "y", alpha = dot.categ), # not dot.categ here because the classes of dot.categ create new separations
-position = ggplot2::position_dodge(width = box.width), 
-binpositions = "all", 
-binaxis = "y", 
-stackdir = "center", 
-fill = NA, 
-stroke = NA, 
-color = NA, 
-# WARNING: do not use show.legend = TRUE because it uses the arguments outside aes() as aesthetics (here color and fill). Thus I must find a way using ggplot2::scale_discrete_manual()
-binwidth = (y.lim[2] - y.lim[1]) / dot.tidy.bin.nb
-)) # geom_dotplot ggplot2 v3.3.0: I had to remove rev() in fill and color # very weird behavior of geom_dotplot ggplot2 v3.2.1, (1) because with aes group = (to avoid legend), the dot plotting is not good in term of coordinates, and (2) because data1 seems reorderer according to x = categ[1] before plotting. Thus, I have to use fill = dot.coord[rev(order(dot.coord[, categ[1]], decreasing = TRUE)), "dot.color"] to have the good corresponding colors # show.legend option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
-# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "linetype", name = dot.legend.name, values = rep(1, length(categ.color)))) # values = rep("black", length(categ.color)) are the values of color (which is the border color of dots), and this modify the border color on the plot. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor
-coord.names <- c(coord.names, "bad_remove")
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "alpha", name = dot.legend.name, values = rep(dot.alpha, length(dot.categ.class.order)), labels = dot.categ.class.order, guide = ggplot2::guide_legend(title = if(ini.dot.categ == categ[length(categ)]){dot.categ}else{ini.dot.categ}, override.aes = list(fill = levels(dot.coord$dot.color), color = if(is.null(dot.border.color)){levels(dot.coord$dot.color)}else{dot.border.color}, stroke = dot.border.size, alpha = dot.alpha)))) # values are the values of color (which is the border color in geom_box. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor
-}
-# coordinates of tidy dots
-tempo.coord <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))$data # to have the tidy dot coordinates
-if(length(which(sapply(X = tempo.coord, FUN = function(X){any(names(X) == "binwidth", na.rm = TRUE)}))) != 1){ # detect the compartment of tempo.coord which is the binned data frame
-# if(length(which(sapply(tempo.coord, FUN = nrow) == nrow(data1))) > if(is.null(dot.categ)){1}else{2}){ # this does not work if only one dot per class, thus replaced by above # if(is.null(dot.categ)){1}else{2} because 1 dotplot if dot.categ is NULL and 2 dotplots if not, with the second being a blank dotplot with wrong coordinates. Thus take the first in that situation
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nEITHER MORE THAN 1 OR NO COMPARTMENT HAVING A DATA FRAME WITH binwidth AS COLUMN NAME IN THE tempo.coord LIST (FOR TIDY DOT COORDINATES). CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-# dot.coord.tidy1 <- tempo.coord[[which(sapply(tempo.coord, FUN = nrow) == nrow(data1))[1]]] # this does not work if only one dot per class, thus replaced by above # the second being a blank dotplot with wrong coordinates. Thus take the first whatever situation
-dot.coord.tidy1 <- tempo.coord[[which(sapply(X = tempo.coord, FUN = function(X){any(names(X) == "binwidth", na.rm = TRUE)}))]] # detect the compartment of tempo.coord which is the binned data frame
-dot.coord.tidy1$x <- as.numeric(dot.coord.tidy1$x) # because weird class
-dot.coord.tidy1$PANEL <- as.numeric(dot.coord.tidy1$PANEL) # because numbers as levels. But may be a problem is facet are reordered ?
-}
-# tempo.box.coord <- merge(box.coord, unique(dot.coord[, c("PANEL", "group", categ)]), by = c("PANEL", "group"), sort = FALSE) # not required anymore because box.coord already contains categ do not add dot.categ and tidy_group_coord here because the coordinates are for stats. Add the categ in box.coord. WARNING: by = c("PANEL", "group") without fill column because PANEL & group columns are enough as only one value of x column per group number in box.coord. Thus, no need to consider fill column
-# below inactivated because not true when dealing with dot.categ different from categ
-# if(nrow(tempo.box.coord) != nrow(box.coord)){
-# tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nTHE merge() FUNCTION DID NOT RETURN A CORRECT tempo.box.coord DATA FRAME. CODE HAS TO BE MODIFIED")
-# stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-# }
-dot.coord.tidy2 <- merge(dot.coord.tidy1, box.coord[c("fill", "PANEL", "group", "x", categ)], by = c("PANEL", "group"), sort = FALSE) # send the coord of the boxes into the coord data.frame of the dots (in the column x.y).WARNING: by = c("PANEL", "group") without fill column because PANEL & group columns are enough as only one value of x column per group number in tempo.box.coord. Thus, no need to consider fill colum # DANGER: from here the fill.y and x.y (from tempo.box.coord) are not good in dot.coord.tidy2. It is ok because Categ1 Categ2 from tempo.box.coord are ok with the group column from dot.coord.tidy1. This is due to the fact that dot.coord.tidy resulting from geom_dotplot does not make the same groups as the other functions
-if(nrow(dot.coord.tidy2) != nrow(dot.coord)){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nTHE merge() FUNCTION DID NOT RETURN A CORRECT dot.coord.tidy2 DATA FRAME. CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# From here, check for dot.coord.tidy3 which wil be important for stat over the plot. WARNING: dot.categ has nothing to do here for stat coordinates. Thus, not in tempo.data1
-if(length(categ)== 1L){
-tempo.data1 <- unique(data.frame(data1[categ[1]], group = as.integer(data1[, categ[1]]), stringsAsFactors = TRUE)) # categ[1] is factor
-names(tempo.data1)[names(tempo.data1) == categ[1]] <- paste0(categ[1], ".check")
-verif <- paste0(categ[1], ".check")
-}else if(length(categ) == 2L){
-tempo.data1 <- unique(
-data.frame(
-data1[c(categ[1], categ[2])], 
-group = as.integer(factor(paste0(
-formatC(as.integer(data1[, categ[2]]), width = nchar(max(as.integer(data1[, categ[2]]), na.rm = TRUE)), flag = "0"), # convert factor into numeric with leading zero for proper ranking
-".", 
-formatC(as.integer(data1[, categ[1]]), width = nchar(max(as.integer(data1[, categ[1]]), na.rm = TRUE)), flag = "0")# convert factor into numeric with leading zero for proper ranking
-)), stringsAsFactors = TRUE) # merge the 2 formatC() to create a new factor. The convertion to integer should recreate the correct group number
-)
-) # categ[2] first if categ[2] is used to make the categories in ggplot and categ[1] is used to make the x-axis
-names(tempo.data1)[names(tempo.data1) == categ[1]] <- paste0(categ[1], ".check")
-names(tempo.data1)[names(tempo.data1) == categ[2]] <- paste0(categ[2], ".check")
-verif <- c(paste0(categ[1], ".check"), paste0(categ[2], ".check"))
-}else{
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 4")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-dot.coord.tidy3 <- merge(dot.coord.tidy2, tempo.data1, by = intersect("group", "group"), sort = FALSE) # send the factors of data1 into coord. WARNING: I have tested intersect("group", "group") instead of by = "group". May be come back to by = "group" in case of error. But I did this because of an error in dot.coord.rd3 above
-if(nrow(dot.coord.tidy3) != nrow(dot.coord) | ( ! fun_comp_2d(dot.coord.tidy3[categ], dot.coord.tidy3[verif])$identical.content)){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nTHE merge() FUNCTION DID NOT RETURN A CORRECT dot.coord.tidy3 DATA FRAME. CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end coordinates of tidy dots
-}
-}
-# end dot display
-
-
-
-# boxplot display (if box.fill = FALSE, otherwise, already plotted above)
-if(box.fill == TRUE){
-# overcome "work only for the filling of boxes, not for the frame. See https://github.com/tidyverse/ggplot2/issues/252"
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "fill", name = box.legend.name, values = if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[length(categ)]])))}else{categ.color}, guide = ggplot2::guide_legend(order = 1))) #, guide = ggplot2::guide_legend(override.aes = list(fill = levels(tempo.polygon$COLOR), color = "black")))) # values are the values of color (which is the border color in geom_box. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "color", name = box.legend.name, values = rep(hsv(0, 0, 0, alpha = box.alpha), length(unique(data1[, categ[length(categ)]]))), guide = ggplot2::guide_legend(order = 1))) # , guide = ggplot2::guide_legend(override.aes = list(color = "black", alpha = box.alpha)))) # values are the values of color (which is the border color in geom_box. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor # outline of the polygon in black but with alpha
-}else{
-# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, color = categ[length(categ)], fill = categ[length(categ)]), position = ggplot2::position_dodge(width = NULL), width = box.width, size = box.line.size, notch = box.notch, alpha = box.alpha, coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf}, outlier.shape = if( ! is.null(dot.color)){NA}else{21}, outlier.color = if( ! is.null(dot.color)){NA}else{if(dot.border.size == 0){NA}else{dot.border.color}}, outlier.fill = if( ! is.null(dot.color)){NA}else{NULL}, outlier.size = if( ! is.null(dot.color)){NA}else{dot.size}, outlier.stroke = if( ! is.null(dot.color)){NA}else{dot.border.size}, outlier.alpha = if( ! is.null(dot.color)){NA}else{dot.alpha})) # the color, size, etc. of the outliers are dealt here. outlier.color = NA to do not plot outliers when dots are already plotted
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_path(
-data = tempo.polygon, 
-mapping = ggplot2::aes_string(x = "X", y = "Y", group = "BOX", color = categ[length(categ)]), 
-size = box.line.size, 
-alpha = box.alpha, 
-lineend = "round", 
-linejoin = "round"
-))
-coord.names <- c(coord.names, "main.box")
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = if(box.notch == FALSE){X_BOX_INF}else{X_NOTCH_INF}, xend = if(box.notch == FALSE){X_BOX_SUP}else{X_NOTCH_SUP}, y = MEDIAN, yend = MEDIAN, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size * 2, alpha = box.alpha)) # 
-coord.names <- c(coord.names, "median")
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X, xend = X, y = BOX_SUP, yend = WHISK_SUP, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size, alpha = box.alpha)) # 
-coord.names <- c(coord.names, "sup.whisker")
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X, xend = X, y = BOX_INF, yend = WHISK_INF, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size, alpha = box.alpha)) # 
-coord.names <- c(coord.names, "inf.whisker")
-if(box.whisker.width > 0){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X_WHISK_INF, xend = X_WHISK_SUP, y = WHISK_SUP, yend = WHISK_SUP, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size, alpha = box.alpha, lineend = "round")) # 
-coord.names <- c(coord.names, "sup.whisker.edge")
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X_WHISK_INF, xend = X_WHISK_SUP, y = WHISK_INF, yend = WHISK_INF, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size, alpha = box.alpha, lineend = "round")) # 
-coord.names <- c(coord.names, "inf.whisker.edge")
-}
-if(box.mean == TRUE){
-# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(data = stat, mapping = ggplot2::aes_string(x = "X", y = "MEAN", group = categ[length(categ)]), shape = 23, stroke = box.line.size * 2, color = stat$COLOR, size = box.mean.size, fill = NA, alpha = box.alpha)) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_path(
-data = tempo.diamon.mean, 
-mapping = ggplot2::aes(x = X, y = Y, group = GROUP), 
-color = tempo.diamon.mean[, "COLOR"], 
-size = box.line.size, 
-alpha = box.alpha, 
-lineend = "round", 
-linejoin = "round"
-))
-coord.names <- c(coord.names, "mean")
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "fill", name = box.legend.name, values = rep(NA, length(unique(data1[, categ[length(categ)]]))))) #, guide = ggplot2::guide_legend(override.aes = list(color = categ.color)))) # values are the values of color (which is the border color in geom_box. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "color", name = box.legend.name, values = if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[length(categ)]])))}else{categ.color}, guide = ggplot2::guide_legend(override.aes = list(alpha = if(plot == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list()) == 0L & Sys.info()["sysname"] == "Windows"))){1}else{box.alpha})))) # , guide = ggplot2::guide_legend(override.aes = list(color = as.character(categ.color))))) # values are the values of color (which is the border color in geom_box. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor
-if(plot == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list()) == 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
-# to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE LINES IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-if(box.alpha == 0){ # remove box legend because no boxes drawn
-# add this after the scale_xxx_manual() for boxplots
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::guides(fill = FALSE, color = FALSE)) # inactivate the legend
-}
-# end boxplot display (if box.fill = FALSE, otherwise, already plotted above)
-
-
-
-
-# stat display
-# layer after dots but ok, behind dots on the plot
-if( ! is.null(stat.pos)){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NUMBERS DISPLAYED ARE ", ifelse(stat.mean == FALSE, "MEDIANS", "MEANS"))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-if(stat.pos == "top"){
-tempo.stat <- data.frame(stat, Y = y.lim[2], stringsAsFactors = TRUE) # I had to create a data frame for geom_tex() so that facet is taken into account, (ggplot2::annotate() does not deal with facet because no data and mapping arguments). Of note, facet.categ is in tempo.stat, via tempo.mean, via dot.coord
-if(stat.mean == FALSE){tempo.stat$MEDIAN <- formatC(stat.nolog$MEDIAN, digit = 2, drop0trailing = TRUE, format = "f")}else{tempo.stat$MEAN <- formatC(stat.nolog$MEAN, digit = 2, drop0trailing = TRUE, format = "f")}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_text(
-data = tempo.stat, 
-mapping = ggplot2::aes_string(x = "X", y = "Y", label = ifelse(stat.mean == FALSE, "MEDIAN", "MEAN")),
-size = stat.size, 
-color = "black", 
-angle = stat.angle, 
-hjust = stat.just$hjust, 
-vjust = stat.just$vjust
-)) # stat$X used here because identical to stat.nolog but has the X. WARNING: no need of order() for labels because box.coord$x set the order. For justification, see https://stackoverflow.com/questions/7263849/what-do-hjust-and-vjust-do-when-making-a-plot-using-ggplot
-coord.names <- c(coord.names, "stat.pos")
-}else if(stat.pos == "above"){
-# stat coordinates
-if( ! is.null(dot.color)){ # for text just above max dot
-if(dot.tidy == FALSE){
-tempo.stat.ini <- dot.coord.rd3
-}else if(dot.tidy == TRUE){
-tempo.stat.ini <- dot.coord.tidy3
-tempo.stat.ini$x.y <- tempo.stat.ini$x.x # this is just to be able to use tempo.stat.ini$x.y for untidy or tidy dots (remember that dot.coord.tidy3$x.y is not good, see above)
-}
-stat.coord1 <- aggregate(x = tempo.stat.ini["y"], by = {x.env <- if(length(categ)== 1L){list(tempo.stat.ini$group, tempo.stat.ini$PANEL, tempo.stat.ini$x.y, tempo.stat.ini[, categ[1]])}else if(length(categ) == 2L){list(tempo.stat.ini$group, tempo.stat.ini$PANEL, tempo.stat.ini$x.y, tempo.stat.ini[, categ[1]], tempo.stat.ini[, categ[2]])} ; names(x.env) <- if(length(categ)== 1L){c("group", "PANEL", "x.y", categ[1])}else if(length(categ) == 2L){c("group", "PANEL", "x.y", categ[1], categ[2])} ; x.env}, FUN = min, na.rm = TRUE)
-names(stat.coord1)[names(stat.coord1) == "y"] <- "dot.min"
-stat.coord2 <- aggregate(x = tempo.stat.ini["y"], by = {x.env <- if(length(categ)== 1L){list(tempo.stat.ini$group, tempo.stat.ini$PANEL, tempo.stat.ini$x.y, tempo.stat.ini[, categ[1]])}else if(length(categ) == 2L){list(tempo.stat.ini$group, tempo.stat.ini$PANEL, tempo.stat.ini$x.y, tempo.stat.ini[, categ[1]], tempo.stat.ini[, categ[2]])} ; names(x.env) <- if(length(categ)== 1L){c("group", "PANEL", "x.y", categ[1])}else if(length(categ) == 2L){c("group", "PANEL", "x.y", categ[1], categ[2])} ; x.env}, FUN = max, na.rm = TRUE)
-names(stat.coord2) <- paste0(names(stat.coord2), "_from.dot.max")
-names(stat.coord2)[names(stat.coord2) == "y_from.dot.max"] <- "dot.max"
-stat.coord3 <- cbind(box.coord[order(box.coord$group, box.coord$PANEL), ], stat.coord1[order(stat.coord1$group, stat.coord1$x.y), ], stat.coord2[order(stat.coord2$group, stat.coord2$x.y), ], stringsAsFactors = TRUE) # 
-if( ! all(identical(round(stat.coord3$x, 9), round(as.numeric(stat.coord3$x.y), 9)), na.rm = TRUE)){ # as.numeric() because stat.coord3$x is class "mapped_discrete" "numeric"
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nFUSION OF box.coord, stat.coord1 AND stat.coord2 ACCORDING TO box.coord$x, stat.coord1$x.y AND stat.coord2$x.y IS NOT CORRECT. CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# text.coord <- stat.coord3[, c("x", "group", "dot.min", "dot.max")]
-# names(text.coord)[names(text.coord) == "dot.min"] <- "text.min.pos"
-#names(text.coord)[names(text.coord) == "dot.max"] <- "text.max.pos"
-box.coord <- box.coord[order(box.coord$x, box.coord$group, box.coord$PANEL), ]
-# text.coord <- text.coord[order(text.coord$x), ] # to be sure to have the two objects in the same order for x. WARNING: cannot add identical(as.integer(text.coord$group), as.integer(box.coord$group)) because with error, the correspondence between x and group is not the same
-stat.coord3 <- stat.coord3[order(stat.coord3$x, stat.coord3$group, stat.coord3$PANEL), ] # to be sure to have the two objects in the same order for x. WARNING: cannot add identical(as.integer(text.coord$group), as.integer(box.coord$group)) because with error, the correspondence between x and group is not the same
-if( ! (identical(box.coord$x, stat.coord3$x) & identical(box.coord$group, stat.coord3$group) & identical(box.coord$PANEL, stat.coord3$PANEL))){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\ntext.coord AND box.coord DO NOT HAVE THE SAME x, group AND PANEL COLUMN CONTENT")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}else{
-stat.coord3 <- box.coord
-}
-stat.coord3 <- data.frame(
-stat.coord3, 
-Y = stat.coord3[, ifelse(
-is.null(dot.color), 
-ifelse(diff(y.lim) > 0, "ymax", "ymin"), 
-ifelse(diff(y.lim) > 0, "ymax_final", "ymin_final")
-)], 
-stringsAsFactors = TRUE
-) # ymax is top whisker, ymax_final is top dot
-# stat.coord3 <- data.frame(stat.coord3, Y = vector("numeric", length = nrow(stat.coord3)), stringsAsFactors = TRUE)
-# check.Y <- as.logical(stat.coord3$Y) # convert everything in Y into FALSE (because Y is full of zero)
-# end stat coordinates
-# stat display
-# performed twice: first for y values >=0, then y values < 0, because only a single value allowed for hjust anf vjust
-if(stat.mean == FALSE){
-tempo.center.ref <- "middle"
-}else{
-tempo.center.ref <- "MEAN"
-}
-# if(is.null(dot.color)){
-# tempo.low.ref <- "ymin"
-# tempo.high.ref <- "ymax"
-# }else{
-# tempo.low.ref <- "ymin_final"
-# tempo.high.ref <- "ymax_final"
-# }
-# tempo.log.high <- if(diff(y.lim) > 0){stat.coord3[, tempo.center.ref] >= 0}else{stat.coord3[, tempo.center.ref] < 0}
-# tempo.log.low <- if(diff(y.lim) > 0){stat.coord3[, tempo.center.ref] < 0}else{stat.coord3[, tempo.center.ref] >= 0}
-# stat.coord3$Y[tempo.log.high] <- stat.coord3[tempo.log.high, tempo.high.ref]
-# stat.coord3$Y[tempo.log.low] <- stat.coord3[tempo.log.low, tempo.low.ref]
-# add distance
-stat.coord3$Y <- stat.coord3$Y + diff(y.lim) * stat.dist / 100
-# end add distance
-# correct median or mean text format
-if(y.log != "no"){
-stat.coord3[, tempo.center.ref] <- ifelse(y.log == "log2", 2, 10)^(stat.coord3[, tempo.center.ref])
-}
-stat.coord3[, tempo.center.ref] <- formatC(stat.coord3[, tempo.center.ref], digit = 2, drop0trailing = TRUE, format = "f")
-# end correct median or mean text format
-# if(any(tempo.log.high) == TRUE){
-# tempo.stat <- stat.coord3[tempo.log.high,]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_text(
-data = stat.coord3, 
-mapping = ggplot2::aes_string(x = "x", y = "Y", label = tempo.center.ref),
-size = stat.size, 
-color = "black", 
-angle = stat.angle, 
-hjust = stat.just$hjust, 
-vjust = stat.just$vjust
-)) # WARNING: no need of order() for labels because box.coord$x set the order
-coord.names <- c(coord.names, "stat.pos")
-# }
-# if(any(tempo.log.low) == TRUE){
-# tempo.stat <- stat.coord3[tempo.log.low,]
-# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_text(
-# data = tempo.stat, 
-# mapping = ggplot2::aes_string(x = "x", y = "Y", label = tempo.center.ref),
-# size = stat.size, 
-# color = "black", 
-# hjust = ifelse(vertical == TRUE, 0.5, 0.5 + stat.dist), 
-# vjust = ifelse(vertical == TRUE, 0.5 + stat.dist, 0.5)
-# )) # WARNING: no need of order() for labels because box.coord$x set the order
-# coord.names <- c(coord.names, "stat.pos.negative")
-# }
-# end stat display
-}else{
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 5")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-}
-# end stat display
-# legend management
-if(legend.show == FALSE){ # must be here because must be before bef.final.plot <- 
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::guides(fill = FALSE, color = FALSE, alpha = FALSE)) # inactivate the initial legend
-}
-# end legend management
-
-
-
-# y scale management (cannot be before dot plot management)
-# the rescaling aspect is complicated and not intuitive. See:
-# explaination: https://github.com/tidyverse/ggplot2/issues/3948
-# the oob argument of scale_y_continuous() https://ggplot2.tidyverse.org/reference/scale_continuous.html
-# see also https://github.com/rstudio/cheatsheets/blob/master/data-visualization-2.1.pdf
-# secondary ticks
-bef.final.plot <- ggplot2::ggplot_build(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), ' + if(vertical == TRUE){ggplot2::scale_y_continuous(expand = c(0, 0), limits = sort(y.lim), oob = scales::rescale_none)}else{ggplot2::coord_flip(ylim = y.lim)}')))) # here I do not need the x-axis and y-axis orientation, I just need the number of main ticks and the legend. I DI NOT UNDERSTAND THE COMMENT HERE BECAUSE WE NEED COORD_FLiP
-tempo.coord <- bef.final.plot$layout$panel_params[[1]]
-# y.second.tick.positions: coordinates of secondary ticks (only if y.second.tick.nb argument is non NULL or if y.log argument is different from "no")
-if(y.log != "no"){ # integer main ticks for log2 and log10
-tempo.scale <- (as.integer(min(y.lim, na.rm = TRUE)) - 1):(as.integer(max(y.lim, na.rm = TRUE)) + 1)
-}else{
-tempo <- if(is.null(attributes(tempo.coord$y$breaks))){tempo.coord$y$breaks}else{unlist(attributes(tempo.coord$y$breaks))}
-if(all(is.na(tempo))){# all() without na.rm -> ok because is.na() cannot be NA
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nONLY NA IN tempo.coord$y$breaks")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-tempo.scale <- fun_scale(lim = y.lim, n = ifelse(is.null(y.tick.nb), length(tempo[ ! is.na(tempo)]), y.tick.nb)) # in ggplot 3.3.0, tempo.coord$y.major_source replaced by tempo.coord$y$breaks. If fact: n = ifelse(is.null(y.tick.nb), length(tempo[ ! is.na(tempo)]), y.tick.nb)) replaced by n = ifelse(is.null(y.tick.nb), 4, y.tick.nb))
-}
-y.second.tick.values <- NULL
-y.second.tick.pos <- NULL
-if(y.log != "no"){
-tempo <- fun_inter_ticks(lim = y.lim, log = y.log)
-y.second.tick.values <- tempo$values
-y.second.tick.pos <- tempo$coordinates
-# if(vertical == TRUE){ # do not remove in case the bug is fixed
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", y = y.second.tick.pos, yend = y.second.tick.pos, x = tempo.coord$x.range[1], xend = tempo.coord$x.range[1] + diff(tempo.coord$x.range) / 80))
-# }else{ # not working because of the ggplot2 bug
-# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", x = y.second.tick.pos, xend = y.second.tick.pos, y = tempo.coord$y.range[1], yend = tempo.coord$y.range[1] + diff(tempo.coord$y.range) / 80))
-# }
-coord.names <- c(coord.names, "y.second.tick.positions")
-}else if(( ! is.null(y.second.tick.nb)) & y.log == "no"){
-# if(y.second.tick.nb > 0){ #inactivated because already checked before
-if(length(tempo.scale) < 2){
-tempo.cat1 <- c("y.tick.nb", "y.second.tick.nb")
-tempo.cat2 <- sapply(list(y.tick.nb, y.second.tick.nb), FUN = paste0, collapse = " ")
-tempo.sep <- sapply(mapply(" ", max(nchar(tempo.cat1)) - nchar(tempo.cat1) + 3, FUN = rep, SIMPLIFY = FALSE), FUN = paste0, collapse = "")
-tempo.cat <- paste0("ERROR IN ", function.name, "\nTHE NUMBER OF GENERATED TICKS FOR THE Y-AXIS IS NOT CORRECT: ", length(tempo.scale), "\nUSING THESE ARGUMENT SETTINGS (NO DISPLAY MEANS NULL VALUE):\n", paste0(tempo.cat1, tempo.sep, tempo.cat2, collapse = "\n"), "\nPLEASE, TEST OTHER VALUES")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-tempo <- fun_inter_ticks(lim = y.lim, log = y.log, breaks = tempo.scale, n = y.second.tick.nb)
-}
-y.second.tick.values <- tempo$values
-y.second.tick.pos <- tempo$coordinates
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
-geom = "segment", 
-y = y.second.tick.pos, 
-yend = y.second.tick.pos, 
-x = if(vertical == TRUE){tempo.coord$x.range[1]}else{tempo.coord$y.range[1]}, 
-xend = if(vertical == TRUE){tempo.coord$x.range[1] + diff(tempo.coord$x.range) / 80}else{tempo.coord$y.range[1] + diff(tempo.coord$y.range) / 80}
-))
-coord.names <- c(coord.names, "y.second.tick.positions")
-}
-# end y.second.tick.positions
-# for the ggplot2 bug with y.log, this does not work: eval(parse(text = ifelse(vertical == FALSE & y.log == "log10", "ggplot2::scale_x_continuous", "ggplot2::scale_y_continuous")))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_y_continuous(
-breaks = tempo.scale, 
-minor_breaks = y.second.tick.pos, 
-labels = if(y.log == "log10"){scales::trans_format("identity", scales::math_format(10^.x))}else if(y.log == "log2"){scales::trans_format("identity", scales::math_format(2^.x))}else if(y.log == "no"){ggplot2::waiver()}else{tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 6") ; stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)}, # == in stop() to be able to add several messages between ==
-expand = c(0, 0), # remove space after after axis limits
-limits = sort(y.lim), # NA indicate that limits must correspond to data limits but ylim() already used
-oob = scales::rescale_none, 
-trans = ifelse(diff(y.lim) < 0, "reverse", "identity") # equivalent to ggplot2::scale_y_reverse() but create the problem of y-axis label disappearance with y.lim decreasing. Thus, do not use. Use ylim() below and after this
-))
-if(vertical == TRUE){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::coord_cartesian(ylim = y.lim)) # problem of ggplot2::ylim() is that it redraws new breaks # coord_cartesian(ylim = y.lim)) not used because bug -> y-axis label disappearance with y.lim decreasing I DO NOT UNDERSTAND THIS MESSAGE WHILE I USE COORD_CARTESIAN # clip = "off" to have secondary ticks outside plot region does not work
-}else{
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::coord_flip(ylim = y.lim)) # clip = "off" to have secondary ticks outside plot region does not work # create the problem of y-axis label disappearance with y.lim decreasing. IDEM ABOVE
-
-}
-# end y scale management (cannot be before dot plot management)
-
-
-# legend management
-if( ! is.null(legend.width)){
-legend.final <- fun_gg_get_legend(ggplot_built = bef.final.plot, fun.name = function.name, lib.path = lib.path) # get legend
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::guides(fill = FALSE, color = FALSE, alpha = FALSE)) # inactivate the initial legend
-if(is.null(legend.final) & plot == TRUE){ # even if any(unlist(legend.disp)) is TRUE
-legend.final <- ggplot2::ggplot()+ggplot2::theme_void() # empty graph instead of legend
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") LEGEND REQUESTED (NON NULL categ ARGUMENT OR legend.show ARGUMENT SET TO TRUE)\nBUT IT SEEMS THAT THE PLOT HAS NO LEGEND -> EMPTY LEGEND SPACE CREATED BECAUSE OF THE NON NULL legend.width ARGUMENT\n")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# end legend management
-
-
-# drawing
-fin.plot <- suppressMessages(suppressWarnings(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + ")))))
-grob.save <- NULL
-if(plot == TRUE){
-# following lines inactivated because of problem in warn.recov and message.recov
-# assign("env_fun_get_message", new.env())
-# assign("tempo.gg.name", tempo.gg.name, envir = env_fun_get_message)
-# assign("tempo.gg.count", tempo.gg.count, envir = env_fun_get_message)
-# assign("add", add, envir = env_fun_get_message)
-# two next line: for the moment, I cannot prevent the warning printing
-# warn.recov <- fun_get_message(paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if(is.null(add)){NULL}else{add}), kind = "warning", header = FALSE, print.no = FALSE, env = env_fun_get_message) # for recovering warnings printed by ggplot() functions
-# message.recov <- fun_get_message('print(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if(is.null(add)){NULL}else{add}))))', kind = "message", header = FALSE, print.no = FALSE, env = env_fun_get_message) # for recovering messages printed by ggplot() functions
-# if( ! (return == TRUE & return.ggplot == TRUE)){ # because return() plots when return.ggplot is TRUE # finally not used -> see return.ggplot description
-if(is.null(legend.width)){
-grob.save <- suppressMessages(suppressWarnings(gridExtra::grid.arrange(fin.plot)))
-}else{
-grob.save <-suppressMessages(suppressWarnings(gridExtra::grid.arrange(fin.plot, legend.final, ncol=2, widths=c(1, legend.width))))
-}
-# }
-# suppressMessages(suppressWarnings(print(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if(is.null(add)){NULL}else{add}))))))
-}else{
-# following lines inactivated because of problem in warn.recov and message.recov
-# message.recov <- NULL
-# warn.recov <- NULL
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") PLOT NOT SHOWN AS REQUESTED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# end drawing
-
-
-
-# output
-# following lines inactivated because of problem in warn.recov and message.recov
-# if( ! (is.null(warn) & is.null(warn.recov) & is.null(message.recov))){
-# warn <- paste0(warn, "\n\n", if(length(warn.recov) > 0 | length(message.recov) > 0){paste0(paste0("MESSAGES FROM ggplot2 FUNCTIONS: ", ifelse( ! is.null(warn.recov), unique(message.recov), ""), ifelse( ! is.null(message.recov), unique(message.recov), ""), collapse = "\n\n"), "\n\n")})
-# }else if( ! (is.null(warn) & is.null(warn.recov)) & is.null(message.recov)){
-# warn <- paste0(warn, "\n\n", if(length(warn.recov) > 0){paste0(paste0("MESSAGES FROM ggplot2 FUNCTIONS: ", unique(warn.recov), collapse = "\n\n"), "\n\n")})
-# }else if( ! (is.null(warn) & is.null(message.recov)) & is.null(warn.recov)){
-# warn <- paste0(warn, "\n\n", if(length(message.recov) > 0){paste0(paste0("MESSAGES FROM ggplot2 FUNCTIONS: ", unique(message.recov), collapse = "\n\n"), "\n\n")})
-# }
-if(warn.print == TRUE & ! is.null(warn)){
-on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
-}
-on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
-if(return == TRUE){
-tempo.output <- ggplot2::ggplot_build(fin.plot)
-tempo.output$data <- tempo.output$data[-1] # remove the first data because corresponds to the initial empty boxplot
-if(length(tempo.output$data) != length(coord.names)){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nlength(tempo.output$data) AND length(coord.names) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-names(tempo.output$data) <- coord.names
-tempo.output$data <- tempo.output$data[coord.names != "bad_remove"]
-}
-tempo <- tempo.output$layout$panel_params[[1]]
-output <- list(
-data = data1.ini, 
-stat = stat.nolog, 
-removed.row.nb = removed.row.nb, 
-removed.rows = removed.rows, 
-plot = c(tempo.output$data, y.second.tick.values = list(y.second.tick.values)), 
-panel = facet.categ, 
-axes = list(
-x.range = tempo$x.range, 
-x.labels = if(is.null(attributes(tempo$x$breaks))){tempo$x$breaks}else{tempo$x$scale$get_labels()}, # is.null(attributes(tempo$x$breaks)) test if it is number (TRUE) or character (FALSE)
-x.positions = if(is.null(attributes(tempo$x$breaks))){tempo$x$breaks}else{unlist(attributes(tempo$x$breaks))}, 
-y.range = tempo$y.range, 
-y.labels = if(is.null(attributes(tempo$y$breaks))){tempo$y$breaks}else{tempo$y$scale$get_labels()}, 
-y.positions = if(is.null(attributes(tempo$y$breaks))){tempo$y$breaks}else{unlist(attributes(tempo$y$breaks))}
-), 
-warn = paste0("\n", warn, "\n\n"), 
-ggplot = if(return.ggplot == TRUE){fin.plot}else{NULL}, # fin.plot plots the graph if return == TRUE
-gtable = if(return.gtable == TRUE){grob.save}else{NULL} 
-)
-return(output) # this plots the graph if return.ggplot is TRUE and if no assignment
-}
-# end output
-# end main code
-}
-
-
-
-
-
-
-
-
-
-# add density
-# rasterise all kind: https://cran.r-project.org/web/packages/ggrastr/vignettes/Raster_geoms.html
-# log not good: do not convert as in boxplot
-
-
-fun_gg_scatter <- function(
-data1, 
-x, 
-y, 
-categ = NULL, 
-categ.class.order = NULL, 
-color = NULL, 
-geom = "geom_point", 
-geom.step.dir = "hv", 
-geom.stick.base = NULL, 
-alpha = 0.5, 
-dot.size = 2, 
-dot.shape = 21, 
-dot.border.size = 0.5, 
-dot.border.color = NULL, 
-line.size = 0.5, 
-line.type = "solid", 
-x.lim = NULL, 
-x.lab = NULL, 
-x.log = "no", 
-x.tick.nb = NULL, 
-x.second.tick.nb = NULL, 
-x.include.zero = FALSE, 
-x.left.extra.margin = 0.05, 
-x.right.extra.margin = 0.05, 
-x.text.angle = 0, 
-y.lim = NULL, 
-y.lab = NULL, 
-y.log = "no", 
-y.tick.nb = NULL, 
-y.second.tick.nb = NULL, 
-y.include.zero = FALSE, 
-y.top.extra.margin = 0.05, 
-y.bottom.extra.margin = 0.05, 
-y.text.angle = 0, 
-raster = FALSE, 
-raster.ratio = 1, 
-raster.threshold = NULL, 
-text.size = 12, 
-title = "", 
-title.text.size = 12, 
-legend.show = TRUE, 
-legend.width = 0.5, 
-legend.name = NULL, 
-article = TRUE, 
-grid = FALSE, 
-add = NULL, 
-return = FALSE, 
-return.ggplot = FALSE,
-return.gtable = TRUE,
-plot = TRUE, 
-warn.print = FALSE, 
-lib.path = NULL
-){
-# AIM
-# Plot ggplot2 scatterplot with the possibility to overlay dots from up to 3 different data frames (-> three different legends) and lines from up to 3 different data frames (-> three different legends) -> up to 6 overlays totally
-# For ggplot2 specifications, see: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html
-# WARNINGS
-# Rows containing NA in data1[, c(x, y, categ)] will be removed before processing, with a warning (see below)
-# Size arguments (dot.size, dot.border.size, line.size, text.size and title.text.size) are in mm. See Hadley comment in https://stackoverflow.com/questions/17311917/ggplot2-the-unit-of-size. See also http://sape.inf.usi.ch/quick-reference/ggplot2/size). Unit object are not accepted, but conversion can be used (e.g., grid::convertUnit(grid::unit(0.2, "inches"), "mm", valueOnly = TRUE))
-# ARGUMENTS
-# data1: a dataframe compatible with ggplot2, or a list of data frames. Order matters for the order of the legend and for the layer staking (starting from below to top)
-# x: single character string of the data1 column name for x-axis coordinates. If data1 is a list, then x must be a list of single character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc. Write NULL for each "geom_hline" in geom argument
-# y: single character string of the data1 column name for y-axis coordinates. If data1 is a list, then y must be a list of single character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc. Write NULL for each "geom_vline" in geom argument
-# categ: either NULL or a single character string or a list of single character strings, indicating the data1 column names to use for categories which creates legend display
-# If categ == NULL, no categories -> no legend displayed
-# If data1 is a data frame, categ must be a single character string of the data1 column name for categories
-# If data1 is a list, then categ must be a list of single character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc. Some of the list compartments can be NULL (no legend display for these compartments), and other not
-# categ.class.order: either (1) NULL or (2) a vector of character strings or (3) a list of these vectors, setting the order of the classes of categ in the legend display
-# If categ.class.order is NULL, classes are represented according to the alphabetical order
-# If data1 is a data frame, categ.class.order must be a vector of character strings specifying the different classes in the categ column name of data1
-# If data1 is a list, then categ.class.order must be a list of vector of character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc. Some of the list compartments can be NULL (alphabetical order for these compartments), and other not
-# color: either (1) NULL, or (2) a vector of character strings or integers, or (3) a list of vectors of character strings or integers
-# If color is NULL, default colors of ggplot2
-# If data1 is a data frame, color argument can be either:
-# (1) a single color string. All the dots of the corresponding data1 will have this color, whatever the categ value (NULL or not)
-# (2) if categ is non-null, a vector of string colors, one for each class of categ. Each color will be associated according to the categ.class.order argument if specified, or to the alphabetical order of categ classes otherwise
-# (3) if categ is non-null, a vector or factor of string colors, like if it was one of the column of data1 data frame. WARNING: a single color per class of categ and a single class of categ per color must be respected
-# Positive integers are also accepted instead of character strings, as long as above rules about length are respected. Integers will be processed by fun_gg_palette() using the max integer value among all the integers in color (see fun_gg_palette())
-# If data1 is a list, then color argument must be either: 
-# (1) a list of character strings or integers, of same size as data1, with compartment 1 related to compartment 1 of data1, etc.
-# (2) a single character string or a single integer
-# With a list (first possibility), the rules described for when data1 is a data frame apply to each compartment of the list. Some of the compartments can be NULL. In that case, a different grey color will be used for each NULL compartment. With a single value (second possibility), the same color will be used for all the dots and lines, whatever the data1 list
-# geom: single character string of the kind of plot, or a list of single character strings
-# Either:
-# "geom_point" (scatterplot)
-# "geom_line" (coordinates plotted then line connection, from the lowest to highest x coordinates first and from the lowest to highest y coordinates thenafter)
-# "geom_path" (coordinates plotted then line connection respecting the row order in data1)
-# "geom_step" coordinates plotted then line connection respecting the row order in data1 but drawn in steps). See the geom.step.dir argument
-# "geom_hline" (horizontal line, no x value provided)
-# "geom_vline" (vertical line, no y value provided)
-# "geom_stick" (dots as vertical bars)
-# If data1 is a list, then geom must be either:
-# (1) a list of single character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc.
-# (2) a single character string. In that case the same kind of plot will apply for the different compartments of the data1 list
-# WARNING concerning "geom_hline" or "geom_vline":
-# (1) x or y argument must be NULL, respectively
-# (2) x.lim or y.lim argument must NOT be NULL, respectively, if only these kind of lines are drawn (if other geom present, then x.lim = NULL and y.lim = NULL will generate x.lim and y.lim defined by these other geom, which is not possible with "geom_hline" or "geom_vline" alone)
-# (3) the function will draw n lines for n values in the x argument column name of the data1 data frame. If several colors required, the categ argument must be specified and the corresponding categ column name must exist in the data1 data frame with a different class name for each row
-# geom.step.dir: single character string indicating the direction when using "geom_step" of the geom argument, or a list of single character strings
-# Either:
-# "vh" (vertical then horizontal)
-# "hv" (horizontal then vertical)
-# "mid" (step half-way between adjacent x-values)
-# See https://ggplot2.tidyverse.org/reference/geom_path.html
-# If data1 is a list, then geom.step.dir must be either:
-# (1) a list of single character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc. The value in compartments related to other geom values than "geom_step" will be ignored
-# (2) a single character string, which will be used for all the "geom_step" values of the geom argument, whatever the data1 list
-# geom.stick.base: either (1) NULL or (2) a single numeric value or (3) a list of single numeric values, setting the base of the sticks when using "geom_stick" of the geom argument
-# If geom.stick.base is NULL, the bottom limit of the y-axis is taken as the base
-# If data1 is a list, then geom.stick.base must be either (1) a list of single numeric values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single numeric value. With a list (former possibility), the values in compartments related to other geom values than "geom_stick" will be ignored. With a single value (latter possibility), the same base will be used for all the sticks, whatever the data1 list
-# Warning: the y-axis limits are not modified by the value of geom.stick.base, meaning that this value can be outside of the range of y.lim. Add the value of geom.stick.base also in the y.lim argument if required
-# Warning: if geom.stick.base is NULL, the bottom limit of the y-axis is taken as the base. Thus, be careful with inverted y-axis
-# alpha: single numeric value (from 0 to 1) of transparency. If data1 is a list, then alpha must be either (1) a list of single numeric values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single numeric value. In that case the same transparency will apply for the different compartments of the data1 list
-# dot.size: single numeric value of dot shape radius? in mm. If data1 is a list, then dot.size must be either (1) a list of single numeric values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single numeric value. With a list (former possibility), the value in compartments related to lines will be ignored. With a single value (latter possibility), the same dot.size will be used for all the dots, whatever the data1 list
-# dot.shape: value indicating the shape of the dots (see https://ggplot2.tidyverse.org/articles/ggplot2-specs.html) If data1 is a list, then dot.shape must be either (1) a list of single shape values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single shape value. With a list (former possibility), the value in compartments related to lines will be ignored. With a single value (latter possibility), the same dot.shape will be used for all the dots, whatever the data1 list
-# dot.border.size: single numeric value of border dot width in mm. Write zero for no dot border. If data1 is a list, then dot.border.size must be either (1) a list of single numeric values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single numeric value. With a list (former possibility), the value in compartments related to lines will be ignored. With a single value (latter possibility), the same dot.border.size will be used for all the dots, whatever the data1 list
-# dot.border.color: single character color string defining the color of the dot border (same border color for all the dots, whatever their categories). If dot.border.color == NULL, the border color will be the same as the dot color. A single integer is also accepted instead of a character string, that will be processed by fun_gg_palette()
-# line.size: single numeric value of line width in mm. If data1 is a list, then line.size must be either (1) a list of single numeric values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single numeric value. With a list (former possibility), the value in compartments related to dots will be ignored. With a single value (latter possibility), the same line.size will be used for all the lines, whatever the data1 list
-# line.type: value indicating the kind of lines (see https://ggplot2.tidyverse.org/articles/ggplot2-specs.html) If data1 is a list, then line.type must be either (1) a list of single line kind values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single line kind value. With a list (former possibility), the value in compartments related to dots will be ignored. With a single value (latter possibility), the same line.type will be used for all the lines, whatever the data1 list
-# x.lim: 2 numeric values setting the x-axis range. Order of the 2 values matters (for inverted axis). If NULL, the range of the x column name of data1 will be used
-# x.lab: a character string or expression for x-axis label. If NULL, will use the first value of x (x column name of the first data frame in data1). Warning message if the elements in x are different between data frames in data1
-# x.log: either "no", "log2" (values in the x column name of the data1 data frame will be log2 transformed and x-axis will be log2 scaled) or "log10" (values in the x column name of the data1 data frame will be log10 transformed and x-axis will be log10 scaled)
-# x.tick.nb: approximate number of desired values labeling the x-axis (i.e., main ticks, see the n argument of the the cute::fun_scale() function). If NULL and if x.log is "no", then the number of labeling values is set by ggplot2. If NULL and if x.log is "log2" or "log10", then the number of labeling values corresponds to all the exposant integers in the x.lim range (e.g., 10^1, 10^2 and 10^3, meaning 3 main ticks for x.lim = c(9, 1200)). WARNING: if non-NULL and if x.log is "log2" or "log10", labeling can be difficult to read (e.g., ..., 10^2, 10^2.5, 10^3, ...)
-# x.second.tick.nb: number of desired secondary ticks between main ticks. Ignored if x.log is other than "no" (log scale plotted). Use argument return = TRUE and see $plot$x.second.tick.values to have the values associated to secondary ticks. IF NULL, no secondary ticks
-# x.include.zero: logical. Does x.lim range include 0? Ignored if x.log is "log2" or "log10"
-# x.left.extra.margin: single proportion (between 0 and 1) indicating if extra margins must be added to x.lim. If different from 0, add the range of the axis multiplied by x.left.extra.margin (e.g., abs(x.lim[2] - x.lim[1]) * x.left.extra.margin) to the left of x-axis
-# x.right.extra.margin: idem as x.left.extra.margin but to the right of x-axis
-# x.text.angle: integer value of the text angle for the x-axis labeling values, using the same rules as in ggplot2. Use positive value for clockwise rotation: 0 for horizontal, 90 for vertical, 180 for upside down etc. Use negative values for counterclockwise rotation: 0 for horizontal, -90 for vertical, -180 for upside down etc.
-# y.lim: 2 numeric values setting the y-axis range. Order of the 2 values matters (for inverted axis). If NULL, the range of the y column name of data1 will be used
-# y.lab: a character string or expression for y-axis label. If NULL, will use the first value of y (y column name of the first data frame in data1). Warning message if the elements in y are different between data frames in data1
-# y.log: either "no", "log2" (values in the y column name of the data1 data frame will be log2 transformed and y-axis will be log2 scaled) or "log10" (values in the y column name of the data1 data frame will be log10 transformed and y-axis will be log10 scaled)
-# y.tick.nb: approximate number of desired values labeling the y-axis (i.e., main ticks, see the n argument of the the cute::fun_scale() function). If NULL and if y.log is "no", then the number of labeling values is set by ggplot2. If NULL and if y.log is "log2" or "log10", then the number of labeling values corresponds to all the exposant integers in the y.lim range (e.g., 10^1, 10^2 and 10^3, meaning 3 main ticks for y.lim = c(9, 1200)). WARNING: if non-NULL and if y.log is "log2" or "log10", labeling can be difficult to read (e.g., ..., 10^2, 10^2.5, 10^3, ...)
-# y.second.tick.nb: number of desired secondary ticks between main ticks. Ignored if y.log is other than "no" (log scale plotted). Use argument return = TRUE and see $plot$y.second.tick.values to have the values associated to secondary ticks. IF NULL, no secondary ticks
-# y.include.zero: logical. Does y.lim range include 0? Ignored if y.log is "log2" or "log10"
-# y.top.extra.margin: single proportion (between 0 and 1) indicating if extra margins must be added to y.lim. If different from 0, add the range of the axis multiplied by y.top.extra.margin (e.g., abs(y.lim[2] - y.lim[1]) * y.top.extra.margin) to the top of y-axis
-# y.bottom.extra.margin: idem as y.top.extra.margin but to the bottom of y-axis
-# y.text.angle: integer value of the text angle for the y-axis labeling values, using the same rules as in ggplot2. Use positive value for clockwise rotation: 0 for horizontal, 90 for vertical, 180 for upside down etc. Use negative values for counterclockwise rotation: 0 for horizontal, -90 for vertical, -180 for upside down etc.
-# raster: logical. Dots in raster mode? If FALSE, dots from each "geom_point" from geom argument are plotted in vectorial mode (bigger pdf and long to display if lots of dots). If TRUE, dots from each "geom_point" from geom argument are plotted in matricial mode (smaller pdf and easy display if lots of dots, but it takes time to generate the layer). If TRUE, the raster.ratio argument is used to avoid an ellipsoid representation of the dots. If TRUE, solve the transparency problem with some GUI. Overriden by the non-NULL raster.threshold argument
-# raster.ratio: single numeric value indicating the height / width ratio of the graphic device used (for instance provided by the $dim compartment in the output of the fun_open() function). The default value is 1 because by default R opens a square graphic device. But this argument has to be set when using other device dimensions. Ignored if raster == FALSE
-# raster.threshold: positive integer value indicating the limit of the dot number above which "geom_point" layers from the geom argument switch from vectorial mode to matricial mode (see the raster argument). If any layer is matricial, then the raster.ratio argument is used to avoid an ellipsoid representation of the dots. If non-NULL, it overrides the raster argument
-# text.size: numeric value of the font size of the (1) axis numbers and axis legends and (2) texts in the graphic legend (in mm)
-# title: character string of the graph title
-# title.text.size: numeric value of the title font size in mm
-# legend.show: logical. Show legend? Not considered if categ argument is NULL, because this already generate no legend, excepted if legend.width argument is non-NULL. In that specific case (categ is NULL, legend.show is TRUE and legend.width is non-NULL), an empty legend space is created. This can be useful when desiring graphs of exactly the same width, whatever they have legends or not
-# legend.width: single proportion (between 0 and 1) indicating the relative width of the legend sector (on the right of the plot) relative to the width of the plot. Value 1 means that the window device width is split in 2, half for the plot and half for the legend. Value 0 means no room for the legend, which will overlay the plot region. Write NULL to inactivate the legend sector. In such case, ggplot2 will manage the room required for the legend display, meaning that the width of the plotting region can vary between graphs, depending on the text in the legend
-# legend.name: character string of the legend title. If legend.name is NULL and categ argument is not NULL, then legend.name <- categ. If data1 is a list, then legend.name must be a list of character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc. Some of the list compartments can be NULL, and other not
-# article: logical. If TRUE, use an article theme (article like). If FALSE, use a classic related ggplot theme. Use the add argument (e.g., add = "+ggplot2::theme_classic()" for the exact classic ggplot theme
-# grid: logical. Draw lines in the background to better read the box values? Not considered if article == FALSE (grid systematically present)
-# add: character string allowing to add more ggplot2 features (dots, lines, themes, facet, etc.). Ignored if NULL
-# WARNING: (1) the string must start with "+", (2) the string must finish with ")" and (3) each function must be preceded by "ggplot2::". Example: "+ ggplot2::coord_flip() + ggplot2::theme_bw()"
-# If the character string contains the "ggplot2::theme" string, then the article argument of fun_gg_scatter() (see above) is ignored with a warning. In addition, some arguments can be overwritten, like x.angle (check all the arguments)
-# Handle the add argument with caution since added functions can create conflicts with the preexisting internal ggplot2 functions
-# WARNING: the call of objects inside the quotes of add can lead to an error if the name of these objects are some of the fun_gg_scatter() arguments. Indeed, the function will use the internal argument instead of the global environment object. Example article <- "a" in the working environment and add = '+ ggplot2::ggtitle(article)'. The risk here is to have TRUE as title. To solve this, use add = '+ ggplot2::ggtitle(get("article", envir = .GlobalEnv))'
-# return: logical. Return the graph parameters?
-# return.ggplot: logical. Return the ggplot object in the output list? Ignored if return argument is FALSE. WARNING: always assign the fun_gg_scatter() function (e.g., a <- fun_gg_scatter()) if return.ggplot argument is TRUE, otherwise, double plotting is performed. See $ggplot in the RETURN section below for more details
-# return.gtable: logical. Return the ggplot object as gtable of grobs in the output list? Ignored if plot argument is FALSE. Indeed, the graph must be plotted to get the grobs dispositions. See $gtable in the RETURN section below for more details
-# plot: logical. Plot the graphic? If FALSE and return argument is TRUE, graphical parameters and associated warnings are provided without plotting
-# warn.print: logical. Print warnings at the end of the execution? ? If FALSE, warning messages are never printed, but can still be recovered in the returned list. Some of the warning messages (those delivered by the internal ggplot2 functions) are not apparent when using the argument plot = FALSE
-# lib.path: character string indicating the absolute path of the required packages (see below). if NULL, the function will use the R library default folders
-# RETURN
-# a scatter plot if plot argument is TRUE
-# a list of the graph info if return argument is TRUE:
-# $data: the initial data with graphic information added. WARNING: if the x.log or y.log argument is not "no", x or y argument column of the data1 data frame are log2 or log10 converted in $data, respectively. Use 2^values or 10^$values to recover the initial values
-# $removed.row.nb: a list of the removed rows numbers in data frames (because of NA). NULL if no row removed
-# $removed.rows: a list of the removed rows in data frames (because of NA). NULL if no row removed
-# $plot: the graphic box and dot coordinates
-# $dots: dot coordinates
-# y.second.tick.positions: coordinates of secondary ticks (only if y.second.tick.nb argument is non-null or if y.log argument is different from "no")
-# y.second.tick.values: values of secondary ticks. NULL except if y.second.tick.nb argument is non-null or if y.log argument is different from "no")
-# $panel: the variable names used for the panels (NULL if no panels). WARNING: NA can be present according to ggplot2 upgrade to v3.3.0
-# $axes: the x-axis and y-axis info
-# $warn: the warning messages. Use cat() for proper display. NULL if no warning. WARNING: warning messages delivered by the internal ggplot2 functions are not apparent when using the argument plot = FALSE
-# $ggplot: ggplot object that can be used for reprint (use print($ggplot) or update (use $ggplot + ggplot2::...). NULL if return.ggplot argument is FALSE. Of note, a non-null $ggplot in the output list is sometimes annoying as the manipulation of this list prints the plot
-# $gtable: gtable object that can be used for reprint (use gridExtra::grid.arrange(...$ggplot) or with additionnal grobs (see the grob decomposition in the examples). NULL if return.ggplot argument is FALSE. Contrary to $ggplot, a non-NULL $gtable in the output list is not annoying as the manipulation of this list does not print the plot
-# REQUIRED PACKAGES
-# ggplot2
-# gridExtra
-# lemon (in case of use in the add argument)
-# scales
-# if raster plots are drawn (see the raster and raster.threshold arguments):
-# Cairo
-# grid
-# REQUIRED FUNCTIONS FROM THE cute PACKAGE
-# fun_gg_empty_graph()
-# fun_gg_palette()
-# fun_gg_point_rast()
-# fun_pack()
-# fun_check()
-# fun_round()
-# fun_scale()
-# fun_inter_ticks()
-# EXAMPLES
-# set.seed(1) ; obs1 <- data.frame(Km = c(2, 1, 6, 5, 4, 7), Time = c(2, 1, 6, 5, 4, 7)^2, Car = c("TUUT", "TUUT", "TUUT", "WIIM", "WIIM", "WIIM"), Color1 = rep(c("coral", "lightblue"), each = 3), stringsAsFactors = TRUE) ; fun_gg_scatter(data1 = obs1, x = "Km", y = "Time")
-# DEBUGGING
-# set.seed(1) ; obs1 <- data.frame(km = rnorm(1000, 10, 3), time = rnorm(1000, 10, 3), group1 = rep(c("A1", "A2"), 500), stringsAsFactors = TRUE) ; obs2 <-data.frame(km = rnorm(1000, 15, 3), time = rnorm(1000, 15, 3), group2 = rep(c("G1", "G2"), 500), stringsAsFactors = TRUE) ; set.seed(NULL) ; obs1$km[2:3] <- NA ; data1 = list(L1 = obs1, L2 = obs2) ; x = list(L1 = "km", L2 = "km") ; y = list(L1 = "time", L2 = "time") ; categ = list(L1 = "group1", L2 = "group2") ; categ = NULL ; categ.class.order = NULL ; color = NULL ; geom = "geom_point" ; geom.step.dir = "hv" ; geom.stick.base = NULL ; alpha = 0.5 ; dot.size = 2 ; dot.shape = 21 ; dot.border.size = 0.5 ; dot.border.color = NULL ; line.size = 0.5 ; line.type = "solid" ; x.lim = NULL ; x.lab = NULL ; x.log = "no" ; x.tick.nb = NULL ; x.second.tick.nb = NULL ; x.include.zero = FALSE ; x.left.extra.margin = 0.05 ; x.right.extra.margin = 0.05 ; x.text.angle = 0 ; y.lim = NULL ; y.lab = NULL ; y.log = "no" ; y.tick.nb = NULL ; y.second.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0.05 ; y.text.angle = 0 ; raster = FALSE ; raster.ratio = 1 ; raster.threshold = NULL ; text.size = 12 ; title = "" ; title.text.size = 12 ; legend.show = TRUE ; legend.width = 0.5 ; legend.name = NULL ; article = TRUE ; grid = FALSE ; add = NULL ; return = FALSE ; return.ggplot = FALSE ; return.gtable = TRUE ; plot = TRUE ; warn.print = FALSE ; lib.path = NULL
-# function name
-function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
-arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
-arg.user.setting <- as.list(match.call(expand.dots=FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
-# end function name
-# required function checking
-req.function <- c(
-"fun_check", 
-"fun_gg_just", 
-"fun_gg_empty_graph", 
-"fun_gg_palette", 
-"fun_gg_point_rast", 
-"fun_round", 
-"fun_pack", 
-"fun_scale", 
-"fun_inter_ticks"
-)
-tempo <- NULL
-for(i1 in req.function){
-if(length(find(i1, mode = "function"))== 0L){
-tempo <- c(tempo, i1)
-}
-}
-if( ! is.null(tempo)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end required function checking
-# reserved words to avoid bugs (used in this function)
-reserved.words <- c("fake_x", "fake_y", "fake_categ")
-# end reserved words to avoid bugs (used in this function)
-# arg with no default values
-mandat.args <- c(
-"data1", 
-"x", 
-"y"
-)
-tempo <- eval(parse(text = paste0("missing(", paste0(mandat.args, collapse = ") | missing("), ")")))
-if(any(tempo)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(length(mandat.args) > 1, "S HAVE", "HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end arg with no default values
-# argument primary checking
-arg.check <- NULL #
-text.check <- NULL #
-checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
-ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
-tempo1 <- fun_check(data = data1, class = "data.frame", na.contain = TRUE, fun.name = function.name)
-tempo2 <- fun_check(data = data1, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data1 ARGUMENT MUST BE A DATA FRAME OR A LIST OF DATA FRAMES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-if( ! is.null(x)){
-tempo1 <- fun_check(data = x, class = "vector", mode = "character", na.contain = TRUE, length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = x, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = x, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(y)){
-tempo1 <- fun_check(data = y, class = "vector", mode = "character", na.contain = TRUE, length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = y, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": y ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = y, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(categ)){
-tempo1 <- fun_check(data = categ, class = "vector", mode = "character", length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = categ, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": categ ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = categ, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(categ.class.order)){
-if(is.null(categ)){
-tempo.cat <- paste0("ERROR IN ", function.name, ": categ.class.order ARGUMENT IS NOT NULL, BUT categ IS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo1 <- fun_check(data = categ.class.order, class = "vector", mode = "character", fun.name = function.name)
-tempo2 <- fun_check(data = categ.class.order, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": categ.class.order ARGUMENT MUST BE A VECTOR OF CHARACTER STRINGS OR A LIST OF VECTOR OF CHARACTER STRINGS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = categ.class.order, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(legend.name)){
-tempo1 <- fun_check(data = legend.name, class = "vector", mode = "character", na.contain = TRUE, length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = legend.name, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": legend.name ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = legend.name, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(color)){
-tempo1 <- fun_check(data = color, class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name)
-tempo2 <- fun_check(data = color, class = "factor", na.contain = TRUE, fun.name = function.name)
-tempo3 <- fun_check(data = color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name)
-tempo4 <- fun_check(data = color, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo4$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE & tempo3$problem == TRUE & tempo4$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": color ARGUMENT MUST BE A VECTOR (OF CHARACTER STRINGS OR INTEGERS) OR A FACTOR OR A LIST OF THESE POSSIBILITIES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = color, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo1 <- fun_check(data = geom, class = "vector", mode = "character", na.contain = FALSE, length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = geom, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": geom ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo1 <- fun_check(data = geom.step.dir, options = c("vh", "hv", "mid"), na.contain = FALSE, length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = geom.step.dir, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": geom.step.dir ARGUMENT MUST BE A SINGLE CHARACTER STRING (\"vh\" OR \"hv\" OR \"mid\") OR A LIST OF THESE CHARACTER STRINGS")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-if( ! is.null(geom.stick.base)){
-tempo1 <- fun_check(data = geom.stick.base, class = "vector", mode = "numeric", na.contain = FALSE, length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = color, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": geom.stick.base ARGUMENT MUST BE A SINGLE NUMERIC VALUE OR A LIST OF SINGLE NUMERIC VALUES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = geom.stick.base, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo1 <- fun_check(data = alpha, prop = TRUE, length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = alpha, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": alpha ARGUMENT MUST BE A SINGLE NUMERIC VALUE BETWEEN 0 AND 1 OR A LIST OF SUCH VALUES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo1 <- fun_check(data = dot.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name)
-tempo2 <- fun_check(data = dot.size, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": dot.size ARGUMENT MUST BE A SINGLE NUMERIC VALUE OR A LIST OF SINGLE NUMERIC VALUES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo1 <- fun_check(data = dot.shape, class = "vector", length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = dot.shape, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": dot.shape ARGUMENT MUST BE A SINGLE SHAPE VALUE OR A LIST OF SINGLE SHAPE VALUES (SEE https://ggplot2.tidyverse.org/articles/ggplot2-specs.html)")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo1 <- fun_check(data = dot.border.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name)
-tempo2 <- fun_check(data = dot.border.size, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.size ARGUMENT MUST BE A SINGLE NUMERIC VALUE OR A LIST OF SINGLE NUMERIC VALUES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-if( ! is.null(dot.border.color)){
-tempo1 <- fun_check(data = dot.border.color, class = "vector", mode = "character", length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = dot.border.color, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-# integer colors -> gg_palette
-tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.color MUST BE A SINGLE CHARACTER STRING OF COLOR OR A SINGLE INTEGER VALUE")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = dot.border.color, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo1 <- fun_check(data = line.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name)
-tempo2 <- fun_check(data = line.size, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo2$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": line.size ARGUMENT MUST BE A SINGLE NUMERIC VALUE OR A LIST OF SINGLE NUMERIC VALUES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-tempo1 <- fun_check(data = line.type, class = "vector", typeof = "integer", double.as.integer.allowed = FALSE, length = 1, fun.name = function.name)
-tempo2 <- fun_check(data = line.type, class = "vector", mode = "character", length = 1, fun.name = function.name)
-tempo3 <- fun_check(data = line.type, class = "list", na.contain = TRUE, fun.name = function.name)
-checked.arg.names <- c(checked.arg.names, tempo3$object.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE & tempo3$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": line.type ARGUMENT MUST BE A SINGLE LINE KIND VALUE OR A LIST OF SINGLE LINE KIND VALUES (SEE https://ggplot2.tidyverse.org/articles/ggplot2-specs.html)")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-if( ! is.null(x.lim)){
-tempo <- fun_check(data = x.lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & any(x.lim %in% c(Inf, -Inf))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x.lim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = x.lim, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(x.lab)){
-if(all(class(x.lab) %in% "expression")){ # to deal with math symbols
-tempo <- fun_check(data = x.lab, class = "expression", length = 1, fun.name = function.name) ; eval(ee)
-}else{
-tempo <- fun_check(data = x.lab, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = x.lab, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = x.log, options = c("no", "log2", "log10"), length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(x.tick.nb)){
-tempo <- fun_check(data = x.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & x.tick.nb < 0){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x.tick.nb ARGUMENT MUST BE A NON-NULL POSITIVE INTEGER")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = x.tick.nb, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(x.second.tick.nb)){
-tempo <- fun_check(data = x.second.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & x.second.tick.nb <= 0){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x.second.tick.nb ARGUMENT MUST BE A NON-NULL POSITIVE INTEGER")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = x.second.tick.nb, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = x.include.zero, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = x.left.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = x.right.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = x.text.angle, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, neg.values = TRUE, fun.name = function.name) ; eval(ee)
-if( ! is.null(y.lim)){
-tempo <- fun_check(data = y.lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & any(y.lim %in% c(Inf, -Inf))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": y.lim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = y.lim, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(y.lab)){
-if(all(class(y.lab) %in% "expression")){ # to deal with math symbols
-tempo <- fun_check(data = y.lab, class = "expression", length = 1, fun.name = function.name) ; eval(ee)
-}else{
-tempo <- fun_check(data = y.lab, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = y.lab, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = y.log, options = c("no", "log2", "log10"), length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(y.tick.nb)){
-tempo <- fun_check(data = y.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & y.tick.nb < 0){
-tempo.cat <- paste0("ERROR IN ", function.name, ": y.tick.nb ARGUMENT MUST BE A NON-NULL POSITIVE INTEGER")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = y.tick.nb, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if( ! is.null(y.second.tick.nb)){
-tempo <- fun_check(data = y.second.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE & y.second.tick.nb <= 0){
-tempo.cat <- paste0("ERROR IN ", function.name, ": y.second.tick.nb ARGUMENT MUST BE A NON-NULL POSITIVE INTEGER")
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = y.second.tick.nb, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = y.include.zero, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y.top.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y.bottom.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = y.text.angle, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, neg.values = TRUE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = raster, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = raster.ratio, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-if( ! is.null(raster.threshold)){
-tempo <- fun_check(data = raster.threshold, class = "vector", typeof = "integer", neg.values = FALSE, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = raster.threshold, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = title, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = title.text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = legend.show, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(legend.width)){
-tempo <- fun_check(data = legend.width, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = legend.width, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = article, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = grid, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(add)){
-tempo <- fun_check(data = add, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = add, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-tempo <- fun_check(data = return, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = return.ggplot, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = return.gtable, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = plot, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
-if( ! is.null(lib.path)){
-tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
-if(tempo$problem == FALSE){
-if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
-tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
-text.check <- c(text.check, tempo.cat)
-arg.check <- c(arg.check, TRUE)
-}
-}
-}else{
-# no fun_check test here, it is just for checked.arg.names
-tempo <- fun_check(data = lib.path, class = "vector")
-checked.arg.names <- c(checked.arg.names, tempo$object.name)
-}
-if(any(arg.check) == TRUE){
-stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
-}
-# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
-# end argument primary checking
-
-
-# second round of checking and data preparation
-# management of NA arguments
-tempo.arg <- names(arg.user.setting) # values provided by the user
-tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length)== 1L # no argument provided by the user can be just NA
-if(any(tempo.log) == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT JUST BE NA")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NA arguments
-# management of NULL arguments
-tempo.arg <-c(
-"data1", 
-# "x", # inactivated because of hline or vline
-# "y", # inactivated because of hline or vline
-"geom", 
-"geom.step.dir", 
-# "geom.stick.base", # inactivated because can be null
-"alpha", 
-"dot.size", 
-"dot.shape", 
-"dot.border.size", 
-"line.size", 
-"line.type", 
-"x.log", 
-"x.include.zero", 
-"x.left.extra.margin", 
-"x.right.extra.margin", 
-"x.text.angle", 
-"y.log", 
-"y.include.zero", 
-"y.top.extra.margin", 
-"y.bottom.extra.margin", 
-"y.text.angle", 
-"raster", 
-"raster.ratio", 
-"text.size", 
-"title", 
-"title.text.size", 
-"legend.show", 
-# "legend.width", # inactivated because can be null
-"article", 
-"grid", 
-"return", 
-"return.ggplot", 
-"return.gtable", 
-"plot", 
-"warn.print"
-)
-tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
-if(any(tempo.log) == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
-}
-# end management of NULL arguments
-# code that protects set.seed() in the global environment
-# end code that protects set.seed() in the global environment
-# warning initiation
-ini.warning.length <- options()$warning.length
-options(warning.length = 8170)
-warn <- NULL
-warn.count <- 0
-# end warning initiation
-# other checkings
-# check list lengths (and names of data1 compartments if present)
-list.color <- NULL
-list.geom <- NULL
-list.geom.step.dir <- NULL
-list.geom.stick.base <- NULL
-list.alpha <- NULL
-list.dot.size <- NULL
-list.dot.shape <- NULL
-list.dot.border.size <- NULL
-list.dot.border.color <- NULL
-list.line.size <- NULL
-list.line.type <- NULL
-if(all(class(data1) == "list")){
-if(length(data1) > 6){
-tempo.cat <- paste0("ERROR IN ", function.name, ": data1 ARGUMENT MUST BE A LIST OF 6 DATA FRAMES MAXIMUM (6 OVERLAYS MAX)")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-if(is.null(names(data1))){
-names(data1) <- paste0("L", 1:length(data1))
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NULL NAME COMPARTMENT OF data1 LIST -> NAMES RESPECTIVELY ATTRIBUTED TO EACH COMPARTMENT:\n", paste(names(data1), collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-if( ! is.null(x)){
-if( ! (all(class(x) == "list") & length(data1) == length(x))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}else{
-x <- vector("list", length(data1))
-}
-if( ! is.null(y)){
-if( ! (all(class(y) == "list") & length(data1) == length(y))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": y ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}else{
-y <- vector("list", length(data1))
-}
-if( ! is.null(categ)){
-if( ! (all(class(categ) == "list") & length(data1) == length(categ))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": categ ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-if( ! is.null(categ.class.order)){
-if( ! (all(class(categ.class.order) == "list") & length(data1) == length(categ.class.order))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": categ.class.order ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-if( ! is.null(color)){
-if( ! ((all(class(color) == "list") & length(data1) == length(color)) | ((all(mode(color) == "character") | all(mode(color) == "numeric")) & length(color)== 1L))){ # list of same length as data1 or single value
-tempo.cat <- paste0("ERROR IN ", function.name, ": color ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE CHARACTER STRING OR INTEGER")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if((all(mode(color) == "character") | all(mode(color) == "numeric")) & length(color)== 1L){ # convert the single value into a list of single value
-list.color <- vector(mode = "list", length = length(data1))
-list.color[] <- color
-}
-}
-if( ! ((all(class(geom) == "list") & length(data1) == length(geom)) | (all(mode(geom) == "character") & length(geom)== 1L))){ # list of same length as data1 or single value
-tempo.cat <- paste0("ERROR IN ", function.name, ": geom ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE CHARACTER VALUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(all(mode(geom) == "character") & length(geom)== 1L){ # convert the single value into a list of single value
-list.geom <- vector(mode = "list", length = length(data1))
-list.geom[] <- geom
-}
-if( ! ((all(class(geom.step.dir) == "list") & length(data1) == length(geom.step.dir)) | (all(mode(geom.step.dir) == "character") & length(geom.step.dir)== 1L))){ # list of same length as data1 or single value
-tempo.cat <- paste0("ERROR IN ", function.name, ": geom.step.dir ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE CHARACTER VALUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(all(mode(geom.step.dir) == "character") & length(geom.step.dir)== 1L){ # convert the single value into a list of single value
-list.geom.step.dir <- vector(mode = "list", length = length(data1))
-list.geom.step.dir[] <- geom.step.dir
-}
-if( ! is.null(geom.stick.base)){
-if( ! ((all(class(geom.stick.base) == "list") & length(data1) == length(geom.stick.base)) | (all(mode(geom.stick.base) == "numeric") & length(geom.stick.base)== 1L))){ # list of same length as data1 or single value
-tempo.cat <- paste0("ERROR IN ", function.name, ": geom.stick.base ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE NUMERIC VALUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(all(mode(geom.stick.base) == "numeric") & length(geom.stick.base)== 1L){ # convert the single value into a list of single value
-list.geom.stick.base <- vector(mode = "list", length = length(data1))
-list.geom.stick.base[] <- geom.stick.base
-}
-}
-if( ! ((all(class(alpha) == "list") & length(data1) == length(alpha)) | (all(mode(alpha) == "numeric") & length(alpha)== 1L))){ # list of same length as data1 or single value
-tempo.cat <- paste0("ERROR IN ", function.name, ": alpha ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE NUMERIC VALUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(all(mode(alpha) == "numeric") & length(alpha)== 1L){ # convert the single value into a list of single value
-list.alpha <- vector(mode = "list", length = length(data1))
-list.alpha[] <- alpha
-}
-if( ! ((all(class(dot.size) == "list") & length(data1) == length(dot.size)) | (all(mode(dot.size) == "numeric") & length(dot.size)== 1L))){ # list of same length as data1 or single value
-tempo.cat <- paste0("ERROR IN ", function.name, ": dot.size ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE NUMERIC VALUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(all(mode(dot.size) == "numeric") & length(dot.size)== 1L){ # convert the single value into a list of single value
-list.dot.size <- vector(mode = "list", length = length(data1))
-list.dot.size[] <- dot.size
-}
-if( ! ((all(class(dot.shape) == "list") & length(data1) == length(dot.shape)) | (all(mode(dot.shape) != "list") & length(dot.shape)== 1L))){ # list of same length as data1 or single value
-tempo.cat <- paste0("ERROR IN ", function.name, ": dot.shape ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE SHAPE VALUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(all(mode(dot.shape) != "list") & length(dot.shape)== 1L){ # convert the single value into a list of single value
-list.dot.shape <- vector(mode = "list", length = length(data1))
-list.dot.shape[] <- dot.shape
-}
-if( ! ((all(class(dot.border.size) == "list") & length(data1) == length(dot.border.size)) | (all(mode(dot.border.size) == "numeric") & length(dot.border.size)== 1L))){ # list of same length as data1 or single value
-tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.size ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE NUMERIC VALUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(all(mode(dot.border.size) == "numeric") & length(dot.border.size)== 1L){ # convert the single value into a list of single value
-list.dot.border.size <- vector(mode = "list", length = length(data1))
-list.dot.border.size[] <- dot.border.size
-}
-if( ! is.null(dot.border.color)){
-if( ! ((all(class(dot.border.color) == "list") & length(data1) == length(dot.border.color)) | ((all(mode(dot.border.color) == "character") | all(mode(dot.border.color) == "numeric")) & length(dot.border.color)== 1L))){ # list of same length as data1 or single value
-tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.color ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE CHARACTER STRING OR INTEGER")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if((all(mode(dot.border.color) == "character") | all(mode(dot.border.color) == "numeric")) & length(dot.border.color)== 1L){ # convert the single value into a list of single value
-list.dot.border.color <- vector(mode = "list", length = length(data1))
-list.dot.border.color[] <- dot.border.color
-}
-}
-if( ! ((all(class(line.size) == "list") & length(data1) == length(line.size)) | (all(mode(line.size) == "numeric") & length(line.size)== 1L))){ # list of same length as data1 or single value
-tempo.cat <- paste0("ERROR IN ", function.name, ": line.size ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE NUMERIC VALUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(all(mode(line.size) == "numeric") & length(line.size)== 1L){ # convert the single value into a list of single value
-list.line.size <- vector(mode = "list", length = length(data1))
-list.line.size[] <- line.size
-}
-if( ! ((all(class(line.type) == "list") & length(data1) == length(line.type)) | (all(mode(line.type) != "list") & length(line.type)== 1L))){ # list of same length as data1 or single value
-tempo.cat <- paste0("ERROR IN ", function.name, ": line.type ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE LINE KIND VALUE")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(all(mode(line.type) != "list") & length(line.type)== 1L){ # convert the single value into a list of single value
-list.line.type <- vector(mode = "list", length = length(data1))
-list.line.type[] <- line.type
-}
-if( ! is.null(legend.name)){
-if( ! (all(class(legend.name) == "list") & length(data1) == length(legend.name))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": legend.name ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-}
-# end check list lengths (and names of data1 compartments if present)
-# conversion into lists
-if(all(is.data.frame(data1))){
-data1 <- list(L1 = data1)
-if(all(class(x) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": x ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-x <- list(L1 = x)
-}
-if(all(class(y) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": y ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-y <- list(L1 = y)
-}
-if( ! is.null(categ)){
-if(all(class(categ) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": categ ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-categ <- list(L1 = categ)
-}
-}
-if( ! is.null(categ.class.order)){
-if(all(class(categ.class.order) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": categ.class.order ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-categ.class.order <- list(L1 = categ.class.order)
-}
-}
-if( ! is.null(color)){
-if(all(class(color) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": color ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-color <- list(L1 = color)
-}
-}
-if(all(class(geom) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": geom ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-geom <- list(L1 = geom)
-}
-if(all(class(geom.step.dir) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": geom.step.dir ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-geom.step.dir <- list(L1 = geom.step.dir)
-}
-if( ! is.null(geom.stick.base)){
-if(all(class(geom.stick.base) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": geom.stick.base ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-geom.stick.base <- list(L1 = geom.stick.base)
-}
-}
-if(all(class(alpha) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": alpha ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-alpha <- list(L1 = alpha)
-}
-if(all(class(dot.size) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": dot.size ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-dot.size <- list(L1 = dot.size)
-}
-if(all(class(dot.shape) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": dot.shape ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-dot.shape <- list(L1 = dot.shape)
-}
-if(all(class(dot.border.size) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.size ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-dot.border.size <- list(L1 = dot.border.size)
-}
-if( ! is.null(dot.border.color)){
-if(all(class(dot.border.color) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.color ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-dot.border.color <- list(L1 = dot.border.color)
-}
-}
-if(all(class(line.size) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": line.size ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-line.size <- list(L1 = line.size)
-}
-if(all(class(line.type) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": line.type ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-line.type <- list(L1 = line.type)
-}
-if( ! is.null(legend.name)){
-if(all(class(legend.name) == "list")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": legend.name ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-legend.name <- list(L1 = legend.name)
-}
-}
-}else if( ! all(sapply(data1, FUN = "class") == "data.frame")){ # if not a data frame, data1 can only be a list, as tested above
-tempo.cat <- paste0("ERROR IN ", function.name, ": data1 ARGUMENT MUST BE A DATA FRAME OR A LIST OF DATA FRAMES")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-# single value converted into list now reattributed to the argument name
-if( ! is.null(color)){
-if( ! is.null(list.color)){
-color <- list.color
-}
-}
-if( ! is.null(list.geom)){
-geom <- list.geom
-}
-if( ! is.null(list.geom.step.dir)){
-geom.step.dir <- list.geom.step.dir
-}
-if( ! is.null(geom.stick.base)){
-if( ! is.null(list.geom.stick.base)){
-geom.stick.base <- list.geom.stick.base
-}
-}
-if( ! is.null(list.alpha)){
-alpha <- list.alpha
-}
-if( ! is.null(list.dot.size)){
-dot.size <- list.dot.size
-}
-if( ! is.null(list.dot.shape)){
-dot.shape <- list.dot.shape
-}
-if( ! is.null(list.dot.border.size)){
-dot.border.size <- list.dot.border.size
-}
-if( ! is.null(dot.border.color)){
-if( ! is.null(list.dot.border.color)){
-dot.border.color <- list.dot.border.color
-}
-}
-if( ! is.null(list.line.size)){
-line.size <- list.line.size
-}
-if( ! is.null(list.line.type)){
-line.type <- list.line.type
-}
-# end single value converted into list now reattributed to the argument name
-# data, x, y, geom, alpha, dot.size, shape, dot.border.size, line.size, line.type, legend.name are list now
-# if non-null, categ, categ.class.order, legend.name, color, dot.border.color are list now
-# end conversion into lists
-# verif of add
-if( ! is.null(add)){
-if( ! grepl(pattern = "^\\s*\\+", add)){ # check that the add string start by +
-tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST START WITH \"+\": ", paste(unique(add), collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-
-}else if( ! grepl(pattern = "(ggplot2|lemon)\\s*::", add)){ #
-tempo.cat <- paste0("ERROR IN ", function.name, ": FOR EASIER FUNCTION DETECTION, add ARGUMENT MUST CONTAIN \"ggplot2::\" OR \"lemon::\" IN FRONT OF EACH GGPLOT2 FUNCTION: ", paste(unique(add), collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if( ! grepl(pattern = ")\\s*$", add)){ # check that the add string finished by )
-tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST FINISH BY \")\": ", paste(unique(add), collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-# end verif of add
-# management of add containing facet
-facet.categ <- NULL
-if( ! is.null(add)){
-facet.check <- TRUE
-tempo <- unlist(strsplit(x = add, split = "\\s*\\+\\s*(ggplot2|lemon)\\s*::\\s*")) #
-tempo <- sub(x = tempo, pattern = "^facet_wrap", replacement = "ggplot2::facet_wrap")
-tempo <- sub(x = tempo, pattern = "^facet_grid", replacement = "ggplot2::facet_grid")
-tempo <- sub(x = tempo, pattern = "^facet_rep", replacement = "lemon::facet_rep")
-if(length(data1) > 1 & (any(grepl(x = tempo, pattern = "ggplot2::facet_wrap|lemon::facet_rep_wrap")) | grepl(x = add, pattern = "ggplot2::facet_grid|lemon::facet_rep_grid"))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nfacet PANELS CANNOT BE USED IF MORE THAN ONE DATA FRAME IN THE data1 ARGUMENT\nPLEASE REWRITE THE add STRING AND RERUN")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-if(any(grepl(x = tempo, pattern = "ggplot2::facet_wrap|lemon::facet_rep_wrap"))){
-tempo1 <- suppressWarnings(eval(parse(text = tempo[grepl(x = tempo, pattern = "ggplot2::facet_wrap|lemon::facet_rep_wrap")])))
-facet.categ <- list(names(tempo1$params$facets)) # list of length 1
-tempo.text <- "facet_wrap OR facet_rep_wrap"
-facet.check <- FALSE
-}else if(grepl(x = add, pattern = "ggplot2::facet_grid|lemon::facet_rep_grid")){
-tempo1 <- suppressWarnings(eval(parse(text = tempo[grepl(x = tempo, pattern = "ggplot2::facet_grid|lemon::facet_rep_grid")])))
-facet.categ <- list(c(names(tempo1$params$rows), names(tempo1$params$cols))) # list of length 1
-tempo.text <- "facet_grid OR facet_rep_grid"
-facet.check <- FALSE
-}
-if(facet.check == FALSE & ! all(facet.categ %in% names(data1[[1]]))){ # WARNING: all(facet.categ %in% names(data1)) is TRUE when facet.categ is NULL
-tempo.cat <- paste0("ERROR IN ", function.name, "\nDETECTION OF \"", tempo.text, "\" STRING IN THE add ARGUMENT BUT PROBLEM OF VARIABLE DETECTION (COLUMN NAMES OF data1)\nTHE DETECTED VARIABLES ARE:\n", paste(facet.categ, collapse = " "), "\nTHE data1 COLUMN NAMES ARE:\n", paste(names(data1[[1]]), collapse = " "), "\nPLEASE REWRITE THE add STRING AND RERUN")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-}
-# if facet.categ is not NULL, it is a list of length 1 now
-# end management of add containing facet
-# legend name filling
-if(is.null(legend.name) & ! is.null(categ)){
-legend.name <- categ
-}else if(is.null(legend.name) & is.null(categ)){
-legend.name <- vector("list", length(data1)) # null list
-}
-# legend.name not NULL anymore (list)
-# end legend name filling
-# ini categ for legend display
-fin.lg.disp <- vector("list", 6) # will be used at the end to display or not legends
-fin.lg.disp[] <- FALSE
-legend.disp <- vector("list", length(data1))
-if(is.null(categ) | legend.show == FALSE){
-legend.disp[] <- FALSE
-}else{
-for(i2 in 1:length(data1)){
-if(is.null(categ[[i2]])){
-legend.disp[[i2]] <- FALSE
-}else{
-legend.disp[[i2]] <- TRUE
-}
-}
-}
-# end ini categ for legend display
-# integer colors into gg_palette
-tempo.check.color <- NULL
-for(i1 in 1:length(data1)){
-if(any(is.na(color[[i1]]))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), ": color ARGUMENT CANNOT CONTAIN NA")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-tempo.check.color <- c(tempo.check.color, fun_check(data = color[[i1]], data.name = ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name)$problem)
-}
-tempo.check.color <- ! tempo.check.color # invert TRUE and FALSE because if integer, then problem = FALSE
-if(any(tempo.check.color == TRUE)){ # convert integers into colors
-tempo.integer <- unlist(color[tempo.check.color])
-tempo.color <- fun_gg_palette(max(tempo.integer, na.rm = TRUE))
-for(i1 in 1:length(data1)){
-if(tempo.check.color[i1] == TRUE){
-color[[i1]] <-tempo.color[color[[i1]]]
-}
-}
-}
-# end integer colors into gg_palette
-# loop (checking inside list compartment)
-compart.null.color <- 0 # will be used to attribute a color when color is non-null but a compartment of color is NULL
-data1.ini <- data1 # to report NA removal
-removed.row.nb <- vector("list", length = length(data1)) # to report NA removal. Contains NULL
-removed.rows <- vector("list", length = length(data1)) # to report NA removal. Contains NULL
-for(i1 in 1:length(data1)){
-tempo <- fun_check(data = data1[[i1]], data.name = ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), class = "data.frame", na.contain = TRUE, fun.name = function.name)
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-# reserved word checking
-if(any(names(data1[[i1]]) %in% reserved.words)){ # I do not use fun_name_change() because cannot control y before creating "fake_y". But ok because reserved are not that common
-tempo.cat <- paste0("ERROR IN ", function.name, ": COLUMN NAMES OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " ARGUMENT CANNOT BE ONE OF THESE WORDS\n", paste(reserved.words, collapse = " "), "\nTHESE ARE RESERVED FOR THE ", function.name, " FUNCTION")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-if( ! (is.null(add))){
-if(any(sapply(X = reserved.words, FUN = grepl, x = add))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nDETECTION OF COLUMN NAMES OF data1 IN THE add ARGUMENT STRING, THAT CORRESPOND TO RESERVED STRINGS FOR ", function.name, "\nFOLLOWING COLUMN NAMES HAVE TO BE CHANGED:\n", paste(arg.names[sapply(X = reserved.words, FUN = grepl, x = add)], collapse = "\n"), "\nFOR INFORMATION, THE RESERVED WORDS ARE:\n", paste(reserved.words, collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(any(sapply(X = arg.names, FUN = grepl, x = add))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NAMES OF ", function.name, " ARGUMENTS DETECTED IN THE add STRING:\n", paste(arg.names[sapply(X = arg.names, FUN = grepl, x = add)], collapse = "\n"), "\nRISK OF WRONG OBJECT USAGE INSIDE ", function.name)
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# end reserved word checking
-# check of geom now because required for y argument
-tempo <- fun_check(data = geom[[i1]], data.name = ifelse(length(geom)== 1L, "geom", paste0("geom NUMBER ", i1)), options = c("geom_point", "geom_line", "geom_path", "geom_step", "geom_hline", "geom_vline", "geom_stick"), length = 1, fun.name = function.name)
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-if(geom[[i1]] == "geom_step" & is.null(geom.step.dir[[i1]])){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(geom.step.dir)== 1L, "geom.step.dir", paste0("ELEMENT ", i1, " OF geom.step.dir ARGUMENT")), ": geom.step.dir ARGUMENT CANNOT BE NULL IF ", ifelse(length(geom)== 1L, "geom", paste0("ELEMENT ", i1, " OF geom")), " ARGUMENT IS \"geom_step\"\nHERE geom.step.dir ARGUMENT IS: ", paste(geom.step.dir[[i1]], collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(geom[[i1]] == "geom_step" & ! is.null(geom.step.dir[[i1]])){
-tempo <- fun_check(data = geom.step.dir[[i1]], data.name = ifelse(length(geom.step.dir)== 1L, "geom.step.dir", paste0("geom.step.dir NUMBER ", i1)), options = c("vh", "hv", "mid"), length = 1, fun.name = function.name)
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-if( ! (is.null(geom.stick.base))){
-if(geom[[i1]] == "geom_stick" & ! is.null(geom.stick.base[[i1]])){
-tempo <- fun_check(data = geom.stick.base[[i1]], data.name = ifelse(length(geom.stick.base)== 1L, "geom.stick.base", paste0("geom.stick.base NUMBER ", i1)), mode = "numeric", length = 1, na.contain = FALSE, fun.name = function.name)
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-}
-# end check of geom now because required for y argument
-if(is.null(x[[i1]])){
-if(all(geom[[i1]] != "geom_hline")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(x)== 1L, "x", paste0("ELEMENT ", i1, " OF x ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ": x ARGUMENT CANNOT BE NULL EXCEPT IF ", ifelse(length(geom)== 1L, "x", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_hline\"\nHERE geom ARGUMENT IS: ", paste(geom[[i1]], collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-x[[i1]] <- "fake_x"
-data1[[i1]] <- cbind(data1[[i1]], fake_x = NA, stringsAsFactors = TRUE)
-data1[[i1]][, "fake_x"] <- as.numeric(data1[[i1]][, "fake_x"])
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NULL ", ifelse(length(x)== 1L, "x", paste0("ELEMENT ", i1, " OF x")), " ARGUMENT ASSOCIATED TO ", ifelse(length(geom)== 1L, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT ", geom[[i1]], " -> FAKE COLUMN ADDED TO DATA FRAME ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", NAMED \"fake_x\" FOR FINAL DRAWING")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(all(geom[[i1]] == "geom_hline")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(x)== 1L, "x", paste0("ELEMENT ", i1, " OF x ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ": x ARGUMENT MUST BE NULL IF ", ifelse(length(geom)== 1L, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_hline\"")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-tempo <- fun_check(data = x[[i1]], data.name = ifelse(length(x)== 1L, "x", paste0("ELEMENT ", i1, " OF x ARGUMENT")), class = "vector", mode = "character", length = 1, fun.name = function.name)
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-if(is.null(y[[i1]])){
-if(all(geom[[i1]] != "geom_vline")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(y)== 1L, "y", paste0("ELEMENT ", i1, " OF y ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ": y ARGUMENT CANNOT BE NULL EXCEPT IF ", ifelse(length(geom)== 1L, "y", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_vline\"\nHERE geom ARGUMENT IS: ", paste(geom[[i1]], collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-y[[i1]] <- "fake_y"
-data1[[i1]] <- cbind(data1[[i1]], fake_y = NA, stringsAsFactors = TRUE)
-data1[[i1]][, "fake_y"] <- as.numeric(data1[[i1]][, "fake_y"])
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NULL ", ifelse(length(y)== 1L, "y", paste0("ELEMENT ", i1, " OF y")), " ARGUMENT ASSOCIATED TO ", ifelse(length(geom)== 1L, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT ", geom[[i1]], " -> FAKE COLUMN ADDED TO DATA FRAME ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", NAMED \"fake_y\" FOR FINAL DRAWING")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else{
-if(all(geom[[i1]] == "geom_vline")){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(y)== 1L, "y", paste0("ELEMENT ", i1, " OF y ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ": y ARGUMENT MUST BE NULL IF ", ifelse(length(geom)== 1L, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_vline\"")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-tempo <- fun_check(data = y[[i1]], data.name = ifelse(length(y)== 1L, "y", paste0("ELEMENT ", i1, " OF y ARGUMENT")), class = "vector", mode = "character", length = 1, fun.name = function.name)
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-# x[[i1]] and y[[i1]] not NULL anymore
-if( ! (x[[i1]] %in% names(data1[[i1]]))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(x)== 1L, "x", paste0("ELEMENT ", i1, " OF x")), " ARGUMENT MUST BE A COLUMN NAME OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT\nHERE IT IS: ", paste(x[[i1]], collapse = " "))))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-if( ! (y[[i1]] %in% names(data1[[i1]]))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(y)== 1L, "y", paste0("ELEMENT ", i1, " OF y")), " ARGUMENT MUST BE A COLUMN NAME OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT\nHERE IT IS: ", paste(y[[i1]], collapse = " "))))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-tempo <- fun_check(data = data1[[i1]][, x[[i1]]], data.name = ifelse(length(x)== 1L, "x ARGUMENT (AS COLUMN NAME OF data1 DATA FRAME)", paste0("ELEMENT ", i1, " OF x ARGUMENT", " (AS COLUMN NAME OF data1 DATA FRAME NUMBER ", i1, ")")), class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name)
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-tempo <- fun_check(data = data1[[i1]][, y[[i1]]], data.name = ifelse(length(y)== 1L, "y ARGUMENT (AS COLUMN NAME OF data1 DATA FRAME)", paste0("ELEMENT ", i1, " OF y ARGUMENT", " (AS COLUMN NAME OF data1 DATA FRAME NUMBER ", i1, ")")), class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name)
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-if(x[[i1]] == "fake_x" & y[[i1]] == "fake_y"){ # because the code cannot accept to be both "fake_x" and "fake_y" at the same time
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 2\nTHE CODE CANNOT ACCEPT x AND y TO BE \"fake_x\" AND \"fake_y\" IN THE SAME DATA FRAME ", i1, " ")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-
-if(( ! is.null(categ)) & ( ! is.null(categ[[i1]]))){ # is.null(categ[[i1]]) works even if categ is NULL # is.null(categ[[i1]]) works even if categ is NULL # if categ[[i1]] = NULL, fake_categ will be created later on
-tempo <- fun_check(data = categ[[i1]], data.name = ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")),, class = "vector", mode = "character", length = 1, fun.name = function.name)
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-if( ! (categ[[i1]] %in% names(data1[[i1]]))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ")), " ARGUMENT MUST BE A COLUMN NAME OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT\nHERE IT IS: ", paste(categ[[i1]], collapse = " "))))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-tempo1 <- fun_check(data = data1[[i1]][, categ[[i1]]], data.name = ifelse(length(categ)== 1L, "categ OF data1 ARGUMENT", paste0("ELEMENT ", i1, " OF categ ARGUMENT IN DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name)
-tempo2 <- fun_check(data = data1[[i1]][, categ[[i1]]], data.name = ifelse(length(categ)== 1L, "categ OF data1 ARGUMENT", paste0("ELEMENT ", i1, " OF categ ARGUMENT IN DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), class = "factor", na.contain = TRUE, fun.name = function.name)
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(categ)== 1L, "categ OF data1 ARGUMENT", paste0("ELEMENT ", i1, " OF categ ARGUMENT IN DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " MUST BE A FACTOR OR CHARACTER VECTOR")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(tempo1$problem == FALSE){
-data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", THE CHARACTER COLUMN HAS BEEN CONVERTED TO FACTOR")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-
-}
-if(geom[[i1]] == "geom_vline" | geom[[i1]] == "geom_hline"){
-if(length(unique(data1[[i1]][, categ[[i1]]])) != nrow(data1[[i1]])){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(geom)== 1L, "geom OF data1 ARGUMENT", paste0("geom NUMBER ", i1, " OF DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " ARGUMENT IS ", geom[[i1]], ", MEANING THAT ", ifelse(length(categ)== 1L, "categ OF data1 ARGUMENT", paste0("ELEMENT ", i1, " OF categ ARGUMENT IN DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " MUST HAVE A DIFFERENT CLASS PER LINE OF data1 (ONE x VALUE PER CLASS)")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-}else if(( ! is.null(categ)) & is.null(categ[[i1]])){ # is.null(categ[[i1]]) works even if categ is NULL # if categ[[i1]] = NULL, fake_categ will be created. WARNING: is.null(categ[[i1]]) means no legend display (see above), because categ has not been precised. This also means a single color for data1[[i1]]
-if(length(color[[i1]]) > 1){ # 0 means is.null(color[[i1]]) or is.null(color) and 1 is ok -> single color for data1[[i1]]
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NULL ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ")), " ARGUMENT BUT CORRESPONDING COLORS IN ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " HAS LENGTH OVER 1\n", paste(color[[i1]], collapse = " "), "\nWHICH IS NOT COMPATIBLE WITH NULL CATEG -> COLOR RESET TO A SINGLE COLOR")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-color[i1] <- list(NULL) # will provide a single color below # Warning color[[i1]] <- NULL removes the compartment
-}
-categ[[i1]] <- "fake_categ"
-data1[[i1]] <- cbind(data1[[i1]], fake_categ = "", stringsAsFactors = TRUE)
-# inactivated because give a different color to different "Line_" categ while a single color for all the data1[[i1]] required. Thus, put back after the color management
-# if(geom[[i1]] == "geom_hline" | geom[[i1]] == "geom_vline"){
-# data1[[i1]][, "fake_categ"] <- paste0("Line_", 1:nrow(data1[[i1]]))
-# }else{
-data1[[i1]][, "fake_categ"] <- data1[[i1]][, "fake_categ"] # as.numeric("") create a vector of NA but class numeric
-# }
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NULL ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ")), " ARGUMENT -> FOR DATA FRAME ", ifelse(length(data1)== 1L, "data1 ARGUMENT:", paste0("NUMBER ", i1, " OF data1 ARGUMENT:")), "\n- FAKE \"fake_categ\" COLUMN ADDED FILLED WITH \"\"(OR WITH \"Line_...\" FOR LINES)\n- SINGLE COLOR USED FOR PLOTTING\n- NO LEGEND DISPLAYED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# OK: if categ is not NULL, all the non-null categ columns of data1 are factors from here
-
-# management of log scale and Inf removal
-if(x[[i1]] != "fake_x"){
-if(any(( ! is.finite(data1[[i1]][, x[[i1]]])) & ( ! is.na(data1[[i1]][, x[[i1]]])))){ # is.finite also detects NA: ( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])) detects only Inf
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") PRESENCE OF -Inf OR Inf VALUES IN ", ifelse(length(categ)== 1L, "x", paste0("ELEMENT ", i1, " OF x ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-if(y[[i1]] != "fake_y"){
-if(any(( ! is.finite(data1[[i1]][, y[[i1]]])) & ( ! is.na(data1[[i1]][, y[[i1]]])))){ # is.finite also detects NA: ( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])) detects only Inf
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") PRESENCE OF -Inf OR Inf VALUES IN ", ifelse(length(categ)== 1L, "y", paste0("ELEMENT ", i1, " OF y ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# log conversion
-if(x.log != "no"){
-tempo1 <- ! is.finite(data1[[i1]][, x[[i1]]]) # where are initial NA and Inf
-data1[[i1]][, x[[i1]]] <- suppressWarnings(get(x.log)(data1[[i1]][, x[[i1]]]))# no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-if(any( ! (tempo1 | is.finite(data1[[i1]][, x[[i1]]])))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") LOG CONVERSION INTRODUCED -Inf OR Inf OR NaN VALUES IN ", ifelse(length(categ)== 1L, "x", paste0("ELEMENT ", i1, " OF x ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-if(y.log != "no"){
-tempo1 <- ! is.finite(data1[[i1]][, y[[i1]]]) # where are initial NA and Inf
-data1[[i1]][, y[[i1]]] <- suppressWarnings(get(y.log)(data1[[i1]][, y[[i1]]]))# no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-if(any( ! (tempo1 | is.finite(data1[[i1]][, y[[i1]]])))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") LOG CONVERSION INTRODUCED -Inf OR Inf OR NaN VALUES IN ", ifelse(length(categ)== 1L, "y", paste0("ELEMENT ", i1, " OF y ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# Inf removal
-# removed.row.nb[[i1]] <- NULL # already NULL and Warning this removes the compartment
-removed.rows[[i1]] <- data.frame(stringsAsFactors = FALSE)
-if(any(( ! is.finite(data1[[i1]][, x[[i1]]])) & ( ! is.na(data1[[i1]][, x[[i1]]])))){ # is.finite also detects NA: ( ! is.finite(data1[[i1]][, x[[i1]]])) & ( ! is.na(data1[[i1]][, x[[i1]]])) detects only Inf
-removed.row.nb[[i1]] <- c(removed.row.nb[[i1]], which(( ! is.finite(data1[[i1]][, x[[i1]]])) & ( ! is.na(data1[[i1]][, x[[i1]]]))))
-}
-if(any(( ! is.finite(data1[[i1]][, y[[i1]]])) & ( ! is.na(data1[[i1]][, y[[i1]]])))){ # is.finite also detects NA: ( ! is.finite(data1[[i1]][, y[[i1]]])) & ( ! is.na(data1[[i1]][, y[[i1]]])) detects only Inf
-removed.row.nb[[i1]] <- c(removed.row.nb[[i1]], which(( ! is.finite(data1[[i1]][, y[[i1]]])) & ( ! is.na(data1[[i1]][, y[[i1]]]))))
-}
-if( ! is.null(removed.row.nb[[i1]])){
-removed.row.nb[[i1]] <- unique(removed.row.nb[[i1]]) # to remove the duplicated positions (NA in both x and y)
-removed.rows[[i1]] <- rbind(removed.rows[[i1]], data1.ini[[i1]][removed.row.nb[[i1]], ]) # here data1.ini used to have the y = O rows that will be removed because of Inf creation after log transformation
-data1[[i1]] <- data1[[i1]][-removed.row.nb[[i1]], ]
-data1.ini[[i1]] <- data1.ini[[i1]][-removed.row.nb[[i1]], ] #
-}
-# From here, data1 and data.ini have no more Inf
-# end Inf removal
-# x.lim and y.lim dealt later on, after the end f the loop
-# end management of log scale and Inf removal
-# management of log scale
-if(x.log != "no"){
-data1[[i1]][, x[[i1]]] <- suppressWarnings(get(x.log)(data1[[i1]][, x[[i1]]])) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-}
-if(y.log != "no"){
-data1[[i1]][, y[[i1]]] <- suppressWarnings(get(y.log)(data1[[i1]][, y[[i1]]])) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-}
-# end management of log scale
-# na detection and removal
-column.check <- unique(unlist(c( # unlist because creates a list
-if(x[[i1]] == "fake_x"){NULL}else{x[[i1]]}, 
-if(y[[i1]] == "fake_y"){NULL}else{y[[i1]]}, 
-if( ! is.null(categ)){if(is.null(categ[[i1]])){NULL}else{categ[[i1]]}}, 
-if( ! is.null(facet.categ)){if(is.null(facet.categ[[i1]])){NULL}else{facet.categ[[i1]]}}
-))) # dot.categ because can be a 3rd column of data1
-if(any(is.na(data1[[i1]][, column.check]))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NA DETECTED IN COLUMNS ", paste(column.check, collapse = " "), " OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-for(i3 in 1:length(column.check)){
-if(any(is.na(data1[[i1]][, column.check[i3]]))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("NA REMOVAL DUE TO COLUMN ", column.check[i3], " OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-tempo <- unique(unlist(lapply(lapply(c(data1[[i1]][column.check]), FUN = is.na), FUN = which)))
-removed.row.nb[[i1]] <- c(removed.row.nb[[i1]], tempo)
-removed.rows[[i1]] <- rbind(removed.rows[[i1]], data1.ini[[i1]][tempo, ]) #  # tempo used because removed.row.nb is not empty. Here data1.ini used to have the non NA rows that will be removed because of NAN creation after log transformation (neg values for instance)
-column.check <- column.check[ ! (column.check == x[[i1]] | column.check == y[[i1]])] # remove x and y to keep quali columns
-if(length(tempo) != 0){
-data1[[i1]] <- data1[[i1]][-tempo, ] # WARNING tempo here and not removed.row.nb because the latter contain more numbers thant the former
-data1.ini[[i1]] <- data1.ini[[i1]][-tempo, ] # WARNING tempo here and not removed.row.nb because the latter contain more numbers than the former
-for(i4 in 1:length(column.check)){
-if(any( ! unique(removed.rows[[i1]][, column.check[i4]]) %in% unique(data1[[i1]][, column.check[i4]]))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN COLUMN ", column.check[i4], " OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", THE FOLLOWING CLASSES HAVE DISAPPEARED AFTER NA REMOVAL\n(IF COLUMN USED IN THE PLOT, THIS CLASS WILL NOT BE DISPLAYED):\n", paste(unique(removed.rows[[i1]][, column.check[i4]])[ ! unique(removed.rows[[i1]][, column.check[i4]]) %in% unique(data1[[i1]][, column.check[i4]])], collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-tempo.levels <- levels(data1[[i1]][, column.check[i4]])[levels(data1[[i1]][, column.check[i4]]) %in% unique(as.character(data1[[i1]][, column.check[i4]]))]
-data1[[i1]][, column.check[i4]] <- factor(as.character(data1[[i1]][, column.check[i4]]), levels = tempo.levels)
-if(column.check[i4] %in% categ[[i1]] & ! is.null(categ.class.order)){
-categ.class.order[[i1]] <- levels(data1[[i1]][, column.check[i4]])[levels(data1[[i1]][, column.check[i4]]) %in% unique(data1[[i1]][, column.check[i4]])] # remove the absent class in the categ.class.order vector
-data1[[i1]][, column.check[i4]] <- factor(as.character(data1[[i1]][, column.check[i4]]), levels = unique(categ.class.order[[i1]]))
-}
-}
-}
-}
-}
-# end na detection and removal
-# From here, data1 and data.ini have no more NA or NaN in x, y, categ (if categ != NULL) and facet.categ (if categ != NULL)
-if( ! is.null(categ.class.order)){
-# the following check will be done several times but I prefer to keep it here, after the creation of categ
-if(is.null(categ[[i1]]) & ! is.null(categ.class.order[[i1]])){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nCOMPARTMENT ", i1, " OF categ ARGUMENT CANNOT BE NULL IF COMPARTMENT ", i1, " OF categ.class.order ARGUMENT IS NOT NULL: ", paste(categ.class.order, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-if(is.null(categ.class.order[[i1]])){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE categ.class.order COMPARTMENT ", i1, " IS NULL. ALPHABETICAL ORDER WILL BE APPLIED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-data1[[i1]][, categ[[i1]]] <- factor(as.character(data1[[i1]][, categ[[i1]]])) # if already a factor, change nothing, if characters, levels according to alphabetical order
-categ.class.order[[i1]] <- levels(data1[[i1]][, categ[[i1]]]) # character vector that will be used later
-}else{
-tempo <- fun_check(data = categ.class.order[[i1]], data.name = paste0("COMPARTMENT ", i1 , " OF categ.class.order ARGUMENT"), class = "vector", mode = "character", length = length(levels(data1[[i1]][, categ[[i1]]])), fun.name = function.name) # length(data1[, categ[i1]) -> if data1[, categ[i1] was initially character vector, then conversion as factor after the NA removal, thus class number ok. If data1[, categ[i1] was initially factor, no modification after the NA removal, thus class number ok
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-if(any(duplicated(categ.class.order[[i1]]))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nCOMPARTMENT ", i1, " OF categ.class.order ARGUMENT CANNOT HAVE DUPLICATED CLASSES: ", paste(categ.class.order[[i1]], collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if( ! (all(categ.class.order[[i1]] %in% unique(data1[[i1]][, categ[[i1]]])) & all(unique(data1[[i1]][, categ[[i1]]]) %in% categ.class.order[[i1]]))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nCOMPARTMENT ", i1, " OF categ.class.order ARGUMENT MUST BE CLASSES OF COMPARTMENT ", i1, " OF categ ARGUMENT\nHERE IT IS:\n", paste(categ.class.order[[i1]], collapse = " "), "\nFOR COMPARTMENT ", i1, " OF categ.class.order AND IT IS:\n", paste(unique(data1[[i1]][, categ[[i1]]]), collapse = " "), "\nFOR COLUMN ", categ[[i1]], " OF data1 NUMBER ", i1)
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]], levels = categ.class.order[[i1]]) # reorder the factor
-}
-names(categ.class.order)[i1] <- categ[[i1]]
-}
-}
-# OK: if categ.class.order is not NULL, all the NULL categ.class.order columns of data1 are character from here
-
-if( ! is.null(legend.name[[i1]])){
-tempo <- fun_check(data = legend.name[[i1]], data.name = ifelse(length(legend.name)== 1L, "legend.name", paste0("legend.name NUMBER ", i1)),, class = "vector", mode = "character", length = 1, fun.name = function.name)
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-if( ! is.null(color)){ # if color is NULL, will be filled later on
-# check the nature of color
-if(is.null(color[[i1]])){
-compart.null.color <- compart.null.color + 1
-color[[i1]] <- grey(compart.null.color / 8) # cannot be more than 7 overlays. Thus 7 different greys. 8/8 is excluded because white dots
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NULL COLOR IN ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " ASSOCIATED TO ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", SINGLE COLOR ", paste(color[[i1]], collapse = " "), " HAS BEEN ATTRIBUTED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-tempo1 <- fun_check(data = color[[i1]], data.name = ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name) # na.contain = TRUE in case of colum of data1
-tempo2 <- fun_check(data = color[[i1]], data.name = ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), class = "factor", na.contain = TRUE, fun.name = function.name) # idem
-if(tempo1$problem == TRUE & tempo2$problem == TRUE){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST BE A FACTOR OR CHARACTER VECTOR OR INTEGER VECTOR") # integer possible because dealt above
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if( ! (all(color[[i1]] %in% colors() | grepl(pattern = "^#", color[[i1]])))){ # check that all strings of low.color start by #
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors(): ", paste(unique(color[[i1]]), collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-if(any(is.na(color[[i1]]))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), ", THE COLORS:\n", paste(unique(color[[i1]]), collapse = " "), "\nCONTAINS NA")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# end check the nature of color
-# check the length of color
-if(is.null(categ) & length(color[[i1]]) != 1){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST BE A SINGLE COLOR IF categ IS NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if( ! is.null(categ)){
-# No problem of NA management by ggplot2 because already removed
-if(categ[[i1]] == "fake_categ" & length(color[[i1]]) != 1){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST BE A SINGLE COLOR IF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IS NULL")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(length(color[[i1]]) == length(unique(data1[[i1]][, categ[[i1]]]))){ # here length(color) is equal to the different number of categ
-data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", THE FOLLOWING COLORS:\n", paste(color[[i1]], collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(factor(data1[[i1]][, categ[[i1]]])), collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else if(length(color[[i1]]) == length(data1[[i1]][, categ[[i1]]])){# here length(color) is equal to nrow(data1[[i1]]) -> Modif to have length(color) equal to the different number of categ (length(color) == length(levels(data1[[i1]][, categ[[i1]]])))
-data1[[i1]] <- cbind(data1[[i1]], color = color[[i1]], stringsAsFactors = TRUE)
-tempo.check <- unique(data1[[i1]][ , c(categ[[i1]], "color")])
-if( ! (nrow(data1[[i1]]) == length(color[[i1]]) & nrow(tempo.check) == length(unique(data1[[i1]][ , categ[[i1]]])))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color")), " ARGUMENT HAS THE LENGTH OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), "\nBUT IS INCORRECTLY ASSOCIATED TO EACH CLASS OF THIS categ:\n", paste(unique(mapply(FUN = "paste", data1[[i1]][ ,categ[[i1]]], data1[[i1]][ ,"color"])), collapse = "\n"))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
-color[[i1]] <- unique(color[[i1]][order(data1[[i1]][, categ[[i1]]])]) # Modif to have length(color) equal to the different number of categ (length(color) == length(levels(data1[[i1]][, categ[[i1]]])))
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count, ") FROM FUNCTION ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " HAS THE LENGTH OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " COLUMN VALUES\nCOLORS HAVE BEEN RESPECTIVELY ASSOCIATED TO EACH CLASS OF categ AS:\n", paste(levels(factor(data1[[i1]][, categ[[i1]]])), collapse = " "), "\n", paste(color[[i1]], collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else if(length(color[[i1]])== 1L){
-data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
-color[[i1]] <- rep(color[[i1]], length(levels(data1[[i1]][, categ[[i1]]])))
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") IN ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", COLOR HAS LENGTH 1 MEANING THAT ALL THE DIFFERENT CLASSES OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), "\n", paste(levels(factor(data1[[i1]][, categ[[i1]]])), collapse = " "), "\nWILL HAVE THE SAME COLOR\n", paste(color[[i1]], collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST BE\n(1) LENGTH 1\nOR (2) THE LENGTH OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " COLUMN VALUES\nOR (3) THE LENGTH OF THE CLASSES IN THIS COLUMN\nHERE IT IS COLOR LENGTH ", length(color[[i1]]), " VERSUS CATEG LENGTH ", length(data1[[i1]][, categ[[i1]]]), " AND CATEG CLASS LENGTH ", length(unique(data1[[i1]][, categ[[i1]]])), "\nPRESENCE OF NA IN THE COLUMN x, y OR categ OF data1 COULD BE THE PROBLEME")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-}
-if((geom[[i1]] == "geom_hline" | geom[[i1]] == "geom_vline") & ! is.null(categ[[i1]])){ # add here after the color management, to deal with the different lines to plot inside any data[[i1]]
-if(categ[[i1]] == "fake_categ"){
-data1[[i1]][, "fake_categ"] <- factor(paste0("Line_", formatC(1:nrow(data1[[i2]]), width = nchar(nrow(data1[[i2]])), flag = "0")))
-}
-}
-tempo <- fun_check(data = alpha[[i1]], data.name = ifelse(length(alpha)== 1L, "alpha", paste0("alpha NUMBER ", i1)), prop = TRUE, length = 1, fun.name = function.name)
-if(tempo$problem == TRUE){
-stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-# end loop (checking inside list compartment)
-if(length(data1) > 1){
-if(length(unique(unlist(x)[ ! x == "fake_x"])) > 1){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE x ARGUMENT DOES NOT CONTAIN IDENTICAL COLUMN NAMES:\n", paste(unlist(x), collapse = " "), "\nX-AXIS OVERLAYING DIFFERENT VARIABLES?")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-if(length(data1) > 1){
-if(length(unique(unlist(y)[ ! y == "fake_y"])) > 1){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE y ARGUMENT DOES NOT CONTAIN IDENTICAL COLUMN NAMES:\n", paste(unlist(y), collapse = " "), "\nY-AXIS OVERLAYING DIFFERENT VARIABLES?")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-if(sum(geom %in% "geom_point") > 3){
-tempo.cat <- paste0("ERROR IN ", function.name, ": geom ARGUMENT CANNOT HAVE MORE THAN THREE \"geom_point\" ELEMENTS")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(length(geom) - sum(geom %in% "geom_point") > 3){
-tempo.cat <- paste0("ERROR IN ", function.name, ": geom ARGUMENT CANNOT HAVE MORE THAN THREE LINE ELEMENTS")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-# x.lim management before transfo by x.log
-if(x.log != "no" & ! is.null(x.lim)){
-if(any(x.lim <= 0)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nx.lim ARGUMENT CANNOT HAVE ZERO OR NEGATIVE VALUES WITH THE x.log ARGUMENT SET TO ", x.log, ":\n", paste(x.lim, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(any( ! is.finite(if(x.log == "log10"){log10(x.lim)}else{log2(x.lim)}))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nx.lim ARGUMENT RETURNS INF/NA WITH THE x.log ARGUMENT SET TO ", x.log, "\nAS SCALE COMPUTATION IS ", ifelse(x.log == "log10", "log10", "log2"), ":\n", paste(if(x.log == "log10"){log10(x.lim)}else{log2(x.lim)}, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-if(x.log != "no" & x.include.zero == TRUE){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") x.log ARGUMENT SET TO ", x.log, " AND x.include.zero ARGUMENT SET TO TRUE -> x.include.zero ARGUMENT RESET TO FALSE BECAUSE 0 VALUE CANNOT BE REPRESENTED IN LOG SCALE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-x.include.zero <- FALSE
-}
-# end x.lim management before transfo by x.log
-# y.lim management before transfo by y.log
-if(y.log != "no" & ! is.null(y.lim)){
-if(any(y.lim <= 0)){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT CANNOT HAVE ZERO OR NEGATIVE VALUES WITH THE y.log ARGUMENT SET TO ", y.log, ":\n", paste(y.lim, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(any( ! is.finite(if(y.log == "log10"){log10(y.lim)}else{log2(y.lim)}))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT RETURNS INF/NA WITH THE y.log ARGUMENT SET TO ", y.log, "\nAS SCALE COMPUTATION IS ", ifelse(y.log == "log10", "log10", "log2"), ":\n", paste(if(y.log == "log10"){log10(y.lim)}else{log2(y.lim)}, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-if(y.log != "no" & y.include.zero == TRUE){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") y.log ARGUMENT SET TO ", y.log, " AND y.include.zero ARGUMENT SET TO TRUE -> y.include.zero ARGUMENT RESET TO FALSE BECAUSE 0 VALUE CANNOT BE REPRESENTED IN LOG SCALE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-y.include.zero <- FALSE
-}
-# end y.lim management before transfo by y.log
-# end other checkings
-# reserved word checking
-#already done above
-# end reserved word checking
-# end second round of checking and data preparation
-
-
-# package checking
-fun_pack(req.package = c(
-"gridExtra", 
-"ggplot2", 
-"lemon", 
-"scales"
-), lib.path = lib.path)
-# packages Cairo and grid tested by fun_gg_point_rast()
-# end package checking
-
-
-
-
-# main code
-# axes management
-if(is.null(x.lim)){
-if(any(unlist(mapply(FUN = "[[", data1, x, SIMPLIFY = FALSE)) %in% c(Inf, -Inf))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE x COLUMN IN data1 CONTAINS -Inf OR Inf VALUES THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-x.lim <- suppressWarnings(range(unlist(mapply(FUN = "[[", data1, x, SIMPLIFY = FALSE)), na.rm = TRUE, finite = TRUE)) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only. y.lim added here. If NULL, ok if y argument has values
-}else if(x.log != "no"){
-x.lim <- get(x.log)(x.lim) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-}
-if(x.log != "no"){
-if(any( ! is.finite(x.lim))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nx.lim ARGUMENT CANNOT HAVE ZERO OR NEGATIVE VALUES WITH THE x.log ARGUMENT SET TO ", x.log, ":\n", paste(x.lim, collapse = " "), "\nPLEASE, CHECK DATA VALUES (PRESENCE OF ZERO OR INF VALUES)")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-if(suppressWarnings(all(x.lim %in% c(Inf, -Inf)))){ # happen when x is only NULL
-if(all(unlist(geom) %in% c("geom_vline", "geom_stick"))){
-tempo.cat <- paste0("ERROR IN ", function.name, " NOT POSSIBLE TO DRAW geom_vline OR geom_stick KIND OF LINES ALONE IF x.lim ARGUMENT IS SET TO NULL, SINCE NO X-AXIS DEFINED (", ifelse(length(x)== 1L, "x", paste0("ELEMENT ", i1, " OF x")), " ARGUMENT MUST BE NULL FOR THESE KIND OF LINES)")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, " x.lim ARGUMENT MADE OF NA, -Inf OR Inf ONLY: ", paste(x.lim, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-x.lim.order <- order(x.lim) # to deal with inverse axis
-# print(x.lim.order)
-x.lim <- sort(x.lim)
-x.lim[1] <- x.lim[1] - abs(x.lim[2] - x.lim[1]) * ifelse(diff(x.lim.order) > 0, x.right.extra.margin, x.left.extra.margin) # diff(x.lim.order) > 0 means not inversed axis
-x.lim[2] <- x.lim[2] + abs(x.lim[2] - x.lim[1]) * ifelse(diff(x.lim.order) > 0, x.left.extra.margin, x.right.extra.margin) # diff(x.lim.order) > 0 means not inversed axis
-if(x.include.zero == TRUE){ # no need to check x.log != "no" because done before
-x.lim <- range(c(x.lim, 0), na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
-}
-x.lim <- x.lim[x.lim.order]
-if(any(is.na(x.lim))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 3")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-if(is.null(y.lim)){
-if(any(unlist(mapply(FUN = "[[", data1, y, SIMPLIFY = FALSE)) %in% c(Inf, -Inf))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE y COLUMN IN data1 CONTAINS -Inf OR Inf VALUES THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-y.lim <- suppressWarnings(range(unlist(mapply(FUN = "[[", data1, y, SIMPLIFY = FALSE)), na.rm = TRUE, finite = TRUE)) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only. y.lim added here. If NULL, ok if y argument has values
-}else if(y.log != "no"){
-y.lim <- get(y.log)(y.lim) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
-}
-if(y.log != "no"){
-if(any( ! is.finite(y.lim))){
-tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT CANNOT HAVE ZERO OR NEGATIVE VALUES WITH THE y.log ARGUMENT SET TO ", y.log, ":\n", paste(y.lim, collapse = " "), "\nPLEASE, CHECK DATA VALUES (PRESENCE OF ZERO OR INF VALUES)")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-if(suppressWarnings(all(y.lim %in% c(Inf, -Inf)))){ # happen when y is only NULL
-if(all(unlist(geom) == "geom_vline")){
-tempo.cat <- paste0("ERROR IN ", function.name, " NOT POSSIBLE TO DRAW geom_vline KIND OF LINES ALONE IF y.lim ARGUMENT IS SET TO NULL, SINCE NO Y-AXIS DEFINED (", ifelse(length(y)== 1L, "y", paste0("ELEMENT ", i1, " OF y")), " ARGUMENT MUST BE NULL FOR THESE KIND OF LINES)")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, " y.lim ARGUMENT MADE OF NA, -Inf OR Inf ONLY: ", paste(y.lim, collapse = " "))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
-y.lim.order <- order(y.lim) # to deal with inverse axis
-y.lim <- sort(y.lim)
-y.lim[1] <- y.lim[1] - abs(y.lim[2] - y.lim[1]) * ifelse(diff(y.lim.order) > 0, y.bottom.extra.margin, y.top.extra.margin) # diff(y.lim.order) > 0 means not inversed axis
-y.lim[2] <- y.lim[2] + abs(y.lim[2] - y.lim[1]) * ifelse(diff(y.lim.order) > 0, y.top.extra.margin, y.bottom.extra.margin) # diff(y.lim.order) > 0 means not inversed axis
-if(y.include.zero == TRUE){ # no need to check y.log != "no" because done before
-y.lim <- range(c(y.lim, 0), na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
-}
-y.lim <- y.lim[y.lim.order]
-if(any(is.na(y.lim))){
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 4")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+    # AIM
+    # rescale the width of a window to open depending on the number of classes to plot
+    # can be used for height, considering that it is as if it was a width
+    # this order can be used:
+    # fun_width()
+    # fun_open()
+    # fun_prior_plot() # not for ggplot2
+    # plot() or any other plotting
+    # fun_post_plot() if fun_prior_plot() has been used # not for ggplot2
+    # fun_close()
+    # ARGUMENTS
+    # class.nb: number of class to plot
+    # inches.per.class.nb: number of inches per unit of class.nb. 2 means 2 inches for each boxplot for instance
+    # ini.window.width:initial window width in inches
+    # inch.left.space: left horizontal margin of the figure region (in inches)
+    # inch.right.space: right horizontal margin of the figure region (in inches)
+    # boundarie.space: space between the right and left limits of the plotting region and the plot (0.5 means half a class width)
+    # RETURN
+    # the new window width in inches
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # fun_width(class.nb = 10, inches.per.class.nb = 0.2, ini.window.width = 7, inch.left.space = 1, inch.right.space = 1, boundarie.space = 0.5)
+    # DEBUGGING
+    # class.nb = 10 ; inches.per.class.nb = 0.2 ; ini.window.width = 7 ; inch.left.space = 1 ; inch.right.space = 1 ; boundarie.space = 0.5 # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = class.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = inches.per.class.nb, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = ini.window.width, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = inch.left.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = inch.right.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = boundarie.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    range.max <- class.nb + boundarie.space # the max range of the future plot
+    range.min <- boundarie.space # the min range of the future plot
+    window.width <- inch.left.space + inch.right.space + inches.per.class.nb * (range.max - range.min)
+    return(window.width)
 }
-# end axes management
 
 
+######## fun_open() #### open a GUI or pdf graphic window
 
 
-# create a fake categ if NULL to deal with legend display
-if(is.null(categ)){
-categ <- vector("list", length(data1))
-categ[] <- "fake_categ"
-for(i2 in 1:length(data1)){
-data1[[i2]] <- cbind(data1[[i2]], fake_categ = "", stringsAsFactors = TRUE)
-if(geom[[i2]] == "geom_hline" | geom[[i2]] == "geom_vline"){
-data1[[i2]][, "fake_categ"] <- factor(paste0("Line_", 1:nrow(data1[[i2]])))
-}
-}
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NULL categ ARGUMENT -> FAKE \"fake_categ\" COLUMN ADDED TO EACH DATA FRAME OF data1, AND FILLED WITH \"\"")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-# categ is not NULL anymore
-if(is.null(categ.class.order)){
-categ.class.order <- vector("list", length = length(data1))
-tempo.categ.class.order <- NULL
-for(i2 in 1:length(categ.class.order)){
-categ.class.order[[i2]] <- levels(data1[[i2]][, categ[[i2]]])
-names(categ.class.order)[i2] <- categ[[i2]]
-tempo.categ.class.order <- c(tempo.categ.class.order, ifelse(i2 != 1, "\n", ""), categ.class.order[[i2]])
-}
-if(any(unlist(legend.disp))){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") THE categ.class.order SETTING IS NULL. ALPHABETICAL ORDER WILL BE APPLIED FOR CLASS ORDERING:\n", paste(tempo.categ.class.order, collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# end create a fake categ if NULL to deal with legend display
-# categ.class.order is not NULL anymore
-
-
-# vector of color with length as in levels(categ) of data1
-if(is.null(color)){
-color <- vector("list", length(data1))
-length.categ.list <- lapply(lapply(mapply(FUN = "[[", data1, categ, SIMPLIFY = FALSE), FUN = unique), FUN = function(x){length(x[ ! is.na(x)])})
-length.categ.list[sapply(categ, FUN = "==", "fake_categ")] <- 1 # when is.null(color), a single color for all the dots or lines of data[[i1]] that contain "fake_categ" category
-total.categ.length <- sum(unlist(length.categ.list), na.rm = TRUE)
-tempo.color <- fun_gg_palette(total.categ.length)
-tempo.count <- 0
-for(i2 in 1:length(data1)){
-color[[i2]] <- tempo.color[(1:length.categ.list[[i2]]) + tempo.count]
-tempo.count <- tempo.count + length.categ.list[[i2]]
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") NULL color ARGUMENT -> COLORS RESPECTIVELY ATTRIBUTED TO EACH CLASS OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i2, " OF categ ARGUMENT")), " (", categ[[i2]], ") IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i2, " OF data1 ARGUMENT")), ":\n", paste(color[[i2]], collapse = " "), "\n", paste(if(all(levels(data1[[i2]][, categ[[i2]]]) == "")){'\"\"'}else{levels(data1[[i2]][, categ[[i2]]])}, collapse = " "))
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+fun_open <- function(
+    pdf = TRUE, 
+    pdf.path = "working.dir", 
+    pdf.name = "graph", 
+    width = 7, 
+    height = 7, 
+    paper = "special", 
+    pdf.overwrite = FALSE, 
+    rescale = "fixed", 
+    remove.read.only = TRUE, 
+    return.output = FALSE
+){
+    # AIM
+    # open a pdf or screen (GUI) graphic window and return initial graphic parameters
+    # this order can be used:
+    # fun_width()
+    # fun_open()
+    # fun_prior_plot() # not for ggplot2
+    # plot() or any other plotting
+    # fun_post_plot() if fun_prior_plot() has been used # not for ggplot2
+    # fun_close()
+    # WARNINGS
+    # On Linux, use pdf = TRUE, if (GUI) graphic window is not always available, meaning that X is not installed (clusters for instance). Use X11() in R to test if available
+    # ARGUMENTS:
+    # pdf: logical. Use pdf display? If FALSE, a GUI is opened
+    # pdf.path: where the pdf is saved (do not terminate by / or \\). Write "working.dir" if working directory is required (default). Ignored if pdf == FALSE
+    # pdf.name: name of the pdf file containing the graphs (the .pdf extension is added by the function, if not detected in the name end). Ignored if pdf == FALSE
+    # width: width of the window (in inches)
+    # height: height of the window (in inches)
+    # paper: paper argument of the pdf function (paper format). Only used for pdf(). Either "a4", "letter", "legal", "us", "executive", "a4r", "USr" or "special". If "special", means that the paper dimension will be width and height. With another paper format, if width or height is over the size of the paper, width or height will be modified such that the plot is adjusted to the paper dimension (see $dim in the returned list below to see the modified dimensions). Ignored if pdf == FALSE
+    # pdf.overwrite: logical. Existing pdf can be overwritten? . Ignored if pdf == FALSE
+    # rescale: kind of GUI. Either "R", "fit", or "fixed". Ignored on Mac and Linux OS. See ?windows for details
+    # remove.read.only: logical. remove the read only (R.O.) graphical parameters? If TRUE, the graphical parameters are returned without the R.O. parameters. The returned $ini.par list can be used to set the par() of a new graphical device. If FALSE, graphical parameters are returned with the R.O. parameters, which provides information like text dimension (see ?par() ). The returned $ini.par list can be used to set the par() of a new graphical device, but generate a warning message. Ignored if return.output == FALSE. 
+    # return.output: logical. Return output ? If TRUE the output list is displayed
+    # RETURN
+    # a list containing:
+    # $pdf.loc: path of the pdf created
+    # $ini.par: initial par() parameters
+    # $zone.ini: initial window spliting
+    # $dim: dimension of the graphical device (in inches)
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # fun_open(pdf = FALSE, pdf.path = "C:/Users/Gael/Desktop", pdf.name = "graph", width = 7, height = 7, paper = "special", pdf.overwrite = FALSE, return.output = TRUE)
+    # DEBUGGING
+    # pdf = TRUE ; pdf.path = "C:/Users/Gael/Desktop" ; pdf.name = "graphs" ; width = 7 ; height = 7 ; paper = "special" ; pdf.overwrite = FALSE ; rescale = "fixed" ; remove.read.only = TRUE ; return.output = TRUE # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = pdf, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = pdf.path, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = pdf.name, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = width, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = height, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = paper, options = c("a4", "letter", "legal", "us", "executive", "a4r", "USr", "special", "A4", "LETTER", "LEGAL", "US"), length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data =pdf.overwrite, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = rescale, options = c("R", "fit", "fixed"), length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = remove.read.only, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = return.output, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    if(pdf.path == "working.dir"){
+        pdf.path <- getwd()
+    }else{
+        if(grepl(x = pdf.path, pattern = ".+/$")){
+            pdf.path <- sub(x = pdf.path, pattern = "/$", replacement = "") # remove the last /
+        }else if(grepl(x = pdf.path, pattern = ".+[\\]$")){ # or ".+\\\\$" # cannot be ".+\$" because \$ does not exist contrary to \n
+            pdf.path <- sub(x = pdf.path, pattern = "[\\]$", replacement = "") # remove the last /
+        }
+        if(dir.exists(pdf.path) == FALSE){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\npdf.path ARGUMENT DOES NOT CORRESPOND TO EXISTING DIRECTORY\n", pdf.path)
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # par.ini recovery
+    # cannot use pdf(file = NULL), because some small differences between pdf() and other devices. For instance, differences with windows() for par()$fin, par()$pin and par()$plt
+    if(Sys.info()["sysname"] == "Windows"){ # Note that .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
+        open.fail <- NULL
+        grDevices::windows()
+        ini.par <- par(no.readonly = remove.read.only) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
+        invisible(dev.off()) # close the new window
+    }else if(Sys.info()["sysname"] == "Linux"){
+        if(pdf == TRUE){# cannot use pdf(file = NULL), because some small differences between pdf() and other devices. For instance, differences with windows() for par()$fin, par()$pin and par()$plt
+            if(exists(".Random.seed", envir = .GlobalEnv)){ # if .Random.seed does not exists, it means that no random operation has been performed yet in any R environment
+                tempo.random.seed <- .Random.seed
+                on.exit(assign(".Random.seed", tempo.random.seed, env = .GlobalEnv))
+            }else{
+                on.exit(set.seed(NULL)) # inactivate seeding -> return to complete randomness
+            }
+            set.seed(NULL)
+            tempo.code <- sample(x = 1:1e7, size = 1)
+            while(file.exists(paste0(pdf.path, "/recover_ini_par", tempo.code, ".pdf")) == TRUE){
+                tempo.code <- tempo.code + 1
+            }
+            grDevices::pdf(width = width, height = height, file=paste0(pdf.path, "/recover_ini_par", tempo.code, ".pdf"), paper = paper)
+            ini.par <- par(no.readonly = remove.read.only) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
+            invisible(dev.off()) # close the pdf window
+            file.remove(paste0(pdf.path, "/recover_ini_par", tempo.code, ".pdf")) # remove the pdf file
+        }else{
+            # test if X11 can be opened
+            if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\nTHIS FUNCTION CANNOT BE USED ON LINUX IF A Rplots.pdf FILE ALREADY EXISTS HERE\n", getwd())
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }else{
+                open.fail <- suppressWarnings(try(grDevices::X11(), silent = TRUE))[] # try to open a X11 window. If open.fail == NULL, no problem, meaning that the X11 window is opened. If open.fail != NULL, a pdf can be opened here paste0(getwd(), "/Rplots.pdf")
+                if(is.null(open.fail)){
+                    ini.par <- par(no.readonly = remove.read.only) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
+                    invisible(dev.off()) # close the new window
+                }else if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
+                    file.remove(paste0(getwd(), "/Rplots.pdf")) # remove the pdf file
+                    tempo.cat <- ("ERROR IN fun_open()\nTHIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM\nTO OVERCOME THIS, EITHER SET THE X GRAPHIC INTERFACE OF THE SYSTEM OR SET THE pdf ARGUMENT OF THE fun_open() FUNCTION TO TRUE AND RERUN")
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+                }
+            }
+        }
+    }else{
+        open.fail <- NULL
+        grDevices::quartz()
+        ini.par <- par(no.readonly = remove.read.only) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
+        invisible(dev.off()) # close the new window
+    }
+    # end par.ini recovery 
+    zone.ini <- matrix(1, ncol=1) # to recover the initial parameters for next figure region when device region split into several figure regions
+    if(pdf == TRUE){
+        if(grepl(x = pdf.name, pattern = "\\.pdf$")){
+            pdf.name <- sub(x = pdf.name, pattern = "\\.pdf$", replacement = "") # remove the last .pdf
+        }
+        pdf.loc <- paste0(pdf.path, "/", pdf.name, ".pdf")
+        if(file.exists(pdf.loc) == TRUE & pdf.overwrite == FALSE){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\npdf.loc FILE ALREADY EXISTS AND CANNOT BE OVERWRITTEN DUE TO pdf.overwrite ARGUMENT SET TO TRUE\n", pdf.loc)
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            grDevices::pdf(width = width, height = height, file=pdf.loc, paper = paper)
+        }
+    }else if(pdf == FALSE){
+        pdf.loc <- NULL
+        if(Sys.info()["sysname"] == "Windows"){ # .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
+            grDevices::windows(width = width, height = height, rescale = rescale)
+        }else if(Sys.info()["sysname"] == "Linux"){
+            if( ! is.null(open.fail)){
+                tempo.cat <- "ERROR IN fun_open()\nTHIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM\nTO OVERCOME THIS, EITHER SET THE X GRAPHIC INTERFACE OF THE SYSTEM OR SET THE pdf ARGUMENT OF THE fun_open() FUNCTION TO TRUE AND RERUN"
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }else{
+                grDevices::X11(width = width, height = height)
+            }
+        }else{
+            grDevices::quartz(width = width, height = height)
+        }
+    }
+    if(return.output == TRUE){
+        output <- list(pdf.loc = pdf.loc, ini.par = ini.par, zone.ini = zone.ini, dim = dev.size())
+        return(output)
+    }
 }
+
+
+######## fun_prior_plot() #### set graph param before plotting (erase axes for instance)
+
+
+fun_prior_plot <- function(
+    param.reinitial = FALSE, 
+    xlog.scale = FALSE, 
+    ylog.scale = FALSE, 
+    remove.label = TRUE, 
+    remove.x.axis = TRUE, 
+    remove.y.axis = TRUE, 
+    std.x.range = TRUE, 
+    std.y.range = TRUE, 
+    down.space = 1, 
+    left.space = 1, 
+    up.space = 1, 
+    right.space = 1, 
+    orient = 1, 
+    dist.legend = 3.5, 
+    tick.length = 0.5, 
+    box.type = "n", 
+    amplif.label = 1, 
+    amplif.axis = 1, 
+    display.extend = FALSE, 
+    return.par = FALSE
+){
+    # AIM
+    # very convenient to erase the axes for post plot axis redrawing using fun_post_plot()
+    # reinitialize and set the graphic parameters before plotting
+    # CANNOT be used if no graphic device already opened
+    # ARGUMENTS
+    # param.reinitial: reinitialize graphic parameters before applying the new ones, as defined by the other arguments? Either TRUE or FALSE
+    # xlog.scale: Log scale for the x-axis? Either TRUE or FALSE. If TRUE, erases the x-axis, except legend, for further drawing by fun_post_plot()(xlog argument of par())
+    # ylog.scale: Log scale for the y-axis? Either TRUE or FALSE. If TRUE, erases the y-axis, except legend, for further drawing by fun_post_plot()(ylog argument of par())
+    # remove.label: remove labels (axis legend) of the two axes? Either TRUE or FALSE (ann argument of par())
+    # remove.x.axis: remove x-axis except legend? Either TRUE or FALSE (control the xaxt argument of par()). Automately set to TRUE if xlog.scale == TRUE
+    # remove.y.axis: remove y-axis except legend? Either TRUE or FALSE (control the yaxt argument of par()). Automately set to TRUE if ylog.scale == TRUE
+    # std.x.range: standard range on the x-axis? TRUE (no range extend) or FALSE (4% range extend). Controls xaxs argument of par() (TRUE is xaxs = "i", FALSE is xaxs = "r")
+    # std.y.range: standard range on the y-axis? TRUE (no range extend) or FALSE (4% range extend). Controls yaxs argument of par() (TRUE is yaxs = "i", FALSE is yaxs = "r")
+    # down.space: lower vertical margin (in inches, mai argument of par())
+    # left.space: left horizontal margin (in inches, mai argument of par())
+    # up.space: upper vertical margin between plot region and grapical window (in inches, mai argument of par())
+    # right.space: right horizontal margin (in inches, mai argument of par())
+    # orient: scale number orientation (las argument of par()). 0, always parallel to the axis; 1, always horizontal; 2, always perpendicular to the axis; 3, always vertical
+    # dist.legend: numeric value that moves axis legends away in inches (first number of mgp argument of par() but in inches thus / 0.2)
+    # tick.length: length of the ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc. 0 means no tick
+    # box.type: bty argument of par(). Either "o", "l", "7", "c", "u", "]", the resulting box resembles the corresponding upper case letter. A value of "n" suppresses the box
+    # amplif.label: increase or decrease the size of the text in legends
+    # amplif.axis: increase or decrease the size of the scale numbers in axis
+    # display.extend: extend display beyond plotting region? Either TRUE or FALSE (xpd argument of par() without NA)
+    # return.par: return graphic parameter modification?
+    # RETURN
+    # return graphic parameter modification
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # fun_prior_plot(param.reinitial = FALSE, xlog.scale = FALSE, ylog.scale = FALSE, remove.label = TRUE, remove.x.axis = TRUE, remove.y.axis = TRUE, std.x.range = TRUE, std.y.range = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 4.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = FALSE)
+    # DEBUGGING
+    # param.reinitial = FALSE ; xlog.scale = FALSE ; ylog.scale = FALSE ; remove.label = TRUE ; remove.x.axis = TRUE ; remove.y.axis = TRUE ; std.x.range = TRUE ; std.y.range = TRUE ; down.space = 1 ; left.space = 1 ; up.space = 1 ; right.space = 1 ; orient = 1 ; dist.legend = 4.5 ; tick.length = 0.5 ; box.type = "n" ; amplif.label = 1 ; amplif.axis = 1 ; display.extend = FALSE ; return.par = FALSE # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = param.reinitial, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = xlog.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = ylog.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = remove.label, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = remove.x.axis, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = remove.y.axis, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = std.x.range, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = std.y.range, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = down.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = left.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = up.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = right.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = orient, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = dist.legend, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = tick.length, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = box.type, options = c("o", "l", "7", "c", "u", "]", "n"), length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = amplif.label, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = amplif.axis, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = display.extend, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = return.par, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    if(is.null(dev.list())){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": THIS FUNCTION CANNOT BE USED IF NO GRAPHIC DEVICE ALREADY OPENED (dev.list() IS CURRENTLY NULL)")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # par.ini recovery
+    # cannot use pdf(file = NULL), because some small differences between pdf() and other devices. For instance, differences with windows() for par()$fin, par()$pin and par()$plt
+    if(param.reinitial == TRUE){
+        if( ! all(names(dev.cur()) == "null device")){
+            active.wind.nb <- dev.cur()
+        }else{
+            active.wind.nb <- 0
+        }
+        if(Sys.info()["sysname"] == "Windows"){ # Note that .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
+            grDevices::windows()
+            ini.par <- par(no.readonly = FALSE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
+            invisible(dev.off()) # close the new window
+        }else if(Sys.info()["sysname"] == "Linux"){
+            if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": THIS FUNCTION CANNOT BE USED ON LINUX WITH param.reinitial SET TO TRUE IF A Rplots.pdf FILE ALREADY EXISTS HERE: ", getwd())
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }else{
+                open.fail <- suppressWarnings(try(grDevices::X11(), silent = TRUE))[] # try to open a X11 window. If open.fail == NULL, no problem, meaning that the X11 window is opened. If open.fail != NULL, a pdf can be opened here paste0(getwd(), "/Rplots.pdf")
+                if(is.null(open.fail)){
+                    ini.par <- par(no.readonly = FALSE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
+                    invisible(dev.off()) # close the new window
+                }else if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
+                    ini.par <- par(no.readonly = FALSE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
+                    invisible(dev.off()) # close the new window
+                    file.remove(paste0(getwd(), "/Rplots.pdf")) # remove the pdf file
+                }else{
+                    tempo.cat <- ("ERROR IN fun_prior_plot()\nTHIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM\nTO OVERCOME THIS, PLEASE USE A PDF GRAPHIC INTERFACE AND RERUN")
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+                }
+            }
+        }else{ # macOS
+            grDevices::quartz()
+            ini.par <- par(no.readonly = FALSE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened)
+            invisible(dev.off()) # close the new window
+        }
+        if( ! all(names(dev.cur()) == "null device")){
+            invisible(dev.set(active.wind.nb)) # go back to the active window if exists
+            par(ini.par) # apply the initial par to current window
+        }
+    }
+    # end par.ini recovery
+    if(remove.x.axis == TRUE){
+        par(xaxt = "n") # suppress the y-axis label
+    }else{
+        par(xaxt = "s")
+    }
+    if(remove.y.axis == TRUE){
+        par(yaxt = "n") # suppress the y-axis label
+    }else{
+        par(yaxt = "s")
+    }
+    if(std.x.range == TRUE){
+        par(xaxs = "i")
+    }else{
+        par(xaxs = "r")
+    }
+    if(std.y.range == TRUE){
+        par(yaxs = "i")
+    }else{
+        par(yaxs = "r")
+    }
+    par(mai = c(down.space, left.space, up.space, right.space), ann = ! remove.label, las = orient, mgp = c(dist.legend/0.2, 1, 0), xpd = display.extend, bty= box.type, cex.lab = amplif.label, cex.axis = amplif.axis)
+    par(tcl = -par()$mgp[2] * tick.length) # tcl gives the length of the ticks as proportion of line text, knowing that mgp is in text lines. So the main ticks are a 0.5 of the distance of the axis numbers by default. The sign provides the side of the tick (negative for outside of the plot region)
+    if(xlog.scale == TRUE){
+        par(xaxt = "n", xlog = TRUE) # suppress the x-axis label
+    }else{
+        par(xlog = FALSE)
+    }
+    if(ylog.scale == TRUE){
+        par(yaxt = "n", ylog = TRUE) # suppress the y-axis label
+    }else{
+        par(ylog = FALSE)
+    }
+    if(return.par == TRUE){
+        tempo.par <- par()
+        return(tempo.par)
+    }
 }
-# end vector of color with length as in levels(categ) of data1
-# color is not NULL anymore
 
 
+######## fun_scale() #### select nice label numbers when setting number of ticks on an axis
+
 
 
 
-# last check
-for(i1 in 1:length(data1)){
-if(categ[[i1]] != "fake_categ" & length(color[[i1]]) != length(unique(data1[[i1]][, categ[[i1]]]))){
-tempo.cat <- paste0("ERROR IN ", function.name, " LAST CHECK: ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST HAVE THE LENGTH OF LEVELS OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), "\nHERE IT IS COLOR LENGTH ", length(color[[i1]]), " VERSUS CATEG LEVELS LENGTH ", length(unique(data1[[i1]][, categ[[i1]]])), "\nREMINDER: A SINGLE COLOR PER CLASS OF CATEG AND A SINGLE CLASS OF CATEG PER COLOR MUST BE RESPECTED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else if(categ[[i1]] == "fake_categ" & length(color[[i1]]) != 1){
-tempo.cat <- paste0("ERROR IN ", function.name, " LAST CHECK: ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST HAVE LENGTH 1 WHEN ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IS NULL\nHERE IT IS COLOR LENGTH ", length(color[[i1]]))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+
+fun_scale <- function(n, lim, kind = "approx", lib.path = NULL){
+    # AIM
+    # attempt to select nice scale numbers when setting n ticks on a lim axis range
+    # ARGUMENTS
+    # n: desired number of main ticks on the axis (integer above 0)
+    # lim: vector of 2 numbers indicating the limit range of the axis. Order of the 2 values matters (for inverted axis). Can be log transformed values
+    # kind: either "approx" (approximative), "strict" (strict) or "strict.cl" (strict clean). If "approx", use the scales::trans_breaks() function to provide an easy to read scale of approximately n ticks spanning the range of the lim argument. If "strict", cut the range of the lim argument into n + 1 equidistant part and return the n numbers at each boundary. This often generates numbers uneasy to read. If "strict.cl", provide an easy to read scale of exactly n ticks, but sometimes not completely spanning the range of the lim argument
+    # lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
+    # RETURN
+    # a vector of numbers
+    # REQUIRED PACKAGES
+    # if kind = "approx":
+    # ggplot2
+    # scales
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # fun_round()
+    # EXAMPLES
+    # approximate number of main ticks
+    # ymin = 2 ; ymax = 3.101 ; n = 5 ; scale <- fun_scale(n = n, lim = c(ymin, ymax), kind = "approx") ; scale ; par(yaxt = "n", yaxs = "i", las = 1) ; plot(ymin:ymax, ymin:ymax, xlim = range(scale, ymin, ymax)[order(c(ymin, ymax))], ylim = range(scale, ymin, ymax)[order(c(ymin, ymax))], xlab = "DEFAULT SCALE", ylab = "NEW SCALE") ; par(yaxt = "s") ; axis(side = 2, at = scale)
+    # strict number of main ticks
+    # ymin = 2 ; ymax = 3.101 ; n = 5 ; scale <- fun_scale(n = n, lim = c(ymin, ymax), kind = "strict") ; scale ; par(yaxt = "n", yaxs = "i", las = 1) ; plot(ymin:ymax, ymin:ymax, xlim = range(scale, ymin, ymax)[order(c(ymin, ymax))], ylim = range(scale, ymin, ymax)[order(c(ymin, ymax))], xlab = "DEFAULT SCALE", ylab = "NEW SCALE") ; par(yaxt = "s") ; axis(side = 2, at = scale)
+    # strict "clean" number of main ticks
+    # ymin = 2 ; ymax = 3.101 ; n = 5 ; scale <- fun_scale(n = n, lim = c(ymin, ymax), kind = "strict.cl") ; scale ; par(yaxt = "n", yaxs = "i", las = 1) ; plot(ymin:ymax, ymin:ymax, xlim = range(scale, ymin, ymax)[order(c(ymin, ymax))], ylim = range(scale, ymin, ymax)[order(c(ymin, ymax))], xlab = "DEFAULT SCALE", ylab = "NEW SCALE") ; par(yaxt = "s") ; axis(side = 2, at = scale)
+    # approximate number of main ticks, scale inversion
+    # ymin = 3.101 ; ymax = 2 ; n = 5 ; scale <- fun_scale(n = n, lim = c(ymin, ymax), kind = "approx") ; scale ; par(yaxt = "n", yaxs = "i", las = 1) ; plot(ymin:ymax, ymin:ymax, xlim = range(scale, ymin, ymax)[order(c(ymin, ymax))], ylim = range(scale, ymin, ymax)[order(c(ymin, ymax))], xlab = "DEFAULT SCALE", ylab = "NEW SCALE") ; par(yaxt = "s") ; axis(side = 2, at = scale)
+    # DEBUGGING
+    # n = 9 ; lim = c(2, 3.101) ; kind = "approx" ; lib.path = NULL # for function debugging
+    # n = 10 ; lim = c(1e-4, 1e6) ; kind = "approx" ; lib.path = NULL # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # end initial argument checking
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(length(utils::find("fun_round", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_round() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = n, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & isTRUE(all.equal(n, 0))){ # isTRUE(all.equal(n, 0)) equivalent to n == 0 but deals with floats (approx ok)
+        tempo.cat <- paste0("ERROR IN ", function.name, ": n ARGUMENT MUST BE A NON NULL AND POSITIVE INTEGER")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE) # 
+    }
+    tempo <- fun_check(data = lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & all(diff(lim) == 0L)){ # isTRUE(all.equal(diff(lim), rep(0, length(diff(lim))))) not used because we strictly need zero as a result
+        tempo.cat <- paste0("ERROR IN ", function.name, ": lim ARGUMENT HAS A NULL RANGE (2 IDENTICAL VALUES)")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }else if(tempo$problem == FALSE & any(lim %in% c(Inf, -Inf))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": lim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    tempo <- fun_check(data = kind, options = c("approx", "strict", "strict.cl"), length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(lib.path)){
+        tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
+                tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end argument checking with fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    lim.rank <- rank(lim) # to deal with inverted axis
+    lim <- sort(lim)
+    if(kind == "approx"){
+        # package checking
+        fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
+        fun_pack(req.package = c("scales"), lib.path = lib.path)
+        # end package checking
+        output <- ggplot2::ggplot_build(ggplot2::ggplot() + ggplot2::scale_y_continuous(
+            breaks = scales::trans_breaks(
+                trans = "identity", 
+                inv = "identity", 
+                n = n
+            ), 
+            limits = lim
+        ))$layout$panel_params[[1]]$y$breaks # pretty() alone is not appropriate: tempo.pret <-  pretty(seq(lim[1] ,lim[2], length.out = n)) ; tempo.pret[tempo.pret > = lim[1] & tempo.pret < = lim[2]]. # in ggplot 3.3.0, tempo.coord$y.major_source replaced by tempo.coord$y$breaks
+        if( ! is.null(attributes(output))){ # layout$panel_params[[1]]$y$breaks can be characters (labels of the axis). In that case, it has attributes that corresponds to positions
+            output <- unlist(attributes(output))
+        }
+        output <- output[ ! is.na(output)]
+    }else if(kind == "strict"){
+        output <- fun_round(seq(lim[1] ,lim[2], length.out = n), 2)
+    }else if(kind == "strict.cl"){
+        tempo.range <- diff(sort(lim))
+        tempo.max <- max(lim)
+        tempo.min <- min(lim)
+        mid <- tempo.min + (tempo.range/2) # middle of axis
+        tempo.inter <- tempo.range / (n + 1) # current interval between two ticks, between 0 and Inf
+        if(tempo.inter == 0L){ # isTRUE(all.equal(tempo.inter, rep(0, length(tempo.inter)))) not used because we strictly need zero as a result
+            tempo.cat <- paste0("ERROR IN ", function.name, ": THE INTERVAL BETWEEN TWO TICKS OF THE SCALE IS NULL. MODIFY THE lim OR n ARGUMENT")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        log10.abs.lim <- 200
+        log10.range <- (-log10.abs.lim):log10.abs.lim
+        log10.vec <- 10^log10.range
+        round.vec <- c(5, 4, 3, 2.5, 2, 1.25, 1)
+        dec.table <- outer(log10.vec, round.vec) # table containing the scale units (row: power of ten from -201 to +199, column: the 5, 2.5, 2, 1.25, 1 notches
+        
+        
+        
+        # recover the number of leading zeros in tempo.inter
+        ini.scipen <- options()$scipen
+        options(scipen = -1000) # force scientific format
+        if(any(grepl(pattern = "\\+", x = tempo.inter))){ # tempo.inter > 1
+            power10.exp <- as.integer(substring(text = tempo.inter, first = (regexpr(pattern = "\\+", text = tempo.inter) + 1))) # recover the power of 10. Example recover 08 from 1e+08
+            mantisse <- as.numeric(substr(x = tempo.inter, start = 1, stop = (regexpr(pattern = "\\+", text = tempo.inter) - 2))) # recover the mantisse. Example recover 1.22 from 1.22e+08
+        }else if(any(grepl(pattern = "\\-", x = tempo.inter))){ # tempo.inter < 1
+            power10.exp <- as.integer(substring(text = tempo.inter, first = (regexpr(pattern = "\\-", text = tempo.inter)))) # recover the power of 10. Example recover 08 from 1e+08
+            mantisse <- as.numeric(substr(x = tempo.inter, start = 1, stop = (regexpr(pattern = "\\-", text = tempo.inter) - 2))) # recover the mantisse. Example recover 1.22 from 1.22e+08
+        }else{
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 1")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        tempo.scale <- dec.table[log10.range == power10.exp, ]
+        # new interval 
+        inter.select <- NULL
+        for(i1 in 1:length(tempo.scale)){
+            tempo.first.tick <- trunc((tempo.min + tempo.scale[i1]) / tempo.scale[i1]) * (tempo.scale[i1]) # this would be use to have a number not multiple of tempo.scale[i1]: ceiling(tempo.min) + tempo.scale[i1] * 10^power10.exp
+            tempo.last.tick <- tempo.first.tick + tempo.scale[i1] * (n - 1)
+            if((tempo.first.tick >= tempo.min) & (tempo.last.tick <= tempo.max)){
+                inter.select <- tempo.scale[i1]
+                break()
+            }
+        }
+        if(is.null(inter.select)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 2")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        options(scipen = ini.scipen) # restore the initial scientific penalty
+        # end new interval 
+        # centering the new scale 
+        tempo.mid <- trunc((mid + (-1:1) * inter.select) / inter.select) * inter.select # tempo middle tick closest to the middle axis
+        mid.tick <- tempo.mid[which.min(abs(tempo.mid - mid))]
+        if(isTRUE(all.equal(n, rep(1, length(n))))){ # isTRUE(all.equal(n, rep(1, length(n)))) is similar to n == 1L but deals with float
+            output <- mid.tick
+        }else if(isTRUE(all.equal(n, rep(2, length(n))))){ # isTRUE(all.equal(n, rep(0, length(n)))) is similar to n == 2L but deals with float
+            output <- mid.tick
+            tempo.min.dist <- mid.tick - inter.select - tempo.min
+            tempo.max.dist <- tempo.max - mid.tick + inter.select
+            if(tempo.min.dist <= tempo.max.dist){ # distance between lowest tick and bottom axis <= distance between highest tick and top axis. If yes, extra tick but at the top, otherwise at the bottom
+                output <- c(mid.tick, mid.tick + inter.select)
+            }else{
+                output <- c(mid.tick - inter.select, mid.tick)
+            }
+        }else if((n / 2 - trunc(n / 2)) > 0.1){ # > 0.1 to avoid floating point. Because result can only be 0 or 0.5. Thus, > 0.1 means odd number
+            output <- c(mid.tick - (trunc(n / 2):1) * inter.select, mid.tick, mid.tick + (1:trunc(n / 2)) * inter.select)
+        }else if((n / 2 - trunc(n / 2)) < 0.1){ # < 0.1 to avoid floating point. Because result can only be 0 or 0.5. Thus, < 0.1 means even number
+            tempo.min.dist <- mid.tick - trunc(n / 2) * inter.select - tempo.min
+            tempo.max.dist <- tempo.max - mid.tick + trunc(n / 2) * inter.select
+            if(tempo.min.dist <= tempo.max.dist){ # distance between lowest tick and bottom axis <= distance between highest tick and top axis. If yes, extra tick but at the bottom, otherwise at the top
+                output <- c(mid.tick - ((trunc(n / 2) - 1):1) * inter.select, mid.tick, mid.tick + (1:trunc(n / 2)) * inter.select)
+            }else{
+                output <- c(mid.tick - (trunc(n / 2):1) * inter.select, mid.tick, mid.tick + (1:(trunc(n / 2) - 1)) * inter.select)
+            }
+        }else{
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 3")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        # end centering the new scale 
+        # last check
+        if(min(output) < tempo.min){
+            output <- c(output[-1], max(output) + inter.select) # remove the lowest tick and add a tick at the top
+        }else if( max(output) > tempo.max){
+            output <- c(min(output) - inter.select, output[-length(output)])
+        }
+        if(min(output) < tempo.min | max(output) > tempo.max){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 4")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(is.na(output))){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 5 (NA GENERATION)")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        # end last check
+    }else{
+        tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 6")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(diff(lim.rank) < 0){
+        output <- rev(output)
+    }
+    return(output)
 }
+
+
+######## fun_inter_ticks() #### define coordinates of secondary ticks
+
+
+fun_inter_ticks <- function(
+    lim, 
+    log = "log10", 
+    breaks = NULL, 
+    n = NULL, 
+    warn.print = TRUE
+){
+    # AIM
+    # define coordinates and values of secondary ticks
+    # ARGUMENTS
+    # lim: vector of 2 numbers indicating the limit range of the axis. Order of the 2 values matters (for inverted axis). If log argument is "log2" or "log10", values in lim must be already log transformed. Thus, negative or zero values are allowed
+    # log: either "log2" (values in the lim argument are log2 transformed) or "log10" (values in the lim argument are log10 transformed), or "no"
+    # breaks: mandatory vector of numbers indicating the main ticks values/positions when log argument is "no". Ignored when log argument is "log2" or "log10"
+    # n: number of secondary ticks between each main tick when log argument is "no". Ignored when log argument is "log2" or "log10"
+    # warn.print: logical. Print potential warning messages at the end of the execution? If FALSE, warning messages are never printed, but can still be recovered in the returned list
+    # RETURN
+    # a list containing
+    # $log: value of the log argument used
+    # $coordinates: the coordinates of the secondary ticks on the axis, between the lim values
+    # $values: the corresponding values associated to each coordinate (with log scale, 2^$values or 10^$values is equivalent to the labels of the axis)
+    # $warn: the potential warning messages. Use cat() for proper display. NULL if no warning
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # no log scale
+    # fun_inter_ticks(lim = c(-4,4), log = "no", breaks = c(-2, 0, 2), n = 3)
+    # fun_inter_ticks(lim = c(10, 0), log = "no", breaks = c(10, 8, 6, 4, 2, 0), n = 4)
+    # log2
+    # fun_inter_ticks(lim = c(-4,4), log = "log2")
+    # log10
+    # fun_inter_ticks(lim = c(-2,3), log = "log10")
+    # DEBUGGING
+    # lim = c(2, 3.101) ; log = "no" ; breaks = NULL ; n = NULL ; warn.print = TRUE # for function debugging
+    # lim = c(0, 26.5) ; log = "no" ; breaks = c(0, 10, 20) ; n = 3 # for function debugging
+    # lim = c(10, 0); log = "no"; breaks = c(10, 8, 6, 4, 2, 0); n = 4 # for function debugging
+    # lim = c(-10, -20); log = "no"; breaks = c(-20, -15, -10); n = 4 # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    req.function <- c(
+        "fun_check"
+    )
+    for(i1 in req.function){
+        if(length(find(i1, mode = "function")) == 0L){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED ", i1, "() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # end required function checking
+    # argument primary checking
+    # arg with no default values
+    mandat.args <- c(
+        "lim"
+    )
+    tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
+    if(any(tempo)){ # normally no NA for missing() output
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end arg with no default values
+    # using fun_check()
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = log, options = c("no", "log2", "log10"), length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(breaks)){
+        tempo <- fun_check(data = breaks, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(n)){
+        tempo <- fun_check(data = n, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = warn.print, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end using fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument primary checking
+    # second round of checking and data preparation
+    # management of NA
+    if(any(is.na(lim)) | any(is.na(log)) | any(is.na(breaks)) | any(is.na(n)) | any(is.na(warn.print))){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nNO ARGUMENT CAN HAVE NA VALUES")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NA
+    # management of NULL
+    if(is.null(lim) | is.null(log)){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nTHESE ARGUMENTS\nlim\nlog\nCANNOT BE NULL")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NULL
+    if(all(diff(lim) == 0L)){ # isTRUE(all.equal(diff(lim), rep(0, length(diff(lim))))) not used because we strictly need zero as a result
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nlim ARGUMENT HAS A NULL RANGE (2 IDENTICAL VALUES): ", paste(lim, collapse = " "))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else if(any(lim %in% c(Inf, -Inf))){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nlim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(log == "no" & is.null(breaks)){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nbreaks ARGUMENT CANNOT BE NULL IF log ARGUMENT IS \"no\"")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! is.null(breaks)){
+        if(length(breaks) < 2){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nbreaks ARGUMENT MUST HAVE 2 VALUES AT LEAST (OTHERWISE, INTER TICK POSITIONS CANNOT BE COMPUTED): ", paste(breaks, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if( ! isTRUE(all.equal(diff(sort(breaks)), rep(diff(sort(breaks))[1], length(diff(sort(breaks))))))){ # isTRUE(all.equal(n, 0)) equivalent to n == 0 but deals with floats (approx ok)
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nbreaks ARGUMENT MUST HAVE EQUIDISTANT VALUES (OTHERWISE, EQUAL NUMBER OF INTER TICK BETWEEN MAIN TICKS CANNOT BE COMPUTED): ", paste(breaks, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if( ! is.null(n)){
+        if(n <= 0){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nn ARGUMENT MUST BE A POSITIVE AND NON NULL INTEGER: ", paste(n, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # end second round of checking and data preparation
+    # main code
+    ini.warning.length <- options()$warning.length
+    options(warning.length = 8170)
+    warn <- NULL
+    warn.count <- 0
+    lim.rank <- rank(lim) # to deal with inverse axis
+    if(log != "no"){
+        ini.scipen <- options()$scipen
+        options(scipen = -1000) # force scientific format
+        power10.exp <- as.integer(substring(text = 10^lim, first = (regexpr(pattern = "\\+|\\-", text = 10^lim)))) # recover the power of 10, i.e., integer part of lim. Example recover 08 from 1e+08. Works for log2
+        # mantisse <- as.numeric(substr(x = 10^lim, start = 1, stop = (regexpr(pattern = "\\+|\\-", text = 10^lim) - 2))) # recover the mantisse. Example recover 1.22 from 1.22e+08
+        options(scipen = ini.scipen) # restore the initial scientific penalty
+        tick.pos <- unique(as.vector(outer(2:10, ifelse(log == "log2", 2, 10)^((power10.exp[1] - ifelse(diff(lim.rank) > 0, 1, -1)):(power10.exp[2] + ifelse(diff(lim.rank) > 0, 1, -1)))))) # use log10(2:10) even if log2: it is to get log values between 0 and 1
+        tick.pos <- sort(tick.pos, decreasing = ifelse(diff(lim.rank) > 0, FALSE, TRUE))
+        if(log == "log2"){
+            tick.values <- tick.pos[tick.pos >= min(2^lim) & tick.pos <= max(2^lim)]
+            tick.pos <- log2(tick.values)
+        }else if(log == "log10"){
+            tick.values <- tick.pos[tick.pos >= min(10^lim) & tick.pos <= max(10^lim)]
+            tick.pos <- log10(tick.values)
+        }
+    }else{
+        # if(length(breaks) > 1){ # not required because already checked above
+        breaks.rank <- rank(c(breaks[1], breaks[length(breaks)]))
+        if(diff(breaks.rank) != diff(lim.rank)){
+            breaks <- sort(breaks, decreasing = ifelse(diff(lim.rank) < 0, TRUE, FALSE))
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") VALUES IN breaks ARGUMENT NOT IN THE SAME ORDER AS IN lim ARGUMENT -> VALUES REORDERED AS IN lim: ", paste(breaks, collapse = " "))
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            breaks.rank <- rank(c(breaks[1], breaks[length(breaks)]))
+        }
+        # }
+        main.tick.dist <- mean(diff(breaks), na.rm = TRUE)
+        tick.dist <- main.tick.dist / (n + 1)
+        tempo.extra.margin <- max(abs(diff(breaks)), na.rm = TRUE)
+        tick.pos <- seq(
+            if(diff(breaks.rank) > 0){breaks[1] - tempo.extra.margin}else{breaks[1] + tempo.extra.margin}, 
+            if(diff(breaks.rank) > 0){breaks[length(breaks)] + tempo.extra.margin}else{breaks[length(breaks)] - tempo.extra.margin}, 
+            by = tick.dist
+        )
+        tick.pos <- tick.pos[tick.pos >= min(lim) & tick.pos <= max(lim)]
+        tick.values <- tick.pos
+    }
+    if(any(is.na(tick.pos) | ! is.finite(tick.pos))){ 
+        tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, ": NA or Inf GENERATED FOR THE INTER TICK POSITIONS: ", paste(tick.pos, collapse = " "))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(length(tick.pos) == 0L){
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") NO INTER TICKS COMPUTED BETWEEN THE LIMITS INDICATED: ", paste(lim, collapse = " "))
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
+    output <- list(log = log, coordinates = tick.pos, values = tick.values, warn = warn)
+    if(warn.print == TRUE & ! is.null(warn)){
+        on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE)) # to recover the warning messages, see $warn
+    }
+    on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
+    return(output)
 }
-# end last check
 
 
+######## fun_post_plot() #### set graph param after plotting (axes redesign for instance)
 
 
 
-# conversion of geom_hline and geom_vline
-for(i1 in 1:length(data1)){
-if(geom[[i1]] == "geom_hline" | geom[[i1]] == "geom_vline"){
-final.data.frame <- data.frame()
-for(i3 in 1:nrow(data1[[i1]])){
-tempo.data.frame <- rbind(data1[[i1]][i3, ], data1[[i1]][i3, ], stringsAsFactors = TRUE)
-if(geom[[i1]] == "geom_hline"){
-tempo.data.frame[, x[[i1]]] <- x.lim
-}else if(geom[[i1]] == "geom_vline"){
-tempo.data.frame[, y[[i1]]] <- y.lim
-}else{
-tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 5")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-# 3 lines below inactivated because I put that above
-# if(is.null(categ[[i1]])){
-# data1[, "fake_categ"] <- paste0("Line_", i3)
-# }
-final.data.frame <- rbind(final.data.frame, tempo.data.frame, stringsAsFactors = TRUE)
-}
-data1[[i1]] <- final.data.frame
-geom[[i1]] <- "geom_line"
-if(length(color[[i1]])== 1L){
-color[[i1]] <- rep(color[[i1]], length(unique(data1[[i1]][ , categ[[i1]]])))
-}else if(length(color[[i1]]) != length(unique(data1[[i1]][ , categ[[i1]]]))){
-tempo.cat <- paste0("ERROR IN ", function.name, " geom_hline AND geom_vline CONVERSION TO FIT THE XLIM AND YLIM LIMITS OF THE DATA: ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST HAVE THE LENGTH OF LEVELS OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), "\nHERE IT IS COLOR LENGTH ", length(color[[i1]]), " VERSUS CATEG LEVELS LENGTH ", length(unique(data1[[i1]][, categ[[i1]]])))
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-}
+
+
+fun_post_plot <- function(
+    x.side = 0, 
+    x.log.scale = FALSE, 
+    x.categ = NULL, 
+    x.categ.pos = NULL, 
+    x.lab = "", 
+    x.axis.size = 1.5, 
+    x.label.size = 1.5, 
+    x.dist.legend = 0.5, 
+    x.nb.inter.tick = 1, 
+    y.side = 0, 
+    y.log.scale = FALSE, 
+    y.categ = NULL, 
+    y.categ.pos = NULL, 
+    y.lab = "", 
+    y.axis.size = 1.5, 
+    y.label.size = 1.5, 
+    y.dist.legend = 0.5, 
+    y.nb.inter.tick = 1, 
+    text.angle = 90, 
+    tick.length = 0.5, 
+    sec.tick.length = 0.3, 
+    bg.color = NULL, 
+    grid.lwd = NULL, 
+    grid.col = "white", 
+    corner.text = "", 
+    corner.text.size = 1, 
+    just.label.add = FALSE, 
+    par.reset = FALSE, 
+    custom.par = NULL
+){
+    # AIM
+    # redesign axis. If x.side = 0, y.side = 0, the function just adds text at topright of the graph and reset par() for next graphics and provides outputs (see below)
+    # provide also positions for legend or additional text on the graph
+    # use fun_prior_plot() before this function for initial inactivation of the axis drawings
+    # ARGUMENTS
+    # x.side: axis at the bottom (1) or top (3) of the region figure. Write 0 for no change
+    # x.log.scale: Log scale for the x-axis? Either TRUE or FALSE
+    # x.categ: character vector representing the classes (levels()) to specify when the x-axis is qualititative(stripchart, boxplot)
+    # x.categ.pos: position of the classes names (numeric vector of identical length than x.categ). If left NULL, this will be 1:length(levels())
+    # x.lab: label of the x-axis. If x.side == 0 and x.lab != "", then x.lab is printed
+    # x.axis.size: positive numeric. Increase or decrease the size of the x axis numbers. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2. Also control the size of displayed categories
+    # x.label.size: positive numeric. Increase or decrease the size of the x axis legend text. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2
+    # x.dist.legend: increase the number to move x-axis legends away in inches (first number of mgp argument of par() but in inches)
+    # x.nb.inter.tick: number of secondary ticks between main ticks on x-axis (only if not log scale). 0 means no secondary ticks
+    # y.side: axis at the left (2) or right (4) of the region figure. Write 0 for no change
+    # y.log.scale: Log scale for the y-axis? Either TRUE or FALSE
+    # y.categ: classes (levels()) to specify when the y-axis is qualititative(stripchart, boxplot)
+    # y.categ.pos: position of the classes names (numeric vector of identical length than y.categ). If left NULL, this will be 1:length(levels())
+    # y.lab: label of the y-axis. If y.side == 0 and y.lab != "", then y.lab is printed
+    # y.axis.size: positive numeric. Increase or decrease the size of the y axis numbers. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2. Also control the size of displayed categories
+    # y.label.size: positive numeric. Increase or decrease the size of the y axis legend text. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2
+    # y.dist.legend: increase the number to move y-axis legends away in inches (first number of mgp argument of par() but in inches)
+    # y.nb.inter.tick: number of secondary ticks between main ticks on y-axis (only if not log scale). 0 means non secondary ticks
+    # text.angle: angle of the text when axis is qualitative
+    # tick.length: length of the main ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc., 0 for no ticks)
+    # sec.tick.length: length of the secondary ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc., 0 for no ticks)
+    # bg.color: background color of the plot region. NULL for no color. BEWARE: cover/hide an existing plot !
+    # grid.lwd: if non NULL, activate the grid line (specify the line width)
+    # grid.col: grid line color (only if grid.lwd non NULL)
+    # corner.text: text to add at the top right corner of the window
+    # corner.text.size: positive numeric. Increase or decrease the size of the text. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2
+    # par.reset: to reset all the graphics parameters. BEWARE: TRUE can generate display problems, mainly in graphic devices with multiple figure regions
+    # just.label.add: just add axis labels (legend)? Either TRUE or FALSE. If TRUE, at least (x.side == 0 & x.lab != "") or (y.side == 0 & y.lab != "") must be set to display the corresponding x.lab or y.lab
+    # custom.par: list that provides the parameters that reset all the graphics parameters. BEWARE: if NULL and par.reset == TRUE, the default par() parameters are used
+    # RETURN
+    # a list containing: 
+    # $x.mid.left.dev.region: middle of the left margin of the device region, in coordinates of the x-axis
+    # $x.left.dev.region: left side of the left margin (including the potential margin of the device region), in coordinates of the x-axis
+    # $x.mid.right.dev.region: middle of the right margin of the device region, in coordinates of the x-axis
+    # $x.right.dev.region: right side of the right margin (including the potential margin of the device region), in coordinates of the x-axis
+    # $x.mid.left.fig.region: middle of the left margin of the figure region, in coordinates of the x-axis
+    # $x.left.fig.region: left side of the left margin, in coordinates of the x-axis
+    # $x.mid.right.fig.region: middle of the right margin of the figure region, in coordinates of the x-axis
+    # $x.right.fig.region: right side of the right margin, in coordinates of the x-axis
+    # $x.left.plot.region: left side of the plot region, in coordinates of the x-axis
+    # $x.right.plot.region: right side of the plot region, in coordinates of the x-axis
+    # $x.mid.plot.region: middle of the plot region, in coordinates of the x-axis
+    # $y.mid.bottom.dev.region: middle of the bottom margin of the device region, in coordinates of the y-axis
+    # $y.bottom.dev.region: bottom side of the bottom margin (including the potential margin of the device region), in coordinates of the y-axis
+    # $y.mid.top.dev.region: middle of the top margin of the device region, in coordinates of the y-axis
+    # $y.top.dev.region: top side of the top margin (including the potential margin of the device region), in coordinates of the y-axis
+    # $y.mid.bottom.fig.region: middle of the bottom margin of the figure region, in coordinates of the y-axis
+    # $y.bottom.fig.region: bottom of the bottom margin of the figure region, in coordinates of the y-axis
+    # $y.mid.top.fig.region: middle of the top margin of the figure region, in coordinates of the y-axis
+    # $y.top.fig.region: top of the top margin of the figure region, in coordinates of the y-axis
+    # $y.top.plot.region: top of the plot region, in coordinates of the y-axis
+    # $y.bottom.plot.region: bottom of the plot region, in coordinates of the y-axis
+    # $y.mid.plot.region: middle of the plot region, in coordinates of the y-axis
+    # $text: warning text
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # fun_open() to reinitialize graph parameters if par.reset = TRUE and custom.par = NULL
+    # EXAMPLES
+    # Example of log axis with log y-axis and unmodified x-axis:
+    # prior.par <- fun_prior_plot(param.reinitial = TRUE, xlog.scale = FALSE, ylog.scale = TRUE, remove.label = TRUE, remove.x.axis = FALSE, remove.y.axis = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 0.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = TRUE) ; plot(1:100, log = "y") ; fun_post_plot(y.side = 2, y.log.scale = prior.par$ylog, x.lab = "Values", y.lab = "TEST", y.axis.size = 1.25, y.label.size = 1.5, y.dist.legend = 0.7, just.label.add = ! prior.par$ann)
+    # Example of log axis with redrawn x-axis and y-axis:
+    # prior.par <- fun_prior_plot(param.reinitial = TRUE) ; plot(1:100) ; fun_post_plot(x.side = 1, x.lab = "Values", y.side = 2, y.lab = "TEST", y.axis.size = 1, y.label.size = 2, y.dist.legend = 0.6)
+    # Example of title easily added to a plot:
+    # plot(1:100) ; para <- fun_post_plot(corner.text = "TITLE ADDED") # try also: par(xpd = TRUE) ; text(x = para$x.mid.left.fig.region, y = para$y.mid.top.fig.region, labels = "TITLE ADDED", cex = 0.5)
+    # example with margins in the device region:
+    # windows(5,5) ; fun_prior_plot(box.type = "o") ; par(mai=c(0.5,0.5,0.5,0.5), omi = c(0.25,0.25,1,0.25), xaxs = "i", yaxs = "i") ; plot(0:10) ; a <- fun_post_plot(x.side = 0, y.side = 0) ; x <- c(a$x.mid.left.dev.region, a$x.left.dev.region, a$x.mid.right.dev.region, a$x.right.dev.region, a$x.mid.left.fig.region, a$x.left.fig.region, a$x.mid.right.fig.region, a$x.right.fig.region, a$x.right.plot.region, a$x.left.plot.region, a$x.mid.plot.region) ; y <- c(a$y.mid.bottom.dev.region, a$y.bottom.dev.region, a$y.mid.top.dev.region, a$y.top.dev.region, a$y.mid.bottom.fig.region, a$y.bottom.fig.region, a$y.mid.top.fig.region, a$y.top.fig.region, a$y.top.plot.region, a$y.bottom.plot.region, a$y.mid.plot.region) ; par(xpd = NA) ; points(x = rep(5, length(y)), y = y, pch = 16, col = "red") ; text(x = rep(5, length(y)), y = y, c("y.mid.bottom.dev.region", "y.bottom.dev.region", "y.mid.top.dev.region", "y.top.dev.region", "y.mid.bottom.fig.region", "y.bottom.fig.region", "y.mid.top.fig.region", "y.top.fig.region", "y.top.plot.region", "y.bottom.plot.region", "y.mid.plot.region"), cex = 0.65, col = grey(0.25)) ; points(y = rep(5, length(x)), x = x, pch = 16, col = "blue") ; text(y = rep(5, length(x)), x = x, c("x.mid.left.dev.region", "x.left.dev.region", "x.mid.right.dev.region", "x.right.dev.region", "x.mid.left.fig.region", "x.left.fig.region", "x.mid.right.fig.region", "x.right.fig.region", "x.right.plot.region", "x.left.plot.region", "x.mid.plot.region"), cex = 0.65, srt = 90, col = grey(0.25))
+    # DEBUGGING
+    # x.side = 0 ; x.log.scale = FALSE ; x.categ = NULL ; x.categ.pos = NULL ; x.lab = "" ; x.axis.size = 1.5 ; x.label.size = 1.5 ; x.dist.legend = 1 ; x.nb.inter.tick = 1 ; y.side = 0 ; y.log.scale = FALSE ; y.categ = NULL ; y.categ.pos = NULL ; y.lab = "" ; y.axis.size = 1.5 ; y.label.size = 1.5 ; y.dist.legend = 0.7 ; y.nb.inter.tick = 1 ; text.angle = 90 ; tick.length = 0.5 ; sec.tick.length = 0.3 ; bg.color = NULL ; grid.lwd = NULL ; grid.col = "white" ; corner.text = "" ; corner.text.size = 1 ; just.label.add = FALSE ; par.reset = FALSE ; custom.par = NULL # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(length(utils::find("fun_open", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_open() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = x.side, options = c(0, 1, 3), length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = x.log.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(x.categ)){
+        tempo <- fun_check(data = x.categ, class = "character", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(x.categ.pos)){
+        tempo <- fun_check(data = x.categ.pos, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = x.lab, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = x.axis.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = x.label.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = x.dist.legend, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = x.nb.inter.tick, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y.side, options = c(0, 2, 4), length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y.log.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(y.categ)){
+        tempo <- fun_check(data = y.categ, class = "character", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(y.categ.pos)){
+        tempo <- fun_check(data = y.categ.pos, class = "vector", mode = "numeric", fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = y.lab, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y.axis.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y.label.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y.dist.legend, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y.nb.inter.tick, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = text.angle, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = tick.length, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = sec.tick.length, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
+    if( ! is.null(bg.color)){
+        tempo <- fun_check(data = bg.color, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+        if( ! (bg.color %in% colors() | grepl(pattern = "^#", bg.color))){ # check color
+            tempo.cat <- paste0("ERROR IN ", function.name, ": bg.color ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # OR A COLOR NAME GIVEN BY colors()")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }
+    if( ! is.null(grid.lwd)){
+        tempo <- fun_check(data = grid.lwd, class = "vector", mode = "numeric", neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(grid.col)){
+        tempo <- fun_check(data = grid.col, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+        if( ! (grid.col %in% colors() | grepl(pattern = "^#", grid.col))){ # check color
+            tempo.cat <- paste0("ERROR IN ", function.name, ": grid.col ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # OR A COLOR NAME GIVEN BY colors()")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }
+    tempo <- fun_check(data = corner.text, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = corner.text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = just.label.add, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = par.reset, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(custom.par)){
+        tempo <- fun_check(data = custom.par, typeof = "list", length = 1, fun.name = function.name) ; eval(ee)
+    }
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    text <- NULL
+    par(tcl = -par()$mgp[2] * tick.length)
+    if(x.log.scale == TRUE){
+        grid.coord.x <- c(10^par("usr")[1], 10^par("usr")[2])
+    }else{
+        grid.coord.x <- c(par("usr")[1], par("usr")[2])
+    }
+    if(y.log.scale == TRUE){
+        grid.coord.y <- c(10^par("usr")[3], 10^par("usr")[4])
+    }else{
+        grid.coord.y <- c(par("usr")[3], par("usr")[4])
+    }
+    if( ! is.null(bg.color)){
+        rect(grid.coord.x[1], grid.coord.y[1], grid.coord.x[2], grid.coord.y[2], col = bg.color, border = NA)
+    }
+    if( ! is.null(grid.lwd)){
+        grid(nx = NA, ny = NULL, col = grid.col, lty = 1, lwd = grid.lwd)
+    }
+    if(x.log.scale == TRUE){
+        x.mid.left.dev.region <- 10^(par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1] / 2) # in x coordinates, to position axis labeling at the bottom of the graph (according to x scale)
+        x.left.dev.region <- 10^(par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1]) # in x coordinates
+        x.mid.right.dev.region <- 10^(par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) + ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * (1 - par("omd")[2]) / 2) # in x coordinates, to position axis labeling at the top of the graph (according to x scale)
+        x.right.dev.region <- 10^(par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) + ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * (1 - par("omd")[2])) # in x coordinates
+        x.mid.left.fig.region <- 10^(par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] / 2) # in x coordinates, to position axis labeling at the bottom of the graph (according to x scale)
+        x.left.fig.region <- 10^(par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1]) # in x coordinates
+        x.mid.right.fig.region <- 10^(par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) / 2) # in x coordinates, to position axis labeling at the top of the graph (according to x scale)
+        x.right.fig.region <- 10^(par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2])) # in x coordinates
+        x.left.plot.region <- 10^par("usr")[1] # in x coordinates, left of the plot region (according to x scale)
+        x.right.plot.region <- 10^par("usr")[2] # in x coordinates, right of the plot region (according to x scale)
+        x.mid.plot.region <- 10^((par("usr")[2] + par("usr")[1]) / 2) # in x coordinates, right of the plot region (according to x scale)
+    }else{
+        x.mid.left.dev.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1] / 2) # in x coordinates, to position axis labeling at the bottom of the graph (according to x scale)
+        x.left.dev.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1]) # in x coordinates
+        x.mid.right.dev.region <- (par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) + ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * (1 - par("omd")[2]) / 2) # in x coordinates, to position axis labeling at the top of the graph (according to x scale)
+        x.right.dev.region <- (par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) + ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * (1 - par("omd")[2])) # in x coordinates
+        x.mid.left.fig.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] / 2) # in x coordinates, to position axis labeling at the bottom of the graph (according to x scale)
+        x.left.fig.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1]) # in x coordinates
+        x.mid.right.fig.region <- (par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2]) / 2) # in x coordinates, to position axis labeling at the top of the graph (according to x scale)
+        x.right.fig.region <- (par("usr")[2] + ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * (1 - par("plt")[2])) # in x coordinates
+        x.left.plot.region <- par("usr")[1] # in x coordinates, left of the plot region (according to x scale)
+        x.right.plot.region <- par("usr")[2] # in x coordinates, right of the plot region (according to x scale)
+        x.mid.plot.region <- (par("usr")[2] + par("usr")[1]) / 2 # in x coordinates, right of the plot region (according to x scale)
+    }
+    if(y.log.scale == TRUE){
+        y.mid.bottom.dev.region <- 10^(par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] - ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (par("omd")[3] / 2)) # in y coordinates, to position axis labeling at the bottom of the graph (according to y scale). Ex mid.bottom.space
+        y.bottom.dev.region <- 10^(par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] - ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * par("omd")[3]) # in y coordinates
+        y.mid.top.dev.region <- 10^(par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4]) / 2) # in y coordinates, to position axis labeling at the top of the graph (according to y scale). Ex mid.top.space
+        y.top.dev.region <- 10^(par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4])) # in y coordinates
+        y.mid.bottom.fig.region <- 10^(par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] / 2) # in y coordinates, to position axis labeling at the bottom of the graph (according to y scale). Ex mid.bottom.space
+        y.bottom.fig.region <- 10^(par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3]) # in y coordinates
+        y.mid.top.fig.region <- 10^(par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) / 2) # in y coordinates, to position axis labeling at the top of the graph (according to y scale). Ex mid.top.space
+        y.top.fig.region <- 10^(par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4])) # in y coordinates
+        y.top.plot.region <- 10^par("usr")[4] # in y coordinates, top of the plot region (according to y scale)
+        y.bottom.plot.region <- 10^par("usr")[3] # in y coordinates, bottom of the plot region (according to y scale)
+        y.mid.plot.region <- (par("usr")[3] + par("usr")[4]) / 2 # in x coordinates, right of the plot region (according to x scale)
+    }else{
+        y.mid.bottom.dev.region <- (par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] - ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (par("omd")[3] / 2)) # in y coordinates, to position axis labeling at the bottom of the graph (according to y scale). Ex mid.bottom.space
+        y.bottom.dev.region <- (par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] - ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * par("omd")[3]) # in y coordinates
+        y.mid.top.dev.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4]) / 2) # in y coordinates, to position axis labeling at the top of the graph (according to y scale). Ex mid.top.space
+        y.top.dev.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4])) # in y coordinates
+        y.mid.bottom.fig.region <- (par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3] / 2) # in y coordinates, to position axis labeling at the bottom of the graph (according to y scale). Ex mid.bottom.space
+        y.bottom.fig.region <- (par("usr")[3] - ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * par("plt")[3]) # in y coordinates
+        y.mid.top.fig.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) / 2) # in y coordinates, to position axis labeling at the top of the graph (according to y scale). Ex mid.top.space
+        y.top.fig.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4])) # in y coordinates
+        y.top.plot.region <- par("usr")[4] # in y coordinates, top of the plot region (according to y scale)
+        y.bottom.plot.region <- par("usr")[3] # in y coordinates, bottom of the plot region (according to y scale)
+        y.mid.plot.region <- ((par("usr")[3] + par("usr")[4]) / 2) # in x coordinates, right of the plot region (according to x scale)
+    }
+    if(any(sapply(FUN = all.equal, c(1, 3), x.side) == TRUE)){
+        par(xpd=FALSE, xaxt="s")
+        if(is.null(x.categ) & x.log.scale == TRUE){
+            if(any(par()$xaxp[1:2] == 0L)){ # any(sapply(FUN = all.equal, par()$xaxp[1:2], 0) == TRUE) not used because we strictly need zero as a result. Beware: write "== TRUE", because the result is otherwise character and a warning message appears using any()
+                if(par()$xaxp[1] == 0L){ # isTRUE(all.equal(par()$xaxp[1], 0)) not used because we strictly need zero as a result
+                    par(xaxp = c(10^-30, par()$xaxp[2:3])) # because log10(par()$xaxp[1] == 0) == -Inf
+                }
+                if(par()$xaxp[2] == 0L){ # isTRUE(all.equal(par()$xaxp[1], 0)) not used because we strictly need zero as a result
+                    par(xaxp = c(par()$xaxp[1], 10^-30, par()$xaxp[3])) # because log10(par()$xaxp[2] == 0) == -Inf
+                }
+            }
+            axis(side = x.side, at = c(10^par()$usr[1], 10^par()$usr[2]), labels=rep("", 2), lwd=1, lwd.ticks = 0) # draw the axis line
+            mtext(side = x.side, text = x.lab, line = x.dist.legend / 0.2, las = 0, cex = x.label.size)
+            par(tcl = -par()$mgp[2] * sec.tick.length) # length of the secondary ticks are reduced
+            suppressWarnings(rug(10^outer(c((log10(par("xaxp")[1]) -1):log10(par("xaxp")[2])), log10(1:10), "+"), ticksize = NA, side = x.side)) # ticksize = NA to allow the use of par()$tcl value
+            par(tcl = -par()$mgp[2] * tick.length) # back to main ticks
+            axis(side = x.side, at = c(1e-15, 1e-14, 1e-13, 1e-12, 1e-11, 1e-10, 1e-9, 1e-8, 1e-7, 1e-6, 1e-5, 1e-4, 1e-3, 1e-2, 1e-1, 1e0, 1e1, 1e2, 1e3, 1e4, 1e5, 1e6, 1e7, 1e8, 1e9, 1e10), labels = expression(10^-15, 10^-14, 10^-13, 10^-12, 10^-11, 10^-10, 10^-9, 10^-8, 10^-7, 10^-6, 10^-5, 10^-4, 10^-3, 10^-2, 10^-1, 10^0, 10^1, 10^2, 10^3, 10^4, 10^5, 10^6, 10^7, 10^8, 10^9, 10^10), lwd = 0, lwd.ticks = 1, cex.axis = x.axis.size)
+            x.text <- 10^par("usr")[2]
+        }else if(is.null(x.categ) & x.log.scale == FALSE){
+            axis(side=x.side, at=c(par()$usr[1], par()$usr[2]), labels=rep("", 2), lwd=1, lwd.ticks=0) # draw the axis line
+            axis(side=x.side, at=round(seq(par()$xaxp[1], par()$xaxp[2], length.out=par()$xaxp[3]+1), 2), cex.axis = x.axis.size) # axis(side=x.side, at=round(seq(par()$xaxp[1], par()$xaxp[2], length.out=par()$xaxp[3]+1), 2), labels = format(round(seq(par()$xaxp[1], par()$xaxp[2], length.out=par()$xaxp[3]+1), 2), big.mark=','), cex.axis = x.axis.size) # to get the 1000 comma separator
+            mtext(side = x.side, text = x.lab, line = x.dist.legend / 0.2, las = 0, cex = x.label.size)
+            if(x.nb.inter.tick > 0){
+                inter.tick.unit <- (par("xaxp")[2] - par("xaxp")[1]) / par("xaxp")[3]
+                par(tcl = -par()$mgp[2] * sec.tick.length) # length of the ticks are reduced
+                suppressWarnings(rug(seq(par("xaxp")[1] - 10 * inter.tick.unit, par("xaxp")[2] + 10 * inter.tick.unit, by = inter.tick.unit / (1 + x.nb.inter.tick)), ticksize = NA, x.side)) # ticksize = NA to allow the use of par()$tcl value
+                par(tcl = -par()$mgp[2] * tick.length) # back to main ticks
+            }
+            x.text <- par("usr")[2]
+        }else if(( ! is.null(x.categ)) & x.log.scale == FALSE){
+            if(is.null(x.categ.pos)){
+                x.categ.pos <- 1:length(x.categ)
+            }else if(length(x.categ.pos) != length(x.categ)){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": x.categ.pos MUST BE THE SAME LENGTH AS x.categ")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            par(xpd = TRUE)
+            if(isTRUE(all.equal(x.side, 1))){ #isTRUE(all.equal(x.side, 1)) is similar to x.side == 1L but deals with float
+                segments(x0 = x.left.plot.region, x1 = x.right.plot.region, y0 = y.bottom.plot.region, y1 = y.bottom.plot.region) # draw the line of the axis
+                text(x = x.categ.pos, y = y.mid.bottom.fig.region, labels = x.categ, srt = text.angle, cex = x.axis.size)
+            }else if(isTRUE(all.equal(x.side, 3))){ #isTRUE(all.equal(x.side, 1)) is similar to x.side == 3L but deals with float
+                segments(x0 = x.left.plot.region, x1 = x.right.plot.region, y0 = y.top.plot.region, y1 = y.top.plot.region) # draw the line of the axis
+                text(x = x.categ.pos, y = y.mid.top.fig.region, labels = x.categ, srt = text.angle, cex = x.axis.size)
+            }else{
+                tempo.cat <- paste0("ERROR IN ", function.name, ": ARGUMENT x.side CAN ONLY BE 1 OR 3")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            par(xpd = FALSE)
+            x.text <- par("usr")[2]
+        }else{
+            tempo.cat <- paste0("ERROR IN ", function.name, ": PROBLEM WITH THE x.side (", x.side ,") OR x.log.scale (", x.log.scale,") ARGUMENTS")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }else{
+        x.text <- par("usr")[2]
+    }
+    if(any(sapply(FUN = all.equal, c(2, 4), y.side) == TRUE)){
+        par(xpd=FALSE, yaxt="s")
+        if(is.null(y.categ) & y.log.scale == TRUE){
+            if(any(par()$yaxp[1:2] == 0L)){ # any(sapply(FUN = all.equal, par()$yaxp[1:2], 0) == TRUE) not used because we strictly need zero as a result. Beware: write "== TRUE", because the result is otherwise character and a warning message appears using any()
+                if(par()$yaxp[1] == 0L){ # strict zero needed
+                    par(yaxp = c(10^-30, par()$yaxp[2:3])) # because log10(par()$yaxp[1] == 0) == -Inf
+                }
+                if(par()$yaxp[2] == 0L){ # strict zero needed
+                    par(yaxp = c(par()$yaxp[1], 10^-30, par()$yaxp[3])) # because log10(par()$yaxp[2] == 0) == -Inf
+                }
+            }
+            axis(side=y.side, at=c(10^par()$usr[3], 10^par()$usr[4]), labels=rep("", 2), lwd=1, lwd.ticks=0) # draw the axis line
+            par(tcl = -par()$mgp[2] * sec.tick.length) # length of the ticks are reduced
+            suppressWarnings(rug(10^outer(c((log10(par("yaxp")[1])-1):log10(par("yaxp")[2])), log10(1:10), "+"), ticksize = NA, side = y.side)) # ticksize = NA to allow the use of par()$tcl value
+            par(tcl = -par()$mgp[2] * tick.length) # back to main tick length
+            axis(side = y.side, at = c(1e-15, 1e-14, 1e-13, 1e-12, 1e-11, 1e-10, 1e-9, 1e-8, 1e-7, 1e-6, 1e-5, 1e-4, 1e-3, 1e-2, 1e-1, 1e0, 1e1, 1e2, 1e3, 1e4, 1e5, 1e6, 1e7, 1e8, 1e9, 1e10), labels = expression(10^-15, 10^-14, 10^-13, 10^-12, 10^-11, 10^-10, 10^-9, 10^-8, 10^-7, 10^-6, 10^-5, 10^-4, 10^-3, 10^-2, 10^-1, 10^0, 10^1, 10^2, 10^3, 10^4, 10^5, 10^6, 10^7, 10^8, 10^9, 10^10), lwd = 0, lwd.ticks = 1, cex.axis = y.axis.size)
+            y.text <- 10^(par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
+            mtext(side = y.side, text = y.lab, line = y.dist.legend / 0.2, las = 0, cex = y.label.size)
+        }else if(is.null(y.categ) & y.log.scale == FALSE){
+            axis(side=y.side, at=c(par()$usr[3], par()$usr[4]), labels=rep("", 2), lwd=1, lwd.ticks=0) # draw the axis line
+            axis(side=y.side, at=round(seq(par()$yaxp[1], par()$yaxp[2], length.out=par()$yaxp[3]+1), 2), cex.axis = y.axis.size)
+            mtext(side = y.side, text = y.lab, line = y.dist.legend / 0.2, las = 0, cex = y.label.size)
+            if(y.nb.inter.tick > 0){
+                inter.tick.unit <- (par("yaxp")[2] - par("yaxp")[1]) / par("yaxp")[3]
+                par(tcl = -par()$mgp[2] * sec.tick.length) # length of the ticks are reduced
+                suppressWarnings(rug(seq(par("yaxp")[1] - 10 * inter.tick.unit, par("yaxp")[2] + 10 * inter.tick.unit, by = inter.tick.unit / (1 + y.nb.inter.tick)), ticksize = NA, side=y.side)) # ticksize = NA to allow the use of par()$tcl value
+                par(tcl = -par()$mgp[2] * tick.length) # back to main tick length
+            }
+            y.text <- (par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
+        }else if(( ! is.null(y.categ)) & y.log.scale == FALSE){
+            if(is.null(y.categ.pos)){
+                y.categ.pos <- 1:length(y.categ)
+            }else if(length(y.categ.pos) != length(y.categ)){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": y.categ.pos MUST BE THE SAME LENGTH AS y.categ")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            axis(side = y.side, at = y.categ.pos, labels = rep("", length(y.categ)), lwd=0, lwd.ticks=1) # draw the line of the axis
+            par(xpd = TRUE)
+            if(isTRUE(all.equal(y.side, 2))){ #isTRUE(all.equal(y.side, 2)) is similar to y.side == 2L but deals with float
+                text(x = x.mid.left.fig.region, y = y.categ.pos, labels = y.categ, srt = text.angle, cex = y.axis.size)
+            }else if(isTRUE(all.equal(y.side, 4))){ # idem
+                text(x = x.mid.right.fig.region, y = y.categ.pos, labels = y.categ, srt = text.angle, cex = y.axis.size)
+            }else{
+                tempo.cat <- paste0("ERROR IN ", function.name, ": ARGUMENT y.side CAN ONLY BE 2 OR 4")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            par(xpd = FALSE)
+            y.text <- (par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
+        }else{
+            tempo.cat <- paste0("ERROR IN ", function.name, ": PROBLEM WITH THE y.side (", y.side ,") OR y.log.scale (", y.log.scale,") ARGUMENTS")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }else{
+        y.text <- (par("usr")[4] + (par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3]) * (1 - par("plt")[4]))
+    }
+    par(xpd=NA)
+    text(x = x.mid.right.fig.region, y = y.text, corner.text, adj=c(1, 1.1), cex = corner.text.size) # text at the topright corner. Replace x.right.fig.region by x.text if text at the right edge of the plot region
+    if(just.label.add == TRUE & isTRUE(all.equal(x.side, 0)) & x.lab != ""){
+        text(x = x.mid.plot.region, y = y.mid.bottom.fig.region, x.lab, adj=c(0.5, 0.5), cex = x.label.size) # x label
+    }
+    if(just.label.add == TRUE & isTRUE(all.equal(y.side, 0)) & y.lab != ""){
+        text(x = y.mid.plot.region, y = x.mid.left.fig.region, y.lab, adj=c(0.5, 0.5), cex = y.label.size) # x label
+    }
+    par(xpd=FALSE)
+    if(par.reset == TRUE){
+        tempo.par <- fun_open(pdf = FALSE, return.output = TRUE)
+        invisible(dev.off()) # close the new window
+        if( ! is.null(custom.par)){
+            if( ! names(custom.par) %in% names(tempo.par$ini.par)){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": custom.par ARGUMENT SHOULD HAVE THE NAMES OF THE COMPARTMENT LIST COMING FROM THE par() LIST")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            par(custom.par)
+            text <- c(text, "\nGRAPH PARAMETERS SET TO VALUES DEFINED BY custom.par ARGUMENT\n")
+        }else{
+            par(tempo.par$ini.par)
+            text <- c(text, "\nGRAPH PARAMETERS RESET TO par() DEFAULT VALUES\n")
+        }
+    }
+    output <- list(x.mid.left.dev.region = x.mid.left.dev.region, x.left.dev.region = x.left.dev.region, x.mid.right.dev.region = x.mid.right.dev.region, x.right.dev.region = x.right.dev.region, x.mid.left.fig.region = x.mid.left.fig.region, x.left.fig.region = x.left.fig.region, x.mid.right.fig.region = x.mid.right.fig.region, x.right.fig.region = x.right.fig.region, x.left.plot.region = x.left.plot.region, x.right.plot.region = x.right.plot.region, x.mid.plot.region = x.mid.plot.region, y.mid.bottom.dev.region = y.mid.bottom.dev.region, y.bottom.dev.region = y.bottom.dev.region, y.mid.top.dev.region = y.mid.top.dev.region, y.top.dev.region = y.top.dev.region, y.mid.bottom.fig.region = y.mid.bottom.fig.region, y.bottom.fig.region = y.bottom.fig.region, y.mid.top.fig.region = y.mid.top.fig.region, y.top.fig.region = y.top.fig.region, y.top.plot.region = y.top.plot.region, y.bottom.plot.region = y.bottom.plot.region, y.mid.plot.region = y.mid.plot.region, text = text)
+    return(output)
 }
-# end conversion of geom_hline and geom_vline
 
 
+######## fun_close() #### close specific graphic windows
 
 
-# kind of geom_point (vectorial or raster)
-scatter.kind <- vector("list", length = length(data1)) # list of same length as data1, that will be used to use either ggplot2::geom_point() (vectorial dot layer) or fun_gg_point_rast() (raster dot layer)
-fix.ratio <- FALSE
-if(is.null(raster.threshold)){
-if(raster == TRUE){
-scatter.kind[] <- "fun_gg_point_rast" # not important to fill everything: will be only used when geom == "geom_point"
-fix.ratio <- TRUE
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") RASTER PLOT GENERATED -> ASPECT RATIO OF THE PLOT REGION SET BY THE raster.ratio ARGUMENT (", fun_round(raster.ratio, 2), ") TO AVOID A BUG OF ELLIPSOID DOT DRAWING")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}else{
-scatter.kind[] <- "ggplot2::geom_point"
-}
-}else{
-for(i2 in 1:length(data1)){
-if(geom[[i2]] == "geom_point"){
-if(nrow(data1[[i2]]) <= raster.threshold){
-scatter.kind[[i2]] <- "ggplot2::geom_point"
-}else{
-scatter.kind[[i2]] <- "fun_gg_point_rast"
-fix.ratio <- TRUE
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i2, " OF data1 ARGUMENT")), " LAYER AS RASTER (NOT VECTORIAL)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-}
-if(any(unlist(scatter.kind) == "fun_gg_point_rast")){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") RASTER PLOT GENERATED -> ASPECT RATIO OF THE PLOT REGION SET BY THE raster.ratio ARGUMENT (", fun_round(raster.ratio, 2), ") TO AVOID A BUG OF ELLIPSOID DOT DRAWING")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}
-# end kind of geom_point (vectorial or raster)
-
-
-
-
-# no need loop part
-coord.names <- NULL
-tempo.gg.name <- "gg.indiv.plot."
-tempo.gg.count <- 0
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::ggplot()", if(is.null(add)){""}else{add})))) # add added here to have the facets
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::xlab(if(is.null(x.lab)){x[[1]]}else{x.lab}))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ylab(if(is.null(y.lab)){y[[1]]}else{y.lab}))
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggtitle(title))
-# text angle management
-x.tempo.just <- fun_gg_just(angle = x.text.angle, pos = "bottom", kind = "axis")
-y.tempo.just <- fun_gg_just(angle = y.text.angle, pos = "left", kind = "axis")
-# end text angle management
-add.check <- TRUE
-if( ! is.null(add)){ # if add is NULL, then = 0
-if(grepl(pattern = "ggplot2::theme", add) == TRUE){
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") \"ggplot2::theme\" STRING DETECTED IN THE add ARGUMENT\n-> INTERNAL GGPLOT2 THEME FUNCTIONS theme() AND theme_classic() HAVE BEEN INACTIVATED, TO BE USED BY THE USER\n-> article ARGUMENT WILL BE IGNORED\nIT IS RECOMMENDED TO USE \"+ theme(aspect.ratio = raster.ratio)\" IF RASTER MODE IS ACTIVATED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-add.check <- FALSE
-}
-}
-if(add.check == TRUE & article == TRUE){
-# WARNING: not possible to add several times theme(). NO message but the last one overwrites the others
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::theme_classic(base_size = text.size))
-if(grid == TRUE){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
-text = ggplot2::element_text(size = text.size), 
-plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
-legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
-line = ggplot2::element_line(size = 0.5), 
-axis.line.y.left = ggplot2::element_line(colour = "black"), # draw lines for the y axis
-axis.line.x.bottom = ggplot2::element_line(colour = "black"), # draw lines for the x axis
-panel.grid.major.x = ggplot2::element_line(colour = "grey85", size = 0.75), 
-panel.grid.minor.x = ggplot2::element_line(colour = "grey90", size = 0.25), 
-panel.grid.major.y = ggplot2::element_line(colour = "grey85", size = 0.75), 
-panel.grid.minor.y = ggplot2::element_line(colour = "grey90", size = 0.25), 
-axis.text.x = ggplot2::element_text(angle = x.tempo.just$angle, hjust = x.tempo.just$hjust, vjust = x.tempo.just$vjust),
-axis.text.y = ggplot2::element_text(angle = y.tempo.just$angle, hjust = y.tempo.just$hjust, vjust = y.tempo.just$vjust), 
-aspect.ratio = if(fix.ratio == TRUE){raster.ratio}else{NULL} # for raster
-))
-}else{
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
-text = ggplot2::element_text(size = text.size), 
-plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
-line = ggplot2::element_line(size = 0.5), 
-legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
-axis.line.y.left = ggplot2::element_line(colour = "black"), 
-axis.line.x.bottom = ggplot2::element_line(colour = "black"), 
-axis.text.x = ggplot2::element_text(angle = x.tempo.just$angle, hjust = x.tempo.just$hjust, vjust = x.tempo.just$vjust),
-axis.text.y = ggplot2::element_text(angle = y.tempo.just$angle, hjust = y.tempo.just$hjust, vjust = y.tempo.just$vjust), 
-aspect.ratio = if(fix.ratio == TRUE){raster.ratio}else{NULL} # for raster
-))
-}
-}else if(add.check == TRUE & article == FALSE){
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
-text = ggplot2::element_text(size = text.size), 
-plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
-line = ggplot2::element_line(size = 0.5), 
-legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
-panel.background = ggplot2::element_rect(fill = "grey95"), 
-axis.line.y.left = ggplot2::element_line(colour = "black"), 
-axis.line.x.bottom = ggplot2::element_line(colour = "black"), 
-panel.grid.major.x = ggplot2::element_line(colour = "grey85", size = 0.75), 
-panel.grid.minor.x = ggplot2::element_line(colour = "grey90", size = 0.25), 
-panel.grid.major.y = ggplot2::element_line(colour = "grey85", size = 0.75), 
-panel.grid.minor.y = ggplot2::element_line(colour = "grey90", size = 0.25), 
-strip.background = ggplot2::element_rect(fill = "white", colour = "black"), 
-axis.text.x = ggplot2::element_text(angle = x.tempo.just$angle, hjust = x.tempo.just$hjust, vjust = x.tempo.just$vjust),
-axis.text.y = ggplot2::element_text(angle = y.tempo.just$angle, hjust = y.tempo.just$hjust, vjust = y.tempo.just$vjust), 
-aspect.ratio = if(fix.ratio == TRUE){raster.ratio}else{NULL} # for raster
-# do not work -> legend.position = "none" # to remove the legend completely: https://www.datanovia.com/en/blog/how-to-remove-legend-from-a-ggplot/
-))
-}
-# end no need loop part
-
-
-# loop part
-point.count <- 0
-line.count <- 0
-lg.order <- vector(mode = "list", length = 6) # order of the legend
-lg.order <- lapply(lg.order, as.numeric) # order of the legend
-lg.color <- vector(mode = "list", length = 6) # color of the legend
-lg.dot.shape <- vector(mode = "list", length = 6) # etc.
-lg.dot.size <- vector(mode = "list", length = 6) # etc.
-lg.dot.size <- lapply(lg.dot.size, as.numeric) # etc.
-lg.dot.border.size <- vector(mode = "list", length = 6) # etc.
-lg.dot.border.size <- lapply(lg.dot.border.size, as.numeric) # etc.
-lg.dot.border.color <- vector(mode = "list", length = 6) # etc.
-lg.line.size <- vector(mode = "list", length = 6) # etc.
-lg.line.size <- lapply(lg.line.size, as.numeric) # etc.
-lg.line.type <- vector(mode = "list", length = 6) # etc.
-lg.alpha <- vector(mode = "list", length = 6) # etc.
-lg.alpha <- lapply(lg.alpha, as.numeric) # etc.
-for(i1 in 1:length(data1)){
-if(geom[[i1]] == "geom_point"){
-point.count <- point.count + 1
-if(point.count== 1L){
-fin.lg.disp[[1]] <- legend.disp[[point.count + line.count]]
-lg.order[[1]] <- point.count + line.count
-lg.color[[1]] <- color[[i1]] # if color == NULL -> NULL
-lg.dot.shape[[1]] <- dot.shape[[i1]]
-lg.dot.size[[1]] <- dot.size[[i1]]
-lg.dot.border.size[[1]] <- dot.border.size[[i1]]
-lg.dot.border.color[[1]] <- dot.border.color[[i1]] # if dot.border.color == NULL -> NULL
-if(plot == TRUE & fin.lg.disp[[1]] == TRUE & dot.shape[[1]] %in% 0:14 & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list())== 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE DOTS (DOT LAYER NUMBER ", point.count, ") IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-lg.alpha[[1]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
-}else{
-lg.alpha[[1]] <- alpha[[i1]]
-}
-class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
-for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
-tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = scatter.kind[[i1]]))(data = tempo.data.frame, mapping = ggplot2::aes_string(x = x[[i1]], y = y[[i1]], fill = categ[[i1]]), shape = dot.shape[[i1]], size = dot.size[[i1]], stroke = dot.border.size[[i1]], color = if(dot.shape[[i1]] %in% 21:24 & ! is.null(dot.border.color)){dot.border.color[[i1]]}else{color[[i1]][i5]}, alpha = alpha[[i1]], show.legend = if(i5== 1L){TRUE}else{FALSE})) # WARNING: a single color allowed for color argument outside aesthetic, but here a single color for border --> loop could be inactivated but kept for commodity # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.). Used here to avoid multiple layers of legend which corrupt transparency
-coord.names <- c(coord.names, paste0(geom[[i1]], ".", class.categ[i5]))
-}
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_fill_manual(name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = as.character(color[[i1]]), breaks = class.categ)) # values are the values of fill, breaks reorder the classes according to class.categ in the legend, order argument of guide_legend determines the order of the different aesthetics in the legend (not order of classes). See guide_legend settings of scale_..._manual below
-}
-if(point.count== 2L){
-fin.lg.disp[[2]] <- legend.disp[[point.count + line.count]]
-lg.order[[2]] <- point.count + line.count
-lg.color[[2]] <- color[[i1]] # if color == NULL -> NULL
-lg.dot.shape[[2]] <- dot.shape[[i1]]
-lg.dot.size[[2]] <- dot.size[[i1]]
-lg.dot.border.size[[2]] <- dot.border.size[[i1]]
-lg.dot.border.color[[2]] <- dot.border.color[[i1]] # if dot.border.color == NULL -> NULL
-if(plot == TRUE & fin.lg.disp[[2]] == TRUE & dot.shape[[2]] %in% 0:14 & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list())== 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE DOTS (DOT LAYER NUMBER ", point.count, ") IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-lg.alpha[[2]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
-}else{
-lg.alpha[[2]] <- alpha[[i1]]
-}
-class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
-for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
-tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = scatter.kind[[i1]]))(data = tempo.data.frame, mapping = ggplot2::aes_string(x = x[[i1]], y = y[[i1]], shape = categ[[i1]]), size = dot.size[[i1]], stroke = dot.border.size[[i1]], fill = color[[i1]][i5], color = if(dot.shape[[i1]] %in% 21:24 & ! is.null(dot.border.color)){dot.border.color[[i1]]}else{color[[i1]][i5]}, alpha = alpha[[i1]], show.legend = FALSE)) # WARNING: a single color allowed for fill argument outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.). Used here to avoid multiple layers of legend which corrupt transparency
-coord.names <- c(coord.names, paste0(geom[[i1]], ".", class.categ[i5]))
+fun_close <- function(kind = "pdf", return.text = FALSE){
+    # AIM
+    # close only specific graphic windows (devices)
+    # ARGUMENTS:
+    # kind: vector, among c("windows", "quartz", "x11", "X11", "pdf", "bmp", "png", "tiff"), indicating the kind of graphic windows (devices) to close. BEWARE: either "windows", "quartz", "x11" or "X11" means that all the X11 GUI graphics devices will be closed, whatever the OS used
+    # return.text: print text regarding the kind parameter and the devices that were finally closed?
+    # RETURN
+    # text regarding the kind parameter and the devices that were finally closed
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # windows() ; windows() ; pdf() ; dev.list() ; fun_close(kind = c("pdf", "x11"), return.text = TRUE) ; dev.list()
+    # DEBUGGING
+    # kind = c("windows", "pdf") ; return.text = FALSE # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = kind, options = c("windows", "quartz", "x11", "X11", "pdf", "bmp", "png", "tiff"), fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = return.text, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    text <- paste0("THE REQUIRED KIND OF GRAPHIC DEVICES TO CLOSE ARE ", paste(kind, collapse = " "))
+    if(Sys.info()["sysname"] == "Windows"){ # Note that .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
+        if(any(kind %in% c("windows", "quartz", "x11", "X11"))){
+            tempo <- kind %in% c("windows", "quartz", "x11", "X11")
+            kind[tempo] <- "windows" # term are replaced by what is displayed when using a <- dev.list() ; names(a)
+        }
+    }else if(Sys.info()["sysname"] == "Linux"){
+        if(any(kind %in% c("windows", "quartz", "x11", "X11"))){
+            tempo.device <- suppressWarnings(try(X11(), silent = TRUE))[] # open a X11 window to try to recover the X11 system used
+            if( ! is.null(tempo.device)){
+                text <- paste0(text, "\nCANNOT CLOSE GUI GRAPHIC DEVICES AS REQUIRED BECAUSE THIS LINUX SYSTEM DOES NOT HAVE IT")
+            }else{
+                tempo <- kind %in% c("windows", "quartz", "x11", "X11")
+                kind[tempo] <- names(dev.list()[length(dev.list())]) # term are replaced by what is displayed when using a <- dev.list() ; names(a)
+                invisible(dev.off()) # close the X11 opened by tempo
+            }
+        }
+    }else{ # for macOS
+        if(any(kind %in% c("windows", "quartz", "x11", "X11"))){
+            tempo <- kind %in% c("windows", "quartz", "x11", "X11")
+            kind[tempo] <- "quartz" # term are replaced by what is displayed when using a <- dev.list() ; names(a)
+        }
+    }
+    kind <- unique(kind)
+    if(length(dev.list()) != 0){
+        for(i in length(names(dev.list())):1){
+            if(names(dev.list())[i] %in% kind){
+                text <- paste0(text, "\n", names(dev.list())[i], " DEVICE NUMBER ", dev.list()[i], " HAS BEEN CLOSED")
+                invisible(dev.off(dev.list()[i]))
+            }
+        }
+    }
+    if(return.text == TRUE){
+        return(text)
+    }
 }
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_shape_manual(name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(dot.shape[[i1]], length(color[[i1]])), breaks = class.categ)) # values are the values of shape, breaks reorder the classes according to class.categ in the legend. See guide_legend settings of scale_..._manual below
 
+
+################ Standard graphics
+
+
+######## fun_empty_graph() #### text to display for empty graphs
+
+
+
+
+
+fun_empty_graph <- function(
+    text = NULL, 
+    text.size = 1, 
+    title = NULL, 
+    title.size = 1.5
+){
+    # AIM
+    # display an empty plot with a text in the middle of the window (for instance to specify that no plot can be drawn)
+    # ARGUMENTS
+    # text: character string of the message to display
+    # text.size: numeric value of the text size
+    # title: character string of the graph title
+    # title.size: numeric value of the title size (in points)
+    # RETURN
+    # an empty plot
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # simple example
+    # fun_empty_graph(text = "NO GRAPH")
+    # white page
+    # fun_empty_graph() # white page
+    # all the arguments
+    # fun_empty_graph(text = "NO GRAPH", text.size = 2, title = "GRAPH1", title.size = 1)
+    # DEBUGGING
+    # text = "NO GRAPH" ; title = "GRAPH1" ; text.size = 1
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    if( ! is.null(text)){
+        tempo <- fun_check(data = text, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(title)){
+        tempo <- fun_check(data = title, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = title.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code because always a tempo window opened
+    par(ann=FALSE, xaxt="n", yaxt="n", mar = rep(1, 4), bty = "n", xpd = NA)
+    plot(1, 1, type = "n") # no display with type = "n"
+    x.left.dev.region <- (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / ((par("omd")[2] - par("omd")[1]) * (par("plt")[2] - par("plt")[1]))) * par("omd")[1])
+    y.top.dev.region <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par("omd")[4] - par("omd")[3]) * (par("plt")[4] - par("plt")[3]))) * (1 - par("omd")[4]))
+    if( ! is.null(text)){
+        text(x = 1, y = 1, labels = text, cex = text.size)
+    }
+    if( ! is.null(title)){
+        text(x = x.left.dev.region, y = y.top.dev.region, labels = title, adj=c(0, 1), cex = title.size)
+    }
+    par(ini.par)
 }
-if(point.count== 3L){
-fin.lg.disp[[3]] <- legend.disp[[point.count + line.count]]
-lg.order[[3]] <- point.count + line.count
-lg.color[[3]] <- color[[i1]] # if color == NULL -> NULL
-lg.dot.shape[[3]] <- dot.shape[[i1]]
-lg.dot.size[[3]] <- dot.size[[i1]]
-lg.dot.border.size[[3]] <- dot.border.size[[i1]]
-lg.dot.border.color[[3]] <- dot.border.color[[i1]] # if dot.border.color == NULL -> NULL
-if(plot == TRUE & fin.lg.disp[[3]] == TRUE & dot.shape[[3]] %in% 0:14 & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list())== 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE DOTS (DOT LAYER NUMBER ", point.count, ") IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-lg.alpha[[3]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
-}else{
-lg.alpha[[3]] <- alpha[[i1]]
-}
-class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
-for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
-tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = scatter.kind[[i1]]))(data = tempo.data.frame, mapping = ggplot2::aes_string(x = x[[i1]], y = y[[i1]], stroke = categ[[i1]]), shape = dot.shape[[i1]], size = dot.size[[i1]], fill = color[[i1]][i5], stroke = dot.border.size[[i1]], color = if(dot.shape[[i1]] %in% 21:24 & ! is.null(dot.border.color)){dot.border.color[[i1]]}else{color[[i1]][i5]}, alpha = alpha[[i1]], show.legend = FALSE)) # WARNING: a single color allowed for color argument outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.). Used here to avoid multiple layers of legend which corrupt transparency
-coord.names <- c(coord.names, paste0(geom[[i1]], ".", class.categ[i5]))
+
+
+################ gg graphics
+
+
+######## fun_gg_palette() #### ggplot2 default color palette
+
+
+
+
+
+fun_gg_palette <- function(n, kind = "std"){
+    # AIM
+    # provide colors used by ggplot2
+    # the interest is to use another single color that is not the red one used by default
+    # for ggplot2 specifications, see: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html
+    # ARGUMENTS
+    # n: number of groups on the graph
+    # kind: either "std" for standard gg colors, "dark" for darkened gg colors, or "light" for pastel gg colors
+    # RETURN
+    # the vector of hexadecimal colors
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # output of the function
+    # fun_gg_palette(n = 2)
+    # the ggplot2 palette when asking for 7 different colors
+    # plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7))
+    # selection of the 5th color of the ggplot2 palette made of 7 different colors
+    # plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7)[5])
+    # the ggplot2 palette made of 7 darkened colors
+    # plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7, kind = "dark"))
+    # the ggplot2 palette made of 7 lighten colors
+    # plot(1:7, pch = 16, cex = 5, col = fun_gg_palette(n = 7, kind = "light"))
+    # DEBUGGING
+    # n = 0
+    # kind = "std"
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = n, class = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & isTRUE(all.equal(n, 0))){ # isTRUE(all.equal(n, 0))) is similar to n == 0 but deals with float
+        tempo.cat <- paste0("ERROR IN ", function.name, ": n ARGUMENT MUST BE A NON ZERO INTEGER. HERE IT IS: ", paste(n, collapse = " "))
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+        tempo <- fun_check(data = kind, options = c("std", "dark", "light"), length = 1, fun.name = function.name) ; eval(ee)
+    }
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    hues = seq(15, 375, length = n + 1)
+    hcl(h = hues, l = if(kind == "std"){65}else if(kind == "dark"){35}else if(kind == "light"){85}, c = 100)[1:n]
 }
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "stroke", name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(dot.border.size[[i1]], length(color[[i1]])), breaks = class.categ)) # values are the values of stroke, breaks reorder the classes according to class.categ in the legend. See guide_legend settings of scale_..._manual below
 
+
+######## fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle
+
+
+
+
+
+fun_gg_just <- function(angle, pos, kind = "axis"){
+    # AIM
+    # provide correct justification for text labeling, depending on the chosen angle
+    # WARNINGS
+    # justification behave differently on plot, depending whether it is used for annotayed text or for axis labelling. Indeed the latter has labelling constrained
+    # Of note, a bug in ggplot2: vjust sometimes does not work, i.e., the same justification result is obtained whatever the value used. This is the case with angle = 90, pos = "top", kind = "axis". While everything is fine with angle = 90, pos = "bottom", kind = "axis". At least, everything seems fine for kind = "axis" and pos = c("left", "bottom")
+    # ARGUMENTS
+    # angle: integer value of the text angle, using the same rules as in ggplot2. Positive values for counterclockwise rotation: 0 for horizontal, 90 for vertical, 180 for upside down etc. Negative values for clockwise rotation: 0 for horizontal, -90 for vertical, -180 for upside down etc. 
+    # pos: where text is? Either "top", "right", "bottom" or "left" of the elements to justify from
+    # kind: kind of text? Either "axis" or "text". In the first case, the pos argument refers to the axis position, and in the second to annotated text (using ggplot2::annotate() or ggplot2::geom_text())
+    # RETURN
+    # a list containing:
+    # $angle: the submitted angle (value potentially reduced to fit the [-360 ; 360] interval, e.g., 460 -> 100, without impact on the final angle displayed)
+    # $pos: the selected position (argument pos)
+    # $kind: the selected kind of text (argument kind)
+    # $hjust: the horizontal justification
+    # $vjust: the vertical justification
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # fun_gg_just(angle = 45, pos = "bottom")
+    # fun_gg_just(angle = (360*2 + 45), pos = "left")
+    # output <- fun_gg_just(angle = 45, pos = "bottom") ; obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10), stringsAsFactors = TRUE) ; ggplot2::ggplot() + ggplot2::geom_bar(data = obs1, mapping = ggplot2::aes(x = group, y = time), stat = "identity") + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = output$angle, hjust = output$hjust, vjust = output$vjust))
+    # output <- fun_gg_just(angle = -45, pos = "left") ; obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10), stringsAsFactors = TRUE) ; ggplot2::ggplot() + ggplot2::geom_bar(data = obs1, mapping = ggplot2::aes(x = group, y = time), stat = "identity") + ggplot2::theme(axis.text.y = ggplot2::element_text(angle = output$angle, hjust = output$hjust, vjust = output$vjust)) + ggplot2::coord_flip()
+    # output1 <- fun_gg_just(angle = 90, pos = "bottom") ; output2 <- fun_gg_just(angle = -45, pos = "left") ; obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10), stringsAsFactors = TRUE) ; ggplot2::ggplot() + ggplot2::geom_bar(data = obs1, mapping = ggplot2::aes(x = group, y = time), stat = "identity") + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = output1$angle, hjust = output1$hjust, vjust = output1$vjust), axis.text.y = ggplot2::element_text(angle = output2$angle, hjust = output2$hjust, vjust = output2$vjust))
+    # output <- fun_gg_just(angle = -45, pos = "left") ; obs1 <- data.frame(time = 1, km = 1, bird = "pigeon", stringsAsFactors = FALSE) ; ggplot2::ggplot(data = obs1, mapping = ggplot2::aes(x = time, y = km)) + ggplot2::geom_point() + ggplot2::geom_text(mapping = ggplot2::aes(label = bird), angle = output$angle, hjust = output$hjust, vjust = output$vjust)
+    # obs1 <- data.frame(time = 1:10, km = 1:10, bird = c(NA, NA, NA, "pigeon", NA, "cat", NA, NA, NA, NA), stringsAsFactors = FALSE) ; fun_open(width = 4, height = 4) ; for(i0 in c("text", "axis")){for(i1 in c("top", "right", "bottom", "left")){for(i2 in c(0, 45, 90, 135, 180, 225, 270, 315, 360)){output <- fun_gg_just(angle = i2, pos = i1, kind = i0) ; title <- paste0("kind: ", i0, " | pos: ", i1, " | angle = ", i2, " | hjust: ", output$hjust, " | vjust: ", output$vjust) ; if(i0 == "text"){print(ggplot2::ggplot(data = obs1, mapping = ggplot2::aes(x = time, y = km)) + ggplot2::geom_point(color = fun_gg_palette(1), alpha = 0.5) + ggplot2::ggtitle(title) + ggplot2::geom_text(mapping = ggplot2::aes(label = bird), angle = output$angle, hjust = output$hjust, vjust = output$vjust) + ggplot2::theme(title = ggplot2::element_text(size = 5)))}else{print(ggplot2::ggplot(data = obs1, mapping = ggplot2::aes(x = time, y = km)) + ggplot2::geom_point(color = fun_gg_palette(1), alpha = 0.5) + ggplot2::ggtitle(title) + ggplot2::geom_text(mapping = ggplot2::aes(label = bird)) + ggplot2::scale_x_continuous(position = ifelse(i1 == "top", "top", "bottom")) + ggplot2::scale_y_continuous(position = ifelse(i1 == "right", "right", "left")) + ggplot2::theme(title = ggplot2::element_text(size = 5), axis.text.x = if(i1 %in% c("top", "bottom")){ggplot2::element_text(angle = output$angle, hjust = output$hjust, vjust = output$vjust)}, axis.text.y = if(i1 %in% c("right", "left")){ggplot2::element_text(angle = output$angle, hjust = output$hjust, vjust = output$vjust)}))}}}} ; dev.off()
+    # DEBUGGING
+    # angle = 45 ; pos = "left" ; kind = "axis"
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument primary checking
+    # arg with no default values
+    mandat.args <- c(
+        "angle", 
+        "pos"
+    )
+    tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
+    if(any(tempo)){ # normally no NA for missing() output
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end arg with no default values
+    # using fun_check()
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = angle, class = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = pos, options = c("left", "top", "right", "bottom"), length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = kind, options = c("axis", "text"), length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end using fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument primary checking
+    # second round of checking and data preparation
+    # management of NA arguments
+    tempo.arg <- names(arg.user.setting) # values provided by the user
+    tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
+    if(any(tempo.log) == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT JUST BE NA")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NA arguments
+    # management of NULL arguments
+    tempo.arg <- c(
+        "angle", 
+        "pos", 
+        "kind"
+    )
+    tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
+    if(any(tempo.log) == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NULL arguments
+    # end second round of checking and data preparation
+    # main code
+    # to get angle between -360 and 360
+    while(angle > 360){
+        angle <- angle - 360
+    }
+    while(angle < -360){
+        angle <- angle + 360
+    }
+    # end to get angle between -360 and 360
+    # justifications
+    if(pos %in% c("bottom", "top")){
+        # code below is for if(pos == "bottom"){
+        if(any(sapply(FUN = all.equal, c(-360, -180, 0, 180, 360), angle) == TRUE)){ # equivalent of angle == -360 | angle == -180 | angle == 0 | angle == 180 | angle == 360 but deals with floats
+            hjust <- 0.5
+            if(kind == "text"){
+                if(any(sapply(FUN = all.equal, c(-360, 0, 360), angle) == TRUE)){
+                    vjust <- 1
+                }else if(any(sapply(FUN = all.equal, c(-180, 180), angle) == TRUE)){
+                    vjust <- 0
+                }
+            }else{
+                vjust <- 0.5
+            }
+        }else if(any(sapply(FUN = all.equal, c(-270, 90), angle) == TRUE)){
+            hjust <- 1
+            vjust <- 0.5
+        }else if(any(sapply(FUN = all.equal, c(-90, 270), angle) == TRUE)){
+            hjust <- 0
+            vjust <- 0.5
+        }else if((angle > -360 & angle < -270) | (angle > 0 & angle < 90)){
+            hjust <- 1
+            vjust <- 1
+        }else if((angle > -270 & angle < -180) | (angle > 90 & angle < 180)){
+            hjust <- 1
+            vjust <- 0
+        }else if((angle > -180 & angle < -90) | (angle > 180 & angle < 270)){
+            hjust <- 0
+            vjust <- 0
+            if(kind == "text" & pos == "top"){
+                hjust <- 1
+            }
+        }else if((angle > -90 & angle < 0) | (angle > 270 & angle < 360)){
+            hjust <- 0
+            vjust <- 1
+        }
+        if(pos == "top"){
+            if( ! ((angle > -180 & angle < -90) | (angle > 180 & angle < 270))){
+                hjust <- 1 - hjust
+            }
+            vjust <- 1 - vjust
+        }
+    }else if(pos %in% c("left", "right")){
+        # code below is for if(pos == "left"){
+        if(any(sapply(FUN = all.equal, c(-270, -90, 90, 270), angle) == TRUE)){ # equivalent of angle == -270 | angle == -90 | angle == 90 | angle == 270 but deals with floats
+            hjust <- 0.5
+            if(kind == "text"){
+                if(any(sapply(FUN = all.equal, c(-90, 90), angle) == TRUE)){
+                    vjust <- 0
+                }else if(any(sapply(FUN = all.equal, c(-270, 270), angle) == TRUE)){
+                    vjust <- 1
+                }
+            }else{
+                vjust <- 0.5
+            }
+        }else if(any(sapply(FUN = all.equal, c(-360, 0, 360), angle) == TRUE)){
+            hjust <- 1
+            vjust <- 0.5
+        }else if(any(sapply(FUN = all.equal, c(-180, 180), angle) == TRUE)){
+            hjust <- 0
+            vjust <- 0.5
+        }else if((angle > -360 & angle < -270) | (angle > 0 & angle < 90)){
+            hjust <- 1
+            vjust <- 0
+        }else if((angle > -270 & angle < -180) | (angle > 90 & angle < 180)){
+            hjust <- 0
+            vjust <- 0
+        }else if((angle > -180 & angle < -90) | (angle > 180 & angle < 270)){
+            hjust <- 0
+            vjust <- 1
+        }else if((angle > -90 & angle < 0) | (angle > 270 & angle < 360)){
+            hjust <- 1
+            vjust <- 1
+        }
+        if(pos == "right"){
+            hjust <- 1 - hjust
+            if( ! (((angle > -270 & angle < -180) | (angle > 90 & angle < 180)) | ((angle > -180 & angle < -90) | (angle > 180 & angle < 270)))){
+                vjust <- 1 - vjust
+            }
+        }
+    }
+    # end justifications
+    output <- list(angle = angle, pos = pos, kind = kind, hjust = hjust, vjust = vjust)
+    return(output)
 }
-}else{
-line.count <- line.count + 1
-if(line.count== 1L){
-fin.lg.disp[[4]] <- legend.disp[[point.count + line.count]]
-lg.order[[4]] <- point.count + line.count
-lg.color[[4]] <- color[[i1]] # if color == NULL -> NULL
-lg.line.size[[4]] <- line.size[[i1]]
-lg.line.type[[4]] <- line.type[[i1]]
-if(plot == TRUE & fin.lg.disp[[4]] == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list())== 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE LINES (LINE LAYER NUMBER ", line.count, ") IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-lg.alpha[[4]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
-}else{
-lg.alpha[[4]] <- alpha[[i1]]
+
+
+######## fun_gg_get_legend() #### get the legend of ggplot objects
+
+
+
+
+
+fun_gg_get_legend <- function(ggplot_built, fun.name = NULL, lib.path = NULL){
+    # AIM
+    # get legend of ggplot objects
+    # # from https://stackoverflow.com/questions/12539348/ggplot-separate-legend-and-plot
+    # ARGUMENTS
+    # ggplot_built: a ggplot build object
+    # fun.name: single character string indicating the name of the function using fun_gg_get_legend() for warning and error messages. Ignored if NULL
+    # lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
+    # RETURN
+    # a list of class c("gtable", "gTree", "grob", "gDesc"), providing legend information of ggplot_built objet, or NULL if the ggplot_built object has no legend
+    # REQUIRED PACKAGES
+    # ggplot2
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # fun_pack()
+    # EXAMPLES
+    # Simple example
+    # obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10), stringsAsFactors = TRUE) ; p <- ggplot2::ggplot() + ggplot2::geom_point(data = obs1, mapping = ggplot2::aes(x = group, y = time, fill = group)) ; fun_gg_get_legend(ggplot_built = ggplot2::ggplot_build(p))
+    # Error message because no legend in the ggplot
+    # obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10), stringsAsFactors = TRUE) ; p <- ggplot2::ggplot() + ggplot2::geom_point(data = obs1, mapping = ggplot2::aes(x = group, y = time)) ; fun_gg_get_legend(ggplot_built = ggplot2::ggplot_build(p))
+    # DEBUGGING
+    # obs1 <- data.frame(time = 1:20, group = rep(c("CLASS_1", "CLASS_2"), times = 10), stringsAsFactors = TRUE) ; p <- ggplot2::ggplot() + ggplot2::geom_point(data = obs1, mapping = ggplot2::aes(x = group, y = time)) ; ggplot_built = ggplot2::ggplot_build(p) ; fun.name = NULL ; lib.path = NULL
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    req.function <- c(
+        "fun_check",
+        "fun_pack"
+    )
+    for(i1 in req.function){
+        if(length(find(i1, mode = "function")) == 0L){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED ", i1, "() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # end required function checking
+    # argument primary checking
+    # arg with no default values
+    mandat.args <- c(
+        "ggplot_built"
+    )
+    tempo <- eval(parse(text = paste0("c(missing(", paste0(mandat.args, collapse = "), missing("), "))")))
+    if(any(tempo)){ # normally no NA for missing() output
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(sum(tempo, na.rm = TRUE) > 1, "S HAVE", " HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args[tempo], collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end arg with no default values
+    # using fun_check()
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = ggplot_built, class = "ggplot_built", mode = "list", fun.name = function.name) ; eval(ee)
+    if( ! is.null(fun.name)){
+        tempo <- fun_check(data = fun.name, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(lib.path)){
+        tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(arg.check)){
+        if(any(arg.check) == TRUE){
+            stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+        }
+    }
+    # end using fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument primary checking
+    # second round of checking
+    # management of NA
+    if(any(is.na(ggplot_built)) | any(is.na(fun.name)) | any(is.na(lib.path))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": NO ARGUMENT CAN HAVE NA VALUES")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NA
+    # management of NULL
+    if(is.null(ggplot_built)){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nggplot_built ARGUMENT CANNOT BE NULL")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NULL
+    if( ! is.null(lib.path)){
+        if( ! all(dir.exists(lib.path))){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # end second round of checking
+    # package checking
+    fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
+    # end package checking
+    # main code
+    win.nb <- dev.cur()
+    pdf(file = NULL)
+    tmp <- ggplot2::ggplot_gtable(ggplot_built)
+    # BEWARE with ggplot_gtable : open a blanck device https://stackoverflow.com/questions/17012518/why-does-this-r-ggplot2-code-bring-up-a-blank-display-device
+    invisible(dev.off())
+    if(win.nb > 1){ # to go back to the previous active device, if == 1 means no opened device
+        dev.set(win.nb)
+    }
+    leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
+    if(length(leg) == 0L){
+        legend <- NULL
+    }else{
+        legend <- tmp$grobs[[leg]]
+    }
+    return(legend)
 }
-class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
-for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
-tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::", # no CR here te0("ggpl
-ifelse(geom[[i1]] == 'geom_stick', 'geom_segment', geom[[i1]]), # geom_segment because geom_stick converted to geom_segment for plotting
-"(data = tempo.data.frame, mapping = ggplot2::aes(x = ", 
-x[[i1]], 
-ifelse(geom[[i1]] == 'geom_stick', ", yend = ", ", y = "), 
-y[[i1]], 
-if(geom[[i1]] == 'geom_stick'){paste0(', xend = ', x[[i1]], ', y = ', ifelse(is.null(geom.stick.base), y.lim[1], geom.stick.base[[i1]]))}, 
-", linetype = ", 
-categ[[i1]], 
-"), color = \"", 
-color[[i1]][i5], 
-"\", size = ", 
-line.size[[i1]], 
-ifelse(geom[[i1]] == 'geom_path', ', lineend = \"round\"', ''), 
-ifelse(geom[[i1]] == 'geom_step', paste0(', direction = \"', geom.step.dir[[i1]], '\"'), ''), 
-", alpha = ", 
-alpha[[i1]], 
-", show.legend = ", 
-ifelse(i5== 1L, TRUE, FALSE), 
-")"
-)))) # WARNING: a single color allowed for color argument outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.). Used here to avoid multiple layers of legend which corrupt transparency
-coord.names <- c(coord.names, paste0(geom[[i1]], ".", class.categ[i5]))
+
+
+######## fun_gg_point_rast() #### ggplot2 raster scatterplot layer
+
+
+
+
+
+fun_gg_point_rast <- function(
+    data = NULL, 
+    mapping = NULL, 
+    stat = "identity", 
+    position = "identity", 
+    ..., 
+    na.rm = FALSE, 
+    show.legend = NA, 
+    inherit.aes = TRUE, 
+    raster.width = NULL, 
+    raster.height = NULL, 
+    raster.dpi = 300, 
+    inactivate = TRUE, 
+    lib.path = NULL
+){
+    # AIM
+    # equivalent to ggplot2::geom_point() but in raster mode
+    # use it like ggplot2::geom_point() with the main raster.dpi additional argument
+    # WARNINGS
+    # can be long to generate the plot
+    # use a square plot region. Otherwise, the dots will have ellipsoid shape
+    # solve the transparency problems with some GUI
+    # this function is derived from the geom_point_rast() function, created by Viktor Petukhov , and present in the ggrastr package (https://rdrr.io/github/VPetukhov/ggrastr/src/R/geom-point-rast.R, MIT License, Copyright (c) 2017 Viktor Petukhov). Has been placed here to minimize package dependencies
+    # ARGUMENTS
+    # classical arguments of geom_point(), shown here https://rdrr.io/github/VPetukhov/ggrastr/man/geom_point_rast.html
+    # raster.width : width of the result image (in inches). Default: deterined by the current device parameters
+    # raster.height: height of the result image (in inches). Default: deterined by the current device parameters
+    # raster.dpi: resolution of the result image
+    # inactivate: logical. Inactivate the fun.name argument of the fun_check() function? If TRUE, the name of the fun_check() function in error messages coming from this function. Use TRUE if fun_gg_point_rast() is used like this: eval(parse(text = "fun_gg_point_rast"))
+    # lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
+    # RETURN
+    # a raster scatter plot
+    # REQUIRED PACKAGES
+    # ggplot2
+    # grid (included in the R installation packages but not automatically loaded)
+    # Cairo
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # fun_pack()
+    # EXAMPLES
+    # Two pdf in the current directory
+    # set.seed(1) ; data1 = data.frame(x = rnorm(100000), y = rnorm(10000), stringsAsFactors = TRUE) ; fun_open(pdf.name = "Raster") ; ggplot2::ggplot() + fun_gg_point_rast(data = data1, mapping = ggplot2::aes(x = x, y = y)) ; fun_open(pdf.name = "Vectorial") ; ggplot2::ggplot() + ggplot2::geom_point(data = data1, mapping = ggplot2::aes(x = x, y = y)) ; dev.off() ; dev.off()
+    # DEBUGGING
+    # 
+    # function name
+    if(all(inactivate == FALSE)){ # inactivate has to be used here but will be fully checked below
+        function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    }else if(all(inactivate == TRUE)){
+        function.name <- NULL
+    }else{
+        tempo.cat <- paste0("ERROR IN fun_gg_point_rast(): CODE INCONSISTENCY 1")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(length(utils::find("fun_pack", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    if( ! is.null(data)){
+        tempo <- fun_check(data = data, class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(mapping)){
+        tempo <- fun_check(data = mapping, class = "uneval", typeof = "list", fun.name = function.name) ; eval(ee) # aes() is tested
+    }
+    # stat and position not tested because too complicate
+    tempo <- fun_check(data = na.rm, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = show.legend, class = "vector", mode = "logical", length = 1, na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = inherit.aes, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(raster.width)){
+        tempo <- fun_check(data = raster.width, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(raster.height)){
+        tempo <- fun_check(data = raster.height, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = raster.dpi, class = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = inactivate, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(lib.path)){
+        tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
+                tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # package checking
+    fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
+    fun_pack(req.package = c("grid"), lib.path = lib.path)
+    fun_pack(req.package = c("Cairo"), lib.path = lib.path)
+    # end package checking
+    # additional functions
+    DrawGeomPointRast <- function(data, panel_params, coord, na.rm = FALSE, raster.width = NULL, raster.height= NULL, raster.dpi = raster.dpi){
+        if (is.null(raster.width)){
+            raster.width <- par('fin')[1]
+        }
+        if (is.null(raster.height)){
+            raster.height <- par('fin')[2]
+        }
+        prev_dev_id <- dev.cur()
+        p <- ggplot2::GeomPoint$draw_panel(data, panel_params, coord)
+        dev_id <- Cairo::Cairo(type='raster', width = raster.width*raster.dpi, height = raster.height*raster.dpi, dpi = raster.dpi, units = 'px', bg = "transparent")[1]
+        grid::pushViewport(grid::viewport(width = 1, height = 1))
+        grid::grid.points(x = p$x, y = p$y, pch = p$pch, size = p$size,
+                          name = p$name, gp = p$gp, vp = p$vp, draw = T)
+        grid::popViewport()
+        cap <- grid::grid.cap()
+        invisible(dev.off(dev_id))
+        invisible(dev.set(prev_dev_id))
+        grid::rasterGrob(cap, x = 0, y = 0, width = 1, height = 1, default.units = "native", just = c("left","bottom"))
+    }
+    # end additional functions
+    # main code
+    GeomPointRast <- ggplot2::ggproto("GeomPointRast", ggplot2::GeomPoint, draw_panel = DrawGeomPointRast)
+    ggplot2::layer(
+        data = data, 
+        mapping = mapping, 
+        stat = stat, 
+        geom = GeomPointRast, 
+        position = position, 
+        show.legend = show.legend, 
+        inherit.aes = inherit.aes, 
+        params = list(
+            na.rm = na.rm, 
+            raster.width = raster.width, 
+            raster.height = raster.height, 
+            raster.dpi = raster.dpi, 
+            ...
+        )
+    )
+    # end main code
 }
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "linetype", name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(line.type[[i1]], length(color[[i1]])), breaks = class.categ)) # values are the values of linetype. 1 means solid. Regarding the alpha bug, I have tried different things without success: alpha in guide alone, in geom alone, in both, with different values, breaks reorder the classes according to class.categ in the legend
+
+
+######## fun_gg_boxplot() #### ggplot2 boxplot + background dots if required
+
+
+
+
+######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally)
+
+
+
+
+######## fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required
+
+
+#test plot.margin = margin(up.space.mds, right.space.mds, down.space.mds, left.space.mds, "inches") to set the dim of the region plot ?
+# if matrix is full of zero (or same value I guess), heatmap is complicate. Test it and error message
+
+fun_gg_heatmap <- function(
+    data1, 
+    legend.name1 = "", 
+    low.color1 = "blue", 
+    mid.color1 = "white", 
+    high.color1 = "red", 
+    limit1 = NULL, 
+    midpoint1 = NULL, 
+    data2 = NULL, 
+    color2 = "black", 
+    alpha2 = 0.5, 
+    invert2 = FALSE, 
+    text.size = 12, 
+    title = "", 
+    title.text.size = 12, 
+    show.scale = TRUE, 
+    rotate = FALSE, 
+    return = FALSE, 
+    plot = TRUE, 
+    add = NULL, 
+    warn.print = FALSE, 
+    lib.path = NULL
+){
+    # AIM
+    # ggplot2 heatmap with the possibility to overlay a mask
+    # see also:
+    # draw : http://www.sthda.com/english/wiki/ggplot2-quick-correlation-matrix-heatmap-r-software-and-data-visualization
+    # same range scale : https://stackoverflow.com/questions/44655723/r-ggplot2-heatmap-fixed-scale-color-between-graphs 
+    # for ggplot2 specifications, see: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html
+    # ARGUMENTS
+    # data1: numeric matrix or data frame resulting from the conversion of the numeric matrix by reshape2::melt()
+    # legend.name1: character string of the data1 heatmap scale legend
+    # low.color1: character string of the color (i.e., "blue" or "#0000FF") of the lowest scale value
+    # mid.color1: same as low.color1 but for the middle scale value. If NULL, the middle color is the default color between low.color1 and high.color1. BEWARE: argument midpoint1 is not ignored, even if mid.color1 is NULL, meaning that the default mid color can still be controled
+    # high.color1: same as low.color1 but for the highest scale value
+    # limit1: 2 numeric values defining the lowest and higest color scale values. If NULL, take the range of data1 values
+    # midpoint1: single numeric value defining the value corresponding to the mid.color1 argument. A warning message is returned if midpoint1 does not correspond to the mean of limit1 values, because the color scale is not linear anymore. If NULL, takes the mean of limit1 values. Mean of data1, instead of mean of limit1, can be used here if required
+    # data2: binary mask matrix (made of 0 and 1) of same dimension as data1 or a data frame resulting from the conversion of the binary mask matrix by reshape2::melt(). Value 1 of data2 will correspond to color2 argument (value 0 will be NA color), and the opposite if invert2 argument is TRUE (inverted mask)
+    # color2: color of the 1 values of the binary mask matrix. The 0 values will be color NA
+    # alpha2: numeric value (from 0 to 1) of the mask transparency
+    # invert2: logical. Invert the mask (1 -> 0 and 0 -> 1)?
+    # text.size: numeric value of the size of the texts in scale
+    # title: character string of the graph title
+    # title.text.size: numeric value of the title size (in points)
+    # show.scale: logical. Show color scale?
+    # rotate: logical. Rotate the heatmap 90° clockwise?
+    # return: logical. Return the graph parameters?
+    # plot: logical. Plot the graphic? If FALSE and return argument is TRUE, graphical parameters and associated warnings are provided without plotting
+    # add: character string allowing to add more ggplot2 features (dots, lines, themes, etc.). BEWARE: (1) must start with "+" just after the simple or double opening quote (no space, end of line, carriage return, etc., allowed), (2) must finish with ")" just before the simple or double closing quote (no space, end of line, carriage return, etc., allowed) and (3) each function must be preceded by "ggplot2::" (for instance: "ggplot2::coord_flip()). If the character string contains the "ggplot2::theme" string, then internal ggplot2 theme() and theme_classic() functions will be inactivated to be reused by add. BEWARE: handle this argument with caution since added functions can create conflicts with the preexisting internal ggplot2 functions
+    # warn.print: logical. Print warnings at the end of the execution? No print if no warning messages
+    # lib.path: absolute path of the required packages, if not in the default folders
+    # RETURN
+    # a heatmap if plot argument is TRUE
+    # a list of the graph info if return argument is TRUE:
+    # $data: a list of the graphic info
+    # $axes: a list of the axes info
+    # $scale: the scale info (lowest, mid and highest values)
+    # $warn: the warning messages. Use cat() for proper display. NULL if no warning
+    # REQUIRED PACKAGES
+    # ggplot2
+    # reshape2
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # fun_pack()
+    # fun_round()
+    # EXAMPLES
+    # fun_gg_heatmap(data1 = matrix(1:16, ncol = 4), title = "GRAPH 1")
+    # fun_gg_heatmap(data1 = matrix(1:16, ncol = 4), return = TRUE)
+    # fun_gg_heatmap(data1 = matrix(1:16, ncol = 4), legend.name1 = "VALUE", title = "GRAPH 1", text.size = 5, data2 = matrix(rep(c(1,0,0,0), 4), ncol = 4), invert2 = FALSE, return = TRUE)
+    # diagonal matrix
+    # fun_gg_heatmap(data1 = matrix(c(1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1), ncol = 4))
+    # fun_gg_heatmap(data1 = reshape2::melt(matrix(c(1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1), ncol = 4)))
+    # error message
+    # fun_gg_heatmap(data1 = matrix(1:16, ncol = 4), data2 = matrix(rep(c(1,0,0,0), 5), ncol = 5))
+    # fun_gg_heatmap(data1 = matrix(1:16, ncol = 4), data2 = reshape2::melt(matrix(rep(c(1,0,0,0), 4), ncol = 4)))
+    # fun_gg_heatmap(data1 = reshape2::melt(matrix(1:16, ncol = 4)), data2 = reshape2::melt(matrix(rep(c(1,0,0,0), 4), ncol = 4)))
+    # DEBUGGING
+    # data1 = matrix(1:16, ncol = 4) ; legend.name1 = "" ; low.color1 = "blue" ; mid.color1 = "white" ; high.color1 = "red" ; limit1 = NULL ; midpoint1 = NULL ; data2 = matrix(rep(c(1,0,0,0), 4), ncol = 4) ; color2 = "black" ; alpha2 = 0.5 ; invert2 = FALSE ; text.size = 12 ; title = "" ; title.text.size = 12 ; show.scale = TRUE ; rotate = FALSE ; return = FALSE ; plot = TRUE ; add = NULL ; warn.print = TRUE ; lib.path = NULL
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(length(utils::find("fun_pack", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(length(utils::find("fun_round", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_round() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # no reserved words required for this function
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    if(all(is.matrix(data1))){
+        tempo <- fun_check(data = data1, class = "matrix", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    }else if(all(is.data.frame(data1))){
+        tempo <- fun_check(data = data1, class = "data.frame", length = 3, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            # structure of reshape2::melt() data frame
+            tempo <- fun_check(data = data1[, 1], data.name = "COLUMN 1 OF data1 (reshape2::melt() DATA FRAME)", typeof = "integer", fun.name = function.name) ; eval(ee)
+            tempo <- fun_check(data = data1[, 2], data.name = "COLUMN 2 OF data1 (reshape2::melt() DATA FRAME)", typeof = "integer", fun.name = function.name) ; eval(ee)
+            tempo <- fun_check(data = data1[, 3], data.name = "COLUMN 3 OF data1 (reshape2::melt() DATA FRAME)", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+        }
+    }else{
+        tempo.cat <- paste0("ERROR IN ", function.name, ": THE data1 ARGUMENT MUST BE A NUMERIC MATRIX OR A DATA FRAME OUTPUT OF THE reshape::melt() FUNCTION")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    tempo <- fun_check(data = legend.name1, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = low.color1, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & ! (all(low.color1 %in% colors() | grepl(pattern = "^#", low.color1)))){ # check that all strings of low.color1 start by #
+        tempo.cat <- paste0("ERROR IN ", function.name, ": low.color1 ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors()")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    if( ! is.null(mid.color1)){
+        tempo <- fun_check(data = mid.color1, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & ! (all(mid.color1 %in% colors() | grepl(pattern = "^#", mid.color1)))){ # check that all strings of mid.color1 start by #
+            tempo.cat <- paste0("ERROR IN ", function.name, ": mid.color1 ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors()")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }
+    tempo <- fun_check(data = high.color1, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & ! (all(high.color1 %in% colors() | grepl(pattern = "^#", high.color1)))){ # check that all strings of high.color1 start by #
+        tempo.cat <- paste0("ERROR IN ", function.name, ": high.color1 ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors()")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    if( ! is.null(limit1)){
+        tempo <- fun_check(data = limit1, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & any(limit1 %in% c(Inf, -Inf))){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": limit1 ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }
+    if( ! is.null(midpoint1)){
+        tempo <- fun_check(data = midpoint1, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(data2)){
+        if(all(is.matrix(data2))){
+            tempo <- fun_check(data = data2, class = "matrix", mode = "numeric", fun.name = function.name) ; eval(ee)
+            if(tempo$problem == FALSE & ! all(unique(data2) %in% c(0,1))){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": MATRIX IN data2 MUST BE MADE OF 0 AND 1 ONLY (MASK MATRIX)")
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }else if(tempo$problem == FALSE & all(is.matrix(data1)) & ! identical(dim(data1), dim(data2))){ # matrix and matrix
+                tempo.cat <- paste0("ERROR IN ", function.name, ": MATRIX DIMENSION IN data2 MUST BE IDENTICAL AS MATRIX DIMENSION IN data1. HERE IT IS RESPECTIVELY:\n", paste(dim(data2), collapse = " "), "\n", paste(dim(data1), collapse = " "))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }else if(tempo$problem == FALSE & all(is.data.frame(data1)) & nrow(data1) != prod(dim(data2))){ # reshape2 and matrix
+                tempo.cat <- paste0("ERROR IN ", function.name, ": DATA FRAME IN data2 MUST HAVE ROW NUMBER EQUAL TO PRODUCT OF DIMENSIONS OF data1 MATRIX. HERE IT IS RESPECTIVELY:\n", paste(nrow(data1), collapse = " "), "\n", paste(prod(dim(data2)), collapse = " "))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }else if(all(is.data.frame(data2))){
+            tempo <- fun_check(data = data2, class = "data.frame", length = 3, fun.name = function.name) ; eval(ee)
+            if(tempo$problem == FALSE){
+                # structure of reshape2::melt() data frame
+                tempo <- fun_check(data = data2[, 1], data.name = "COLUMN 1 OF data2 (reshape2::melt() DATA FRAME)", typeof = "integer", fun.name = function.name) ; eval(ee)
+                tempo <- fun_check(data = data2[, 2], data.name = "COLUMN 2 OF data2 (reshape2::melt() DATA FRAME)", typeof = "integer", fun.name = function.name) ; eval(ee)
+                tempo <- fun_check(data = data2[, 3], data.name = "COLUMN 3 OF data2 (reshape2::melt() DATA FRAME)", mode = "numeric", fun.name = function.name) ; eval(ee)
+            }
+            if(tempo$problem == FALSE & ! all(unique(data2[, 3]) %in% c(0,1))){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": THIRD COLUMN OF DATA FRAME IN data2 MUST BE MADE OF 0 AND 1 ONLY (MASK DATA FRAME)")
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }else if(tempo$problem == FALSE & all(is.data.frame(data1)) & ! identical(dim(data1), dim(data2))){ # data frame and data frame
+                tempo.cat <- paste0("ERROR IN ", function.name, ": DATA FRAME DIMENSION IN data2 MUST BE IDENTICAL TO DATA FRAME DIMENSION IN data1. HERE IT IS RESPECTIVELY:\n", paste(dim(data2), collapse = " "), "\n", paste(dim(data1), collapse = " "))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }else if(tempo$problem == FALSE & all(is.matrix(data1)) & nrow(data2) != prod(dim(data1))){ # reshape2 and matrix
+                tempo.cat <- paste0("ERROR IN ", function.name, ": DATA FRAME IN data2 MUST HAVE ROW NUMBER EQUAL TO PRODUCT OF DIMENSION OF data1 MATRIX. HERE IT IS RESPECTIVELY:\n", paste(nrow(data2), collapse = " "), "\n", paste(prod(dim(data1)), collapse = " "))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }else{
+            tempo.cat <- paste0("ERROR IN ", function.name, ": THE data2 ARGUMENT MUST BE A NUMERIC MATRIX OR A DATA FRAME OUTPUT OF THE reshape::melt() FUNCTION")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }
+    tempo <- fun_check(data = color2, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & ! (all(color2 %in% colors() | grepl(pattern = "^#", color2)))){ # check that all strings of color2 start by #
+        tempo.cat <- paste0("ERROR IN ", function.name, ": color2 ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors()")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    tempo <- fun_check(data = alpha2, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = invert2, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = title, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = title.text.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = show.scale, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = return, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = plot, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(add)){
+        tempo <- fun_check(data = add, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & ! grepl(pattern = "^\\+", add)){ # check that the add string start by +
+            tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST START WITH \"+\": ", paste(unique(add), collapse = " "))
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }else if(tempo$problem == FALSE & ! grepl(pattern = "ggplot2::", add)){ #
+            tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST CONTAIN \"ggplot2::\" IN FRONT OF EACH GGPLOT2 FUNCTION: ", paste(unique(add), collapse = " "))
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }else if(tempo$problem == FALSE & ! grepl(pattern = ")$", add)){ # check that the add string  finished by )
+            tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST FINISH BY \")\": ", paste(unique(add), collapse = " "))
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }
+    tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(lib.path)){
+        tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
+                tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # package checking
+    fun_pack(req.package = c("reshape2", "ggplot2"), lib.path = lib.path)
+    # end package checking
+    # main code
+    ini.warning.length <- options()$warning.length
+    options(warning.length = 8170)
+    warn <- NULL
+    warn.count <- 0
+    if(all(is.matrix(data1))){
+        data1 <- reshape2::melt(data1) # transform a matrix into a data frame with 2 coordinates columns and the third intensity column
+    }
+    if(rotate == TRUE){
+        data1[, 1] <- rev(data1[, 1])
+    }
+    if(is.null(limit1)){
+        if(any(data1[, 3] %in% c(Inf, -Inf))){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") THE data1 ARGUMENT CONTAINS -Inf OR Inf VALUES IN THE THIRD COLUMN, THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+        limit1 <- range(data1[, 3], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") THE limit1 ARGUMENT IS NULL -> RANGE OF data1 ARGUMENT HAS BEEN TAKEN: ", paste(fun_round(limit1), collapse = " "))
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        if(suppressWarnings(any(limit1 %in% c(Inf, -Inf)))){
+            tempo.cat <- paste0("ERROR IN ", function.name, " COMPUTED LIMIT CONTAINS Inf VALUES, BECAUSE VALUES FROM data1 ARGUMENTS ARE NA OR Inf ONLY")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if(is.null(midpoint1)){
+        midpoint1 <- mean(limit1, na.rm = TRUE)
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") THE midpoint1 ARGUMENT IS NULL -> MEAN OF limit1 ARGUMENT HAS BEEN TAKEN: ", paste(fun_round(midpoint1), collapse = " "))
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }else if(fun_round(midpoint1, 9) != fun_round(mean(limit1), 9)){
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") THE midpoint1 ARGUMENT (", fun_round(mean(midpoint1), 9), ") DOES NOT CORRESPOND TO THE MEAN OF THE limit1 ARGUMENT (", fun_round(mean(limit1), 9), "). COLOR SCALE IS NOT LINEAR")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
+    if( ! is.null(data2)){
+        if(all(is.matrix(data2))){
+            data2 <- reshape2::melt(data2) # transform a matrix into a data frame with 2 coordinates columns and the third intensity column
+        }
+        if(rotate == TRUE){
+            data2[, 1] <- rev(data2[, 1])
+        }
+        data2[, 3] <- factor(data2[, 3]) # to converte continuous scale into discrete scale
+    }
+    tempo.gg.name <- "gg.indiv.plot."
+    tempo.gg.count <- 0 # to facilitate debugging
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggplot())
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_raster(data = data1, mapping = ggplot2::aes_string(x = names(data1)[ifelse(rotate == FALSE, 2, 1)], y = names(data1)[ifelse(rotate == FALSE, 1, 2)], fill = names(data1)[3]), show.legend = show.scale)) # show.legend option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_fill_gradient2(low = low.color1, high = high.color1, mid = mid.color1, midpoint = midpoint1, limit = limit1, breaks = c(limit1[1], midpoint1, limit1[2]), labels = fun_round(c(limit1[1], midpoint1, limit1[2])), name = legend.name1))
+    if( ! is.null(data2)){
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_raster(data = data2, mapping = ggplot2::aes_string(x = names(data2)[ifelse(rotate == FALSE, 2, 1)], y = names(data2)[ifelse(rotate == FALSE, 1, 2)], alpha = names(data2)[3]), fill = color2, show.legend = FALSE))
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "alpha", values = if(invert2 == FALSE){c(0, alpha2)}else{c(alpha2, 0)}, guide = FALSE))
+        # assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_raster(data = data2, mapping = ggplot2::aes_string(x = names(data2)[ifelse(rotate == FALSE, 2, 1)], y = names(data2)[ifelse(rotate == FALSE, 1, 2)], group = names(data2)[3]), fill = data2[, 3], alpha = alpha2, show.legend = FALSE)) # BEWARE: this does not work if NA present, because geom_raster() has a tendency to complete empty spaces, and thus, behave differently than geom_tile(). See https://github.com/tidyverse/ggplot2/issues/3025
+    }
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::coord_fixed()) # x = y
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_y_reverse())
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggtitle(title))
+    add.check <- TRUE
+    if( ! is.null(add)){ # if add is NULL, then = 0
+        if(grepl(pattern = "ggplot2::theme", add) == TRUE){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") \"ggplot2::theme\" STRING DETECTED IN THE add ARGUMENT -> INTERNAL GGPLOT2 THEME FUNCTIONS theme() AND theme_classic() HAVE BEEN INACTIVATED, TO BE USED BY THE USER")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            add.check <- FALSE
+        }
+    }
+    if(add.check == TRUE){
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::theme_classic(base_size = text.size))
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::theme(
+            text = ggplot2::element_text(size = text.size), 
+            plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
+            line = ggplot2::element_blank(),
+            axis.title = ggplot2::element_blank(),
+            axis.text = ggplot2::element_blank(),
+            axis.ticks = ggplot2::element_blank(),
+            panel.background = ggplot2::element_blank()
+        ))
+    }
+    if(plot == TRUE){
+        # suppressWarnings(
+        print(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if(is.null(add)){NULL}else{add}))))
+        # )
+    }else{
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") PLOT NOT SHOWN AS REQUESTED")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
+    if(warn.print == TRUE & ! is.null(warn)){
+        on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
+    }
+    on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
+    if(return == TRUE){
+        output <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))
+        output <- output$data
+        names(output)[1] <- "heatmap"
+        if( ! is.null(data2)){
+            names(output)[2] <- "mask"
+        }
+        return(list(data = output, axes = output$layout$panel_params[[1]], scale = c(limit1[1],  midpoint1, limit1[2]), warn = warn))
+    }
 }
-if(line.count== 2L){
-fin.lg.disp[[5]] <- legend.disp[[point.count + line.count]]
-lg.order[[5]] <- point.count + line.count
-lg.color[[5]] <- color[[i1]] # if color == NULL -> NULL
-lg.line.size[[5]] <- line.size[[i1]]
-lg.line.type[[5]] <- line.type[[i1]]
-if(plot == TRUE & fin.lg.disp[[5]] == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list())== 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE LINES (LINE LAYER NUMBER ", line.count, ") IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-lg.alpha[[5]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
-}else{
-lg.alpha[[5]] <- alpha[[i1]]
+
+
+######## fun_gg_empty_graph() #### text to display for empty graphs
+
+
+
+
+
+fun_gg_empty_graph <- function(
+    text = NULL, 
+    text.size = 12, 
+    title = NULL, 
+    title.size = 8, 
+    lib.path = NULL
+){
+    # AIM
+    # display an empty ggplot2 plot with a text in the middle of the window (for instance to specify that no plot can be drawn)
+    # ARGUMENTS
+    # text: character string of the message to display
+    # text.size: numeric value of the text size (in points)
+    # title: character string of the graph title
+    # title.size: numeric value of the title size (in points)
+    # lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL
+    # RETURN
+    # an empty plot
+    # REQUIRED PACKAGES
+    # ggplot2
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # fun_pack()
+    # EXAMPLES
+    ### simple example
+    # fun_gg_empty_graph(text = "NO GRAPH")
+    ### white page
+    # fun_gg_empty_graph()
+    ### all the arguments
+    # fun_gg_empty_graph(text = "NO GRAPH", text.size = 8, title = "GRAPH1", title.size = 10, lib.path = NULL)
+    # DEBUGGING
+    # text = "NO GRAPH" ; text.size = 12 ; title = "GRAPH1" ; title.size = 8 ; lib.path = NULL
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(length(utils::find("fun_pack", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    if( ! is.null(text)){
+        tempo <- fun_check(data = text, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(title)){
+        tempo <- fun_check(data = title, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = title.size, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # package checking
+    fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
+    # end package checking
+    # main code
+    tempo.gg.name <- "gg.indiv.plot."
+    tempo.gg.count <- 0
+    # no need loop part
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggplot())
+    if( ! is.null(text)){
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_text(data = data.frame(x = 1, y = 1, stringsAsFactors = TRUE), ggplot2::aes(x = x, y = y, label = text), size = text.size))
+    }
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggtitle(title))
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::theme_void())
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
+        plot.title = ggplot2::element_text(size = title.size) # stronger than text
+    ))
+    suppressWarnings(print(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + ")))))
 }
-class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
-for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
-tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::", # no CR here te0("ggpl
-ifelse(geom[[i1]] == 'geom_stick', 'geom_segment', geom[[i1]]), # geom_segment because geom_stick converted to geom_segment for plotting
-"(data = tempo.data.frame, mapping = ggplot2::aes(x = ", 
-x[[i1]], 
-ifelse(geom[[i1]] == 'geom_stick', ", yend = ", ", y = "), 
-y[[i1]], 
-if(geom[[i1]] == 'geom_stick'){paste0(', xend = ', x[[i1]], ', y = ', ifelse(is.null(geom.stick.base), y.lim[1], geom.stick.base[[i1]]))}, 
-", alpha = ", 
-categ[[i1]], 
-"), color = \"", 
-color[[i1]][i5], 
-"\", size = ", 
-line.size[[i1]], 
-", linetype = ", 
-ifelse(is.numeric(line.type[[i1]]), "", "\""), 
-line.type[[i1]], 
-ifelse(is.numeric(line.type[[i1]]), "", "\""), 
-ifelse(geom[[i1]] == 'geom_path', ', lineend = \"round\"', ''), 
-ifelse(geom[[i1]] == 'geom_step', paste0(', direction = \"', geom.step.dir[[i1]], '\"'), ''), 
-", show.legend = FALSE)"
-)))) # WARNING: a single color allowed for color argument outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.). Used here to avoid multiple layers of legend which corrupt transparency
-coord.names <- c(coord.names, paste0(geom[[i1]], ".", class.categ[i5]))
+
+
+################ Graphic extraction
+
+
+######## fun_trim() #### display values from a quantitative variable and trim according to defined cut-offs
+
+# Add name of the variable in the graph
+# not max and min for boxplot but 1.5IQR
+fun_trim <- function(
+    data, 
+    displayed.nb = NULL, 
+    single.value.display = FALSE, 
+    trim.method = "", 
+    trim.cutoffs = c(0.05, 
+                     0.975), 
+    interval.scale.disp = TRUE, 
+    down.space = 0.75, 
+    left.space = 0.75, 
+    up.space = 0.3, 
+    right.space = 0.25, 
+    orient = 1, 
+    dist.legend = 0.37, 
+    box.type = "l", 
+    amplif.label = 1.25, 
+    amplif.axis = 1.25, 
+    std.x.range = TRUE, 
+    std.y.range = TRUE, 
+    cex.pt = 0.2, 
+    col.box = hsv(0.55, 
+                  0.8, 
+                  0.8), 
+    x.nb.inter.tick = 4, 
+    y.nb.inter.tick = 0, 
+    tick.length = 1, 
+    sec.tick.length = 0.75, 
+    corner.text = "", 
+    amplif.legend = 1, 
+    corner.text.size = 0.75, 
+    trim.return = FALSE
+){
+    # AIM
+    # trim and display values from a numeric vector or matrix
+    # plot 4 graphs: stripchart of values, stripchart of rank of values, histogram and normal QQPlot
+    # different kinds of intervals are displayed on the top of graphes to facilitate the analysis of the variable and a trimming setting
+    # the trimming interval chosen is displayed on top of graphs
+    # both trimmed and not trimmed values are returned in a list
+    # ARGUMENTS
+    # data: values to plot (either a numeric vector or a numeric matrix)
+    # displayed.nb: number of values displayed. If NULL, all the values are displayed. Otherwise, if the number of values is over displayed.nb, then displayed.nb values are displayed after random selection
+    # single.value.display: provide the 4 graphs if data is made of a single (potentially repeated value)? If FALSE, an empty graph is displayed if data is made of a single (potentially repeated value). And the return list is made of NULL compartments
+    # trim.method: Write "" if not required. write "mean.sd" if mean +/- sd has to be displayed as a trimming interval (only recommanded for normal distribution). Write "quantile" to display a trimming interval based on quantile cut-offs. No other possibility allowed. See trim.cutoffs below
+    # trim.cutoffs: 2 values cutoff for the trimming interval displayed, each value between 0 and 1. Not used if trim.method == "".The couple of values c(lower, upper) represents the lower and upper boundaries of the trimming interval (in proportion), which represent the interval of distribution kept (between 0 and 1). Example: trim.cutoffs = c(0.05, 0.975). What is strictly kept for the display is ]lower , upper[, boundaries excluded. Using the "mean.sd" method, 0.025 and 0.975 represent 95% CI which is mean +/- 1.96 * sd
+    # interval.scale.disp: display sd and quantiles intervals on top of graphs ?
+    # down.space: lower vertical margin (in inches, mai argument of par())
+    # left.space: left horizontal margin (in inches, mai argument of par())
+    # up.space: upper vertical margin between plot region and grapical window (in inches, mai argument of par())
+    # right.space: right horizontal margin (in inches, mai argument of par())
+    # orient: scale number orientation (las argument of par()). 0, always parallel to the axis; 1, always horizontal; 2, always perpendicular to the axis; 3, always vertical
+    # dist.legend: numeric value that moves axis legends away in inches (first number of mgp argument of par() but in inches thus / 0.2)
+    # box.type: bty argument of par(). Either "o", "l", "7", "c", "u", "]", the resulting box resembles the corresponding upper case letter. A value of "n" suppresses the box
+    # amplif.label: increase or decrease the size of the text in legends
+    # amplif.axis: increase or decrease the size of the scale numbers in axis
+    # std.x.range: standard range on the x-axis? TRUE (no range extend) or FALSE (4% range extend). Controls xaxs argument of par() (TRUE is xaxs = "i", FALSE is xaxs = "r")
+    # std.y.range: standard range on the y-axis? TRUE (no range extend) or FALSE (4% range extend). Controls yaxs argument of par() (TRUE is yaxs = "i", FALSE is yaxs = "r")
+    # cex.pt: size of points in stripcharts (in inches, thus cex.pt will be thereafter / 0.2)
+    # col.box: color of boxplot
+    # x.nb.inter.tick: number of secondary ticks between main ticks on x-axis (only if not log scale). Zero means non secondary ticks
+    # y.nb.inter.tick: number of secondary ticks between main ticks on y-axis (only if not log scale). Zero means non secondary ticks
+    # tick.length: length of the ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc. 0 means no tick
+    # sec.tick.length: length of the secondary ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc., 0 for no ticks)
+    # corner.text: text to add at the top right corner of the window
+    # amplif.legend: increase or decrease the size of the text of legend
+    # corner.text.size: positive numeric. Increase or decrease the size of the text. Value 1 does not change it, 0.5 decreases by half, 2 increases by 2
+    # trim.return: return the trimmed and non trimmed values? NULL returned for trimmed and non trimmed values if trim.method == ""
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # RETURN
+    # a list containing:
+    # $trim.method: correspond to trim.method above
+    # $trim.cutoffs: correspond to trim.cutoffs above
+    # $real.trim.cutoffs: the two boundary values (in the unit of the numeric vector or numeric matrix analyzed). NULL 
+    # $trimmed.values: the values outside of the trimming interval as defined in trim.cutoffs above
+    # $kept.values: the values inside the trimming interval as defined in trim.cutoffs above
+    # EXAMPLES
+    # fun_trim(data = c(1:100, 1:10), displayed.nb = NULL, single.value.display = FALSE, trim.method = "mean.sd", trim.cutoffs = c(0.05, 0.975), interval.scale.disp = TRUE, down.space = 0.75, left.space = 0.75, up.space = 0.3, right.space = 0.25, orient = 1, dist.legend = 0.37, box.type = "l", amplif.label = 1.25, amplif.axis = 1.25, std.x.range = TRUE, std.y.range = TRUE, cex.pt = 0.2, col.box = hsv(0.55, 0.8, 0.8), x.nb.inter.tick = 4, y.nb.inter.tick = 0, tick.length = 0.5, sec.tick.length = 0.3, corner.text = "", amplif.legend = 1, corner.text.size = 0.75, trim.return = TRUE)
+    # DEBUGGING
+    # data = c(1:100, 1:10) ; displayed.nb = NULL ; single.value.display = FALSE ; trim.method = "quantile" ; trim.cutoffs = c(0.05, 0.975) ; interval.scale.disp = TRUE ; down.space = 1 ; left.space = 1 ; up.space = 0.5 ; right.space = 0.25 ; orient = 1 ; dist.legend = 0.5 ; box.type = "l" ; amplif.label = 1 ; amplif.axis = 1 ; std.x.range = TRUE ; std.y.range = TRUE ; cex.pt = 0.1 ; col.box = hsv(0.55, 0.8, 0.8) ; x.nb.inter.tick = 4 ; y.nb.inter.tick = 0 ; tick.length = 0.5 ; sec.tick.length = 0.3 ; corner.text = "" ; amplif.legend = 1 ; corner.text.size = 0.75 ; trim.return = TRUE # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    # argument checking without fun_check()
+    if( ! (all(class(data) == "numeric") | all(class(data) == "integer") | (all(class(data) %in% c("matrix", "array")) & base::mode(data) == "numeric"))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": data ARGUMENT MUST BE A NUMERIC VECTOR OR NUMERIC MATRIX")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end argument checking without fun_check()
+    # argument checking with fun_check()
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    if( ! is.null(displayed.nb)){
+        tempo <- fun_check(data = displayed.nb, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+        if(displayed.nb < 2){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": displayed.nb ARGUMENT MUST BE A SINGLE INTEGER VALUE GREATER THAN 1 AND NOT: ", paste(displayed.nb, collapse = " "))
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }
+    tempo <- fun_check(data = single.value.display, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = trim.method, options = c("", "mean.sd", "quantile"), length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = trim.cutoffs, class = "vector", mode = "numeric", length = 2, prop = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = interval.scale.disp, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = down.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = left.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = up.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = right.space, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = orient, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = dist.legend, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = box.type, options = c("o", "l", "7", "c", "u", "]", "n"), length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = amplif.label, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = amplif.axis, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = std.x.range, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = std.y.range, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = cex.pt, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = col.box, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = x.nb.inter.tick, class = "integer", length = 1, neg.values = FALSE, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y.nb.inter.tick, class = "integer", length = 1, neg.values = FALSE, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = tick.length, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = sec.tick.length, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = corner.text, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = amplif.legend, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = corner.text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = trim.return, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end argument checking with fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    if(all(is.na(data) | ! is.finite(data))){
+        tempo.cat <- paste0("ERROR IN fun_trim FUNCTION\ndata ARGUMENT CONTAINS ONLY NA OR Inf")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end argument checking
+    # main code
+    if(all(class(data)%in% c("matrix", "array"))){
+        data <- as.vector(data)
+    }
+    na.nb <- NULL
+    if(any(is.na(data))){
+        na.nb <- sum(c(is.na(data)))
+        data <- data[ ! is.na(data)]
+    }
+    color.cut <- hsv(0.75, 1, 1) # color of interval selected
+    col.mean <- hsv(0.25, 1, 0.8) # color of interval using mean+/-sd
+    col.quantile <- "orange" # color of interval using quantiles
+    quantiles.selection <- c(0.01, 0.025, 0.05, 0.1, 0.25, 0.5, 0.75, 0.9, 0.95, 0.975, 0.99) # quantiles used in axis to help for choosing trimming cutoffs
+    if(single.value.display == FALSE & length(unique(data)) == 1L){
+        par(bty = "n", xaxt = "n", yaxt = "n", xpd = TRUE)
+        plot(1, pch = 16, col = "white", xlab = "", ylab = "")
+        text(x = 1, y = 1, paste0("No graphic displayed\nBecause data made of a single different value (", formatC(as.double(table(data))), ")"), cex = 2)
+        output <- list(trim.method = NULL, trim.cutoffs = NULL, real.trim.cutoffs = NULL, trimmed.values = NULL, kept.values = NULL)
+    }else{
+        output <- list(trim.method = trim.method, trim.cutoffs = trim.cutoffs, real.trim.cutoffs = NULL, trimmed.values = NULL, kept.values = NULL)
+        fun.rug <- function(sec.tick.length.f = sec.tick.length, x.nb.inter.tick.f = x.nb.inter.tick, y.nb.inter.tick.f = y.nb.inter.tick){
+            if(x.nb.inter.tick.f > 0){
+                inter.tick.unit <- (par("xaxp")[2] - par("xaxp")[1]) / par("xaxp")[3]
+                par.ini <- par()[c("xpd", "tcl")]
+                par(xpd = FALSE)
+                par(tcl = -par()$mgp[2] * sec.tick.length.f) # tcl gives the length of the ticks as proportion of line text, knowing that mgp is in text lines. So the main ticks are a 0.5 of the distance of the axis numbers by default. The sign provides the side of the tick (negative for outside of the plot region)
+                suppressWarnings(rug(seq(par("xaxp")[1] - 10 * inter.tick.unit, par("xaxp")[2] + 10 * inter.tick.unit, by = inter.tick.unit / (1 + x.nb.inter.tick.f)), ticksize = NA, side = 1)) # ticksize = NA to allow the use of par()$tcl value
+                par(par.ini)
+                rm(par.ini)
+            }
+            if(y.nb.inter.tick.f > 0){
+                inter.tick.unit <- (par("yaxp")[2] - par("yaxp")[1]) / par("yaxp")[3]
+                par.ini <- par()[c("xpd", "tcl")]
+                par(xpd = FALSE)
+                par(tcl = -par()$mgp[2] * sec.tick.length.f) # tcl gives the length of the ticks as proportion of line text, knowing that mgp is in text lines. So the main ticks are a 0.5 of the distance of the axis numbers by default. The sign provides the side of the tick (negative for outside of the plot region)
+                suppressWarnings(rug(seq(par("yaxp")[1] - 10 * inter.tick.unit, par("yaxp")[2] + 10 * inter.tick.unit, by = inter.tick.unit / (1 + y.nb.inter.tick.f)), ticksize = NA, side = 2)) # ticksize = NA to allow the use of par()$tcl value
+                par(par.ini)
+                rm(par.ini)
+            }
+        }
+        fun.add.cut <- function(data.f, trim.method.f = trim.method, trim.cutoffs.f = trim.cutoffs, color.cut.f = color.cut, return.f = FALSE){
+            # DEBUGGING
+            # data.f = data ; trim.method.f = "mean.sd"; trim.cutoffs.f = trim.cutoffs ; color.cut.f = color.cut ; return.f = TRUE
+            real.trim.cutoffs.f <- NULL
+            if(trim.method.f != ""){
+                data.f <- sort(data.f)
+                par.ini <- par()$xpd
+                par(xpd = FALSE)
+                if(trim.method.f == "mean.sd"){
+                    real.trim.cutoffs.f <- qnorm(trim.cutoffs.f, mean(data.f, na.rm = TRUE), sd(data.f, na.rm = TRUE))
+                    abline(v = qnorm(trim.cutoffs.f, mean(data.f, na.rm = TRUE), sd(data.f, na.rm = TRUE)), col = color.cut.f)
+                    segments(qnorm(trim.cutoffs.f[1], mean(data.f, na.rm = TRUE), sd(data.f, na.rm = TRUE)), par()$usr[4] * 0.75, qnorm(trim.cutoffs.f[2], mean(data.f, na.rm = TRUE), sd(data.f, na.rm = TRUE)), par()$usr[4] * 0.75, col = color.cut.f)
+                }
+                if(trim.method.f == "quantile"){
+                    real.trim.cutoffs.f <- quantile(data.f, probs = trim.cutoffs.f, type = 7, na.rm = TRUE)
+                    abline(v = quantile(data.f, probs = trim.cutoffs.f, type = 7, na.rm = TRUE), col = color.cut.f)
+                    segments(quantile(data.f, probs = trim.cutoffs.f[1], type = 7, na.rm = TRUE), par()$usr[4] * 0.75, quantile(data.f, probs = trim.cutoffs.f[2], type = 7, na.rm = TRUE), par()$usr[4] * 0.75, col = color.cut.f)
+                }
+                par(par.ini)
+                if(return.f == TRUE){
+                    trimmed.values.f <- data.f[data.f <= real.trim.cutoffs.f[1] | data.f >= real.trim.cutoffs.f[2]]
+                    kept.values.f <- data.f[data.f > real.trim.cutoffs.f[1] & data.f < real.trim.cutoffs.f[2]]
+                }
+            }else{
+                real.trim.cutoffs.f <- NULL
+                trimmed.values.f <- NULL
+                kept.values.f <- NULL
+            }
+            if(return.f == TRUE){
+                output <- list(trim.method = trim.method.f, trim.cutoffs = trim.cutoffs.f, real.trim.cutoffs = real.trim.cutoffs.f, trimmed.values = trimmed.values.f, kept.values = kept.values.f)
+                return(output)
+            }
+        }
+        fun.interval.scale.display <- function(data.f, col.quantile.f = col.quantile, quantiles.selection.f = quantiles.selection, col.mean.f = col.mean){ # intervals on top of graphs
+            par.ini <- par()[c("mgp", "xpd")]
+            par(mgp = c(0.25, 0.25, 0), xpd = NA)
+            axis(side = 3, at = c(par()$usr[1], par()$usr[2]), labels = rep("", 2), col = col.quantile.f, lwd.ticks = 0)
+            par(xpd = FALSE)
+            axis(side = 3, at = quantile(as.vector(data.f), probs = quantiles.selection.f, type = 7, na.rm = TRUE), labels = quantiles.selection.f, col.axis = col.quantile.f, col = col.quantile.f)
+            par(mgp = c(1.75, 1.75, 1.5), xpd = NA)
+            axis(side = 3, at = c(par()$usr[1], par()$usr[2]), labels = rep("", 2), col = col.mean.f, lwd.ticks = 0)
+            par(xpd = FALSE)
+            axis(side = 3, at = m + s * qnorm(quantiles.selection.f), labels = formatC(round(qnorm(quantiles.selection.f), 2)), col.axis = col.mean.f, col = col.mean.f, lwd.ticks = 1)
+            par(par.ini)
+        }
+        zone<-matrix(1:4, ncol=2)
+        layout(zone)
+        par(omi = c(0, 0, 1.5, 0), mai = c(down.space, left.space, up.space, right.space), las = orient, mgp = c(dist.legend / 0.2, 0.5, 0), xpd = FALSE, bty= box.type, cex.lab = amplif.label, cex.axis = amplif.axis, xaxs = ifelse(std.x.range, "i", "r"), yaxs = ifelse(std.y.range, "i", "r"))
+        par(tcl = -par()$mgp[2] * tick.length) # tcl gives the length of the ticks as proportion of line text, knowing that mgp is in text lines. So the main ticks are a 0.5 of the distance of the axis numbers by default. The sign provides the side of the tick (negative for outside of the plot region)
+        if(is.null(displayed.nb)){
+            sampled.data <- as.vector(data)
+            if(corner.text == ""){
+                corner.text <- paste0("ALL VALUES OF THE DATASET DISPLAYED")
+            }else{
+                corner.text <- paste0(corner.text, "\nALL VALUES OF THE DATASET DISPLAYED")
+            }
+        }else{
+            if(length(as.vector(data)) > displayed.nb){
+                sampled.data <- sample(as.vector(data), displayed.nb, replace = FALSE)
+                if(corner.text == ""){
+                    corner.text <- paste0("WARNING: ONLY ", displayed.nb, " VALUES ARE DISPLAYED AMONG THE ", length(as.vector(data)), " VALUES OF THE DATASET ANALYZED")
+                }else{
+                    corner.text <- paste0(corner.text, "\nWARNING: ONLY ", displayed.nb, " VALUES ARE DISPLAYED AMONG THE ", length(as.vector(data)), " VALUES OF THE DATASET ANALYZED")
+                }
+            }else{
+                sampled.data <- as.vector(data)
+                if(corner.text == ""){
+                    corner.text <- paste0("WARNING: THE DISPLAYED NUMBER OF VALUES PARAMETER ", deparse(substitute(displayed.nb)), " HAS BEEN SET TO ", displayed.nb, " WHICH IS ABOVE THE NUMBER OF VALUES OF THE DATASET ANALYZED -> ALL VALUES DISPLAYED")
+                }else{
+                    corner.text <- paste0(corner.text, "\nWARNING: THE DISPLAYED NUMBER OF VALUES PARAMETER ", deparse(substitute(displayed.nb)), " HAS BEEN SET TO ", displayed.nb, " WHICH IS ABOVE THE NUMBER OF VALUES OF THE DATASET ANALYZED -> ALL VALUES DISPLAYED")
+                }
+            }
+        }
+        if( ! is.null(na.nb)){
+            if(corner.text == ""){
+                corner.text <- paste0("WARNING: NUMBER OF NA REMOVED IS ", na.nb)
+            }else{
+                corner.text <- paste0("WARNING: NUMBER OF NA REMOVED IS ", na.nb)
+            }
+        }
+        stripchart(sampled.data, method="jitter", jitter=0.4, vertical=FALSE, ylim=c(0.5, 1.5), group.names = "", xlab = "Value", ylab="", pch=1, cex = cex.pt / 0.2)
+        fun.rug(y.nb.inter.tick.f = 0)
+        boxplot(as.vector(data), horizontal=TRUE, add=TRUE, boxwex = 0.4, staplecol = col.box, whiskcol = col.box, medcol = col.box, boxcol = col.box, range = 0, whisklty = 1)
+        m <- mean(as.vector(data), na.rm = TRUE)
+        s <- sd(as.vector(data), na.rm = TRUE)
+        segments(m, 0.8, m, 1, lwd=2, col="red") # mean 
+        segments(m -1.96 * s, 0.9, m + 1.96 * s, 0.9, lwd=1, col="red") # mean 
+        graph.xlim <- par()$usr[1:2] # for hist() and qqnorm() below
+        if(interval.scale.disp == TRUE){
+            fun.interval.scale.display(data.f = data)
+            if(corner.text == ""){
+                corner.text <- paste0("MULTIPLYING FACTOR DISPLAYED (MEAN +/- SD) ON SCALES: ", paste(formatC(round(qnorm(quantiles.selection), 2))[-(1:(length(quantiles.selection) - 1) / 2)], collapse = ", "), "\nQUANTILES DISPLAYED ON SCALES: ", paste(quantiles.selection, collapse = ", "))
+            }else{
+                corner.text <- paste0(corner.text, "\nMULTIPLYING FACTOR DISPLAYED (MEAN +/- SD) ON SCALES: ", paste(formatC(round(qnorm(quantiles.selection), 2))[-(1:(length(quantiles.selection) - 1) / 2)], collapse = ", "), "\nQUANTILES DISPLAYED ON SCALES: ", paste(quantiles.selection, collapse = ", "))
+            }
+        }
+        output.tempo <- fun.add.cut(data.f = data, return.f = TRUE) # to recover real.trim.cutoffs
+        if(trim.return == TRUE){
+            output <- output.tempo
+        }
+        par(xpd = NA)
+        if(trim.method != ""){
+            if(corner.text == ""){
+                corner.text <- paste0("SELECTED CUT-OFFS (PROPORTION): ", paste(trim.cutoffs, collapse = ", "), "\nSELECTED CUT-OFFS: ", paste(output.tempo$real.trim.cutoffs, collapse = ", "))
+            }else{
+                corner.text <- paste0(corner.text, "\nSELECTED CUT-OFFS (PROPORTION): ", paste(trim.cutoffs, collapse = ", "), "\nSELECTED CUT-OFFS: ", paste(output.tempo$real.trim.cutoffs, collapse = ", "))
+            }
+            if(interval.scale.disp == TRUE){
+                legend(x = (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / (par("omd")[2] - par("omd")[1])) * par("omd")[1]), y = (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / (par("omd")[4] - par("omd")[3])) * (1 - par("omd")[4]) / 2), legend = c(c("min, Q1, Median, Q3, max"), "mean +/- 1.96sd", paste0("Trimming interval: ", paste0(trim.cutoffs, collapse = " , ")), "Mean +/- sd multiplying factor", "Quantile"), yjust = 0, lty=1, col=c(col.box, "red", color.cut, col.mean, col.quantile), bty="n", cex = amplif.legend)
+            }else{
+                legend(x = (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / (par("omd")[2] - par("omd")[1])) * par("omd")[1]), y = (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / (par("omd")[4] - par("omd")[3])) * (1 - par("omd")[4]) / 2), legend = c(c("min, Q1, Median, Q3, max"), "mean +/- 1.96sd", paste0("Trimming interval: ", paste0(trim.cutoffs, collapse = " , "))), yjust = 0, lty=1, col=c(col.box, "red", color.cut), bty="n", cex = amplif.legend, y.intersp=1.25)
+            }
+        }else{
+            if(interval.scale.disp == TRUE){
+                legend(x = (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / (par("omd")[2] - par("omd")[1])) * par("omd")[1]), y = (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / (par("omd")[4] - par("omd")[3])) * (1 - par("omd")[4]) / 2), legend = c(c("min, Q1, Median, Q3, max"), "mean +/- sd", "Mean +/- sd multiplying factor", "Quantile"), yjust = 0, lty=1, col=c(col.box, "red", col.mean, col.quantile), bty="n", cex = amplif.legend)
+            }else{
+                legend(x = (par("usr")[1] - ((par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1])) * par("plt")[1] - ((par("usr")[2] - par("usr")[1]) / (par("omd")[2] - par("omd")[1])) * par("omd")[1]), y = (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / (par("omd")[4] - par("omd")[3])) * (1 - par("omd")[4]) / 2), legend = c(c("min, Q1, Median, Q3, max"), "mean +/- sd"), yjust = 0, lty=1, col=c(col.box, "red"), bty="n", cex = amplif.legend, y.intersp=1.25)
+            }
+        }
+        par(xpd = FALSE, xaxs = ifelse(std.x.range, "i", "r"), yaxs = ifelse(std.y.range, "i", "r"))
+        hist(as.vector(data), main = "", xlim = graph.xlim, xlab = "Value", ylab="Density", col = grey(0.25)) # removed: breaks = seq(min(as.vector(data), na.rm = TRUE), max(as.vector(data), na.rm = TRUE), length.out = length(as.vector(data)) / 10)
+        abline(h = par()$usr[3])
+        fun.rug()
+        if(interval.scale.disp == TRUE){
+            fun.interval.scale.display(data.f = data)
+        }
+        fun.add.cut(data.f = data)
+        par(xaxs = ifelse(std.x.range, "i", "r"))
+        stripchart(rank(sampled.data), method="stack", vertical=FALSE, ylim=c(0.99, 1.3), group.names = "", xlab = "Rank of values", ylab="", pch=1, cex = cex.pt / 0.2)
+        fun.rug(y.nb.inter.tick.f = 0)
+        x.text <- par("usr")[2] + (par("usr")[2] - par("usr")[1]) / (par("plt")[2] - par("plt")[1]) * (1 - par("plt")[2]) / 2
+        y.text <- (par("usr")[4] + ((par("usr")[4] - par("usr")[3]) / (par("plt")[4] - par("plt")[3])) * (1 - par("plt")[4]) + ((par("usr")[4] - par("usr")[3]) / ((par()$omd[4] / 2) * ((par("plt")[4] - par("plt")[3])))) * (1 - par("omd")[4])) # BEWARE. Here in "(par()$omd[4] / 2", division by two because there are 2 graphs staked on the y axis, and not one
+        par(xpd=NA)
+        text(x = x.text, y = y.text, paste0(corner.text), adj=c(1, 1.1), cex = corner.text.size) # text at the topright corner
+        par(xpd=FALSE)
+        par(xaxs = ifelse(std.x.range, "i", "r"), yaxs = ifelse(std.y.range, "i", "r"))
+        qqnorm(as.vector(sampled.data), main = "", datax = TRUE, ylab = "Value", pch = 1, col = "red", cex = cex.pt / 0.2)
+        fun.rug()
+        if(diff(quantile(as.vector(data), probs = c(0.25, 0.75), na.rm = TRUE)) != 0){ # otherwise, error generated
+            qqline(as.vector(data), datax = TRUE)
+        }
+        if(interval.scale.disp == TRUE){
+            fun.interval.scale.display(data.f = data)
+        }
+        fun.add.cut(data.f = data)
+    }
+    if(trim.return == TRUE){
+        return(output)
+    }
 }
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "alpha", name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(alpha[[i1]], length(color[[i1]])), breaks = class.categ)) # values are the values of linetype. 1 means solid. Regarding the alpha bug, I have tried different things without success: alpha in guide alone, in geom alone, in both, with different values, breaks reorder the classes according to class.categ in the legend
+
+
+######## fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation
+
+
+fun_segmentation <- function(
+    data1, 
+    x1, 
+    y1, 
+    x.range.split = NULL, 
+    x.step.factor = 10, 
+    y.range.split = NULL, 
+    y.step.factor = 10, 
+    error = 0, 
+    data2 = NULL, 
+    x2, 
+    y2, 
+    data2.pb.dot = "unknown", 
+    xy.cross.kind = "&", 
+    plot = FALSE, 
+    graph.in.file = FALSE, 
+    raster = TRUE, 
+    warn.print = FALSE, 
+    lib.path = NULL
+){
+    # AIM
+    # if data1 is a data frame corresponding to the data set of a scatterplot (with a x column for x-axis values and a y column for the y-axis column), then fun_segmentation() delimits a frame around the dots cloud using a sliding window set by x.range.split and x.step.factor to frame the top and bottom part of the cloud, and set by y.range.split and y.step.factor to frame the left and right part of the cloud
+    # if a second data frame is provided, corresponding to the data set of a scatterplot (with a x column for x-axis values and a y column for the y-axis column), then fun_segmentation() defines the dots of this data frame, outside of the frame of the first data frame
+    # WARNINGS
+    # if dots from data2 look significant on the graph (outside the frame) but are not (not black on the last figure), this is probably because the frame is flat on the zero coordinate (no volume inside the frame at this position). Thus, no way to conclude that data2 dots here are significant. These dots are refered to as "unknown". The pb.dot argument deals with such dots
+    # dots that are sometimes inside and outside the frame, depending on the sliding window, are treated differently: they are removed. Such dots are neither classified as "signif", "non signif" or "unknown", but as "inconsistent"
+    # unknown dots are treated as finally significant, not significant, or unknown (data2.pb.dot argument) for each x-axis and y-axis separately. Then, the union or intersection of significant dots is performed (argument xy.cross.kind). See the example section
+    # ARGUMENTS
+    # data1: a data frame containing a column of x-axis values and a column of y-axis values
+    # x1: character string of the data1 column name for x-axis (first column of data1 by default)
+    # y1: character string of the data1 column name for y-axis (second column of data1 by default)
+    # x.range.split: positive non null numeric value giving the number of interval on the x value range. if x.range is the range of the dots on the x-axis, then abs(diff(x.range) / x.range.split) gives the window size. Window size decreases when range.split increases. In unit of x-axis. Write NULL if not required. At least one of the x.range.split and y.range.split must be non NULL
+    # x.step.factor: positive non null numeric value giving the shift step of the window. If x.step.factor = 1, no overlap during the sliding (when the window slides from position n to position n+1, no overlap between the two positions). If x.step.factor = 2, 50% of overlap (when the window slides from position n to position n+1, the window on position n+1 overlap 50% of the window when it was on position n)
+    # y.range.split: same as x.range.split for the y-axis. At least one of the x.range.split and y.range.split must be non NULL
+    # y.step.factor: same as x.step.factor for the y-axis
+    # error: proportion (from 0 to 1) of false positives (i.e., proportion of dots from data1 outside of the frame). 0.05 means 5% of the dots from data1 outside of the frame
+    # data2: a data frame containing a column of x-axis values and a column of y-axis values, for which outside dots of the data1 cloud has to be determined. Write NULL if not required
+    # x2: character string of the data1 column name for x-axis (first column of data1 by default)
+    # y2: character string of the data1 column name for y-axis (second column of data1 by default)
+    # data2.pb.dot: unknown dots are explain in the warning section above. If "signif", then the unknown dots are finally considered as significant (outside the frame). If "not.signif", then the unknown dots are finally considered as non significant (inside the frame). If "unknown", no conclusion are drawn from these dots. See the examples below
+    # xy.cross.kind: if data2 is non null and if both x.range.split and y.range.split are non null, which dots are finally significants? Write "&" for intersection of outside dots on x and on y. Write "|" for union of outside dots on x and on y. See the examples below
+    # plot: logical. Print graphs that check the frame?
+    # graph.in.file: logical. Graphs sent into a graphic device already opened? If FALSE, GUI are opened for each graph. If TRUE, no GUI are opended. The graphs are displayed on the current active graphic device. Ignored if plot is FALSE
+    # raster: logical. Dots in raster mode? If FALSE, dots from each geom_point from geom argument are in vectorial mode (bigger pdf and long to display if millions of dots). If TRUE, dots from each geom_point from geom argument are in matricial mode (smaller pdf and easy display if millions of dots, but long to generate the layer). If TRUE, the region plot will be square to avoid a bug in fun_gg_point_rast(). If TRUE, solve the transparency problem with some GUI. Not considered if plot is FALSE
+    # warn.print: logical. Print warnings at the end of the execution? No print if no warning messages
+    # lib.path: character vector specifying the absolute pathways of the directories containing the required packages if not in the default directories. Ignored if NULL. Ignored if plot is FALSE
+    # RETURN
+    # several graphs if plot is TRUE
+    # a list containing:
+    # $data1.removed.row.nb: which rows have been removed due to NA; NaN, -Inf or Inf detection in x1 or y1 columns (NULL if no row removed)
+    # $data1.removed.rows: removed rows (NULL if no row removed)
+    # $data2.removed.row.nb: which rows have been removed due to NA; NaN, -Inf or Inf detection in x2 or y2 columns (NULL if no row removed)
+    # $data2.removed.rows: removed rows (NULL if no row removed)
+    # $hframe: x and y coordinates of the bottom and top frames for frame plotting (frame1 for the left step and frame2 for the right step)
+    # $vframe: x and y coordinates of the left and right frames for frame plotting (frame1 for the down step and frame2 for the top step)
+    # $data1.signif.dot: the significant dots of data1 (i.e., dots outside the frame). A good segmentation should not have any data1.signif.dot
+    # $data1.non.signif.dot: the non significant dots of data1 (i.e., dots inside the frame)
+    # $data1.inconsistent.dot: see the warning section above
+    # $data2.signif.dot: the significant dots of data2 if non NULL (i.e., dots outside the frame)
+    # $data2.non.signif.dot: the non significant dots of data2 (i.e., dots inside the frame)
+    # $data2.unknown.dot: the problematic dots of data2 (i.e., data2 dots outside of the range of data1, or data2 dots in a sliding window without data1 dots). Is systematically NULL except if argument data2.pb.dot = "unknown" and some data2 dots are in such situation. Modifying the segmentation x.range.split, x.step.factor, y.range.split, y.step.factor arguments can solve this problem
+    # $data2.inconsistent.dot: see the warning section above
+    # $axes: the x-axis and y-axis info
+    # $warn: the warning messages. Use cat() for proper display. NULL if no warning
+    # REQUIRED PACKAGES
+    # ggplot2 if plot is TRUE
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # if plot is TRUE:
+    # fun_pack()
+    # fun_open()
+    # fun_gg_palette()
+    # fun_gg_scatter()
+    # fun_gg_empty_graph()
+    # fun_close()
+    # EXAMPLES
+    # example explaining the unknown and inconsistent dots, and the cross 
+    
+    # set.seed(1) ; data1 = data.frame(x = rnorm(500), y = rnorm(500), stringsAsFactors = TRUE) ; data1[5:7, 2] <- NA ; data2 = data.frame(x = rnorm(500, 0, 2), y = rnorm(500, 0, 2), stringsAsFactors = TRUE) ; data2[11:13, 1] <- Inf ; set.seed(NULL) ; fun_segmentation(data1 = data1, x1 = names(data1)[1], y1 = names(data1)[2], x.range.split = 20, x.step.factor = 10, y.range.split = 23, y.step.factor = 10, error = 0, data2 = data2, x2 = names(data2)[1], y2 = names(data2)[2], data2.pb.dot = "not.signif", xy.cross.kind = "|", plot = TRUE, graph.in.file = FALSE, raster = FALSE, lib.path = NULL)
+    # set.seed(1) ; data1 = data.frame(x = rnorm(500), y = rnorm(500), stringsAsFactors = TRUE) ; data2 = data.frame(x = rnorm(500, 0, 2), y = rnorm(500, 0, 2), stringsAsFactors = TRUE) ; set.seed(NULL) ; fun_segmentation(data1 = data1, x1 = names(data1)[1], y1 = names(data1)[2], x.range.split = NULL, x.step.factor = 10, y.range.split = 23, y.step.factor = 10, error = 0, data2 = data2, x2 = names(data2)[1], y2 = names(data2)[2], data2.pb.dot = "unknown", xy.cross.kind = "|", plot = TRUE, graph.in.file = FALSE, raster = FALSE, lib.path = NULL)
+    # set.seed(1) ; data1 = data.frame(x = rnorm(500), y = rnorm(500), stringsAsFactors = TRUE) ; data2 = data.frame(x = rnorm(500, 0, 2), y = rnorm(500, 0, 2), stringsAsFactors = TRUE) ; set.seed(NULL) ; fun_segmentation(data1 = data1, x1 = names(data1)[1], y1 = names(data1)[2], x.range.split = 20, x.step.factor = 10, y.range.split = NULL, y.step.factor = 10, error = 0, data2 = data2, x2 = names(data2)[1], y2 = names(data2)[2], data2.pb.dot = "unknown", xy.cross.kind = "&", plot = TRUE, graph.in.file = FALSE, raster = FALSE, lib.path = NULL)
+    # DEBUGGING
+    # set.seed(1) ; data1 = data.frame(x = rnorm(50), y = rnorm(50), stringsAsFactors = TRUE) ; data1[5:7, 2] <- NA ; x1 = names(data1)[1] ; y1 = names(data1)[2] ; x.range.split = 5 ; x.step.factor = 10 ; y.range.split = 5 ; y.step.factor = 10 ; error = 0 ; data2 = data.frame(x = rnorm(50, 0, 2), y = rnorm(50, 0, 2), stringsAsFactors = TRUE) ; set.seed(NULL) ; x2 = names(data2)[1] ; y2 = names(data2)[2] ; data2.pb.dot = "unknown" ; xy.cross.kind = "|" ; plot = TRUE ; graph.in.file = FALSE ; raster = FALSE ; warn.print = TRUE ; lib.path = NULL
+    # set.seed(1) ; data1 = data.frame(x = rnorm(500), y = rnorm(500), stringsAsFactors = TRUE) ; data2 = data.frame(x = rnorm(500, 0, 2), y = rnorm(500, 0, 2), stringsAsFactors = TRUE) ; set.seed(NULL) ; x1 = names(data1)[1] ; y1 = names(data1)[2] ; x.range.split = 20 ; x.step.factor = 10 ; y.range.split = 23 ; y.step.factor = 10 ; error = 0 ; x2 = names(data2)[1] ; y2 = names(data2)[2] ; data2.pb.dot = "not.signif" ; xy.cross.kind = "|" ; plot = TRUE ; graph.in.file = FALSE ; raster = FALSE ; warn.print = TRUE ; lib.path = NULL
+    # set.seed(1) ; data1 = data.frame(x = rnorm(500), y = rnorm(500), stringsAsFactors = TRUE) ; data2 = data.frame(x = rnorm(500, 0, 2), y = rnorm(500, 0, 2), stringsAsFactors = TRUE) ; set.seed(NULL) ; x1 = names(data1)[1] ; y1 = names(data1)[2] ; x.range.split = 20 ; x.step.factor = 10 ; y.range.split = NULL ; y.step.factor = 10 ; error = 0 ; x2 = names(data2)[1] ; y2 = names(data2)[2] ; data2.pb.dot = "unknown" ; xy.cross.kind = "&" ; plot = TRUE ; graph.in.file = FALSE ; raster = FALSE ; warn.print = TRUE ; lib.path = NULL
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    ini.warning.length <- options()$warning.length
+    warn <- NULL
+    warn.count <- 0
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = data1, class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & length(data1) < 2){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": data1 ARGUMENT MUST BE A DATA FRAME OF AT LEAST 2 COLUMNS")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    tempo <- fun_check(data = x1, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & ! (x1 %in% names(data1))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": x1 ARGUMENT MUST BE A COLUMN NAME OF data1")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }else if(tempo$problem == FALSE & x1 %in% names(data1)){
+        tempo <- fun_check(data = data1[, x1], data.name = "x1 COLUMN OF data1", class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = y1, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & ! (y1 %in% names(data1))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": y1 ARGUMENT MUST BE A COLUMN NAME OF data1")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }else if(tempo$problem == FALSE & y1 %in% names(data1)){
+        tempo <- fun_check(data = data1[, y1], data.name = "y1 COLUMN OF data1", class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    }
+    if(is.null(x.range.split) & is.null(y.range.split)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": AT LEAST ONE OF THE x.range.split AND y.range.split ARGUMENTS MUST BE NON NULL")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    if( ! is.null(x.range.split)){
+        tempo <- fun_check(data = x.range.split, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & x.range.split < 1){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": x.range.split ARGUMENT CANNOT BE LOWER THAN 1")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }
+    if( ! is.null(y.range.split)){
+        tempo <- fun_check(data = y.range.split, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & y.range.split < 1){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": y.range.split ARGUMENT CANNOT BE LOWER THAN 1")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }
+    tempo <- fun_check(data = x.step.factor, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & x.step.factor < 1){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": x.step.factor ARGUMENT CANNOT BE LOWER THAN 1")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    tempo <- fun_check(data = y.step.factor, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & y.step.factor < 1){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": y.step.factor ARGUMENT CANNOT BE LOWER THAN 1")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    tempo <- fun_check(data = error, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(data2)){
+        if(is.null(x2) | is.null(y2)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": x2 AND y2 ARGUMENTS CANNOT BE NULL IF data2 ARGUMENT IS NON NULL")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+        tempo <- fun_check(data = data2, class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & length(data2) < 2){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": data2 ARGUMENT MUST BE A DATA FRAME OF AT LEAST 2 COLUMNS")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+        if( ! is.null(x2)){
+            tempo <- fun_check(data = x2, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+            if(tempo$problem == FALSE & ! (x2 %in% names(data2))){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": x2 ARGUMENT MUST BE A COLUMN NAME OF data2")
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }else if(tempo$problem == FALSE & x2 %in% names(data2)){
+                tempo <- fun_check(data = data2[, x2], data.name = "x2 COLUMN OF data2", class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+            }
+        }
+        if( ! is.null(y2)){
+            tempo <- fun_check(data = y2, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+            if(tempo$problem == FALSE & ! (y2 %in% names(data2))){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": y2 ARGUMENT MUST BE A COLUMN NAME OF data2")
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }else if(tempo$problem == FALSE & y2 %in% names(data2)){
+                tempo <- fun_check(data = data2[, y2], data.name = "y2 COLUMN OF data2", class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+            }
+        }
+    }
+    if( ! is.null(data2)){
+        tempo <- fun_check(data = data2.pb.dot, options = c("signif", "not.signif", "unknown"), length = 1, fun.name = function.name) ; eval(ee)
+    }
+    if( ! (is.null(x.range.split)) & ! (is.null(y.range.split))){
+        tempo <- fun_check(data = xy.cross.kind, options = c("&", "|"), length = 1, fun.name = function.name) ; eval(ee)
+    }
+    tempo <- fun_check(data = plot, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & plot == TRUE){
+        tempo <- fun_check(data = raster, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+        tempo <- fun_check(data = graph.in.file, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & graph.in.file == TRUE & is.null(dev.list())){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": \ngraph.in.file PARAMETER SET TO TRUE BUT NO ACTIVE GRAPHIC DEVICE DETECTED")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }else if(tempo$problem == FALSE & graph.in.file == TRUE & ! is.null(dev.list())){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") GRAPHS PRINTED IN THE CURRENT DEVICE (TYPE ", toupper(names(dev.cur())), ")")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+        if( ! is.null(lib.path)){
+            tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+            if(tempo$problem == FALSE){
+                if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
+                    tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+                    text.check <- c(text.check, tempo.cat)
+                    arg.check <- c(arg.check, TRUE)
+                }
+            }
+        }
+    }
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # other required function checking
+    if(plot == TRUE){
+        if(length(utils::find("fun_pack", mode = "function")) == 0L){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(length(utils::find("fun_open", mode = "function")) == 0L){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_open() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(length(utils::find("fun_gg_palette", mode = "function")) == 0L){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_gg_palette() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(length(utils::find("fun_gg_empty_graph", mode = "function")) == 0L){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_gg_empty_graph() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(length(utils::find("fun_gg_scatter", mode = "function")) == 0L){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_gg_scatter() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(length(utils::find("fun_close", mode = "function")) == 0L){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_close() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # end other required function checking
+    # package checking
+    if(plot == TRUE){
+        fun_pack(req.package = c("ggplot2"), lib.path = lib.path)
+    }
+    # end package checking
+    # main code
+    # na and Inf detection and removal (done now to be sure of the correct length of categ)
+    data1.removed.row.nb <- NULL
+    data1.removed.rows <- NULL
+    data2.removed.row.nb <- NULL
+    data2.removed.rows <- NULL
+    if(any(is.na(data1[, c(x1, y1)])) | any(is.infinite(data1[, x1])) | any(is.infinite(data1[, y1]))){
+        tempo.na <- unlist(lapply(lapply(c(data1[c(x1, y1)]), FUN = is.na), FUN = which))
+        tempo.inf <- unlist(lapply(lapply(c(data1[c(x1, y1)]), FUN = is.infinite), FUN = which))
+        data1.removed.row.nb <- sort(unique(c(tempo.na, tempo.inf)))
+        if(length(data1.removed.row.nb) > 0){
+            data1.removed.rows <- data1[data1.removed.row.nb, ]
+        }
+        if(length(data1.removed.row.nb) == nrow(data1)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": AT LEAST ONE NA, NaN, -Inf OR Inf DETECTED IN EACH ROW OF data1. FUNCTION CANNOT BE USED ON EMPTY DATA FRAME")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(length(data1.removed.row.nb) > 0){
+            data1 <- data1[-data1.removed.row.nb, ]
+        }
+        if(nrow(data1) == 0L){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 1")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") NA, NaN, -Inf OR Inf DETECTED IN COLUMN ", paste(c(x1, y1), collapse = " "), " OF data1 AND CORRESPONDING ROWS REMOVED (SEE $data1.removed.row.nb AND $data1.removed.rows)")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }else{
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") NO NA, NaN, -Inf OR Inf DETECTED IN COLUMN ", paste(c(x1, y1), collapse = " "), " OF data1. NO ROW REMOVED")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
+    if( ! is.null(data2)){
+        if(any(is.na(data2[, c(x2, y2)])) | any(is.infinite(data2[, x2])) | any(is.infinite(data2[, y2]))){
+            tempo.na <- unlist(lapply(lapply(c(data2[c(x2, y2)]), FUN = is.na), FUN = which))
+            tempo.inf <- unlist(lapply(lapply(c(data2[c(x2, y2)]), FUN = is.infinite), FUN = which))
+            data2.removed.row.nb <- sort(unique(c(tempo.na, tempo.inf)))
+            if(length(data2.removed.row.nb) > 0){
+                data2.removed.rows <- data2[data2.removed.row.nb, ]
+            }
+            if(length(data2.removed.row.nb) == nrow(data2)){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": AT LEAST ONE NA, NaN, -Inf OR Inf DETECTED IN EACH ROW OF data2. FUNCTION CANNOT BE USED ON EMPTY DATA FRAME")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            if(length(data2.removed.row.nb) > 0){
+                data2 <- data2[-data2.removed.row.nb, ]
+            }
+            if(nrow(data2) == 0L){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 2")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") NA, NaN, -Inf OR Inf DETECTED IN COLUMN ", paste(c(x2, y2), collapse = " "), " OF data2 AND CORRESPONDING ROWS REMOVED (SEE $data2.removed.row.nb AND $data2.removed.rows)")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }else{
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") NO NA, NaN, -Inf OR Inf DETECTED IN COLUMN ", paste(c(x2, y2), collapse = " "), " OF data2. NO ROW REMOVED")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    # end na and Inf detection and removal (done now to be sure of the correct length of categ)
+    # row annotation (dot number)
+    # data1 <- data1[ ! duplicated(data1[, c(x1, y1)]), ] # do not remove the dots that have same x and y values, because they will have different dot number -> not the same position on the matrices (so true for symmetric matrices)
+    data1 <- cbind(data1, DOT_NB = 1:nrow(data1), stringsAsFactors = TRUE)
+    if( ! is.null(data2)){
+        # data2 <- data2[ ! duplicated(data2[, c(x2, y2)]), ] # do not remove the dots that have same x and y values, because they will have different dot number -> not the same position on the matrices (so true for symmetric matrices)
+        data2 <- cbind(data2, DOT_NB = 1:nrow(data2), stringsAsFactors = TRUE)
+    }
+    # end row annotation (dot number)
+    
+    
+    
+    
+    # Method using x unit interval 
+    # may be create vector of each column to increase speed
+    x.data1.l <- NULL # x coord of the y upper and lower limits defined on the data1 cloud for left step line
+    x.data1.r <- NULL # x coord of the y upper and lower limits defined on the data1 cloud for right step line
+    y.data1.down.limit.l <- NULL # lower limit of the data1 cloud for left step line
+    y.data1.top.limit.l <- NULL # upper limit of the data1 cloud for left step line
+    y.data1.down.limit.r <- NULL # lower limit of the data1 cloud for right step line
+    y.data1.top.limit.r <- NULL # upper limit of the data1 cloud for left step line
+    if(any(data1[, x1] %in% c(Inf, -Inf))){
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") THE data1 ARGUMENT CONTAINS -Inf OR Inf VALUES IN THE x1 COLUMN, THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
+    x.range <- range(data1[, x1], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+    if(suppressWarnings(any(x.range %in% c(Inf, -Inf)))){
+        tempo.cat <- paste0("ERROR IN ", function.name, " COMPUTED x.range CONTAINS Inf VALUES, BECAUSE VALUES FROM data1 ARGUMENTS ARE NA OR Inf ONLY")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(any(data1[, y1] %in% c(Inf, -Inf))){
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") THE data1 ARGUMENT CONTAINS -Inf OR Inf VALUES IN THE y1 COLUMN, THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
+    y.range <- range(data1[, y1], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+    if(suppressWarnings(any(x.range %in% c(Inf, -Inf)))){
+        tempo.cat <- paste0("ERROR IN ", function.name, " COMPUTED y.range CONTAINS Inf VALUES, BECAUSE VALUES FROM data1 ARGUMENTS ARE NA OR Inf ONLY")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    x.range.plot <- range(data1[, x1], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+    y.range.plot <- range(data1[, y1], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+    if( ! is.null(data2)){
+        if(any(data2[, x2] %in% c(Inf, -Inf))){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") THE data2 ARGUMENT CONTAINS -Inf OR Inf VALUES IN THE x2 COLUMN, THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+        x.range.plot <- range(data1[, x1], data2[, x2], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+        if(any(data2[, y2] %in% c(Inf, -Inf))){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") THE data2 ARGUMENT CONTAINS -Inf OR Inf VALUES IN THE y2 COLUMN, THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+        y.range.plot <- range(data1[, y1], data2[, y2], na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+    }
+    if(suppressWarnings(any(x.range.plot %in% c(Inf, -Inf)))){
+        tempo.cat <- paste0("ERROR IN ", function.name, " COMPUTED x.range.plot CONTAINS Inf VALUES, BECAUSE VALUES FROM data1 (AND data2?) ARGUMENTS ARE NA OR Inf ONLY")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(suppressWarnings(any(y.range.plot %in% c(Inf, -Inf)))){
+        tempo.cat <- paste0("ERROR IN ", function.name, " COMPUTED y.range.plot CONTAINS Inf VALUES, BECAUSE VALUES FROM data1 (AND data2?) ARGUMENTS ARE NA OR Inf ONLY")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! is.null(x.range.split)){
+        # data.frame ordering to slide the window from small to big values + sliding window definition
+        data1 <- data1[order(data1[, x1], na.last = TRUE), ]
+        if( ! is.null(data2)){
+            data2 <- data2[order(data2[, x2], na.last = TRUE), ]
+        }
+        x.win.size <- abs(diff(x.range) / x.range.split) # in unit of x-axis
+        step <- x.win.size / x.step.factor
+        # end data.frame ordering to slide the window from small to big values + sliding window definition
+        # x-axis sliding and y-axis limits of the data1 cloud -> y significant data2
+        loop.nb <- ceiling((diff(x.range) - x.win.size) / step) # x.win.size + n * step covers the x range if x.win.size + n * step >= diff(x.range), thus if n >= (diff(x.range) - x.win.size) / step 
+        y.outside.data1.dot.nb <- integer() # vector that will contain the selected rows numbers of data1 that are upper or lower than the frame
+        y.inside.data1.dot.nb <- integer() # vector that will contain the selected rows numbers of data1 that are not upper or lower than the frame
+        y.data1.median <- median(data1[, y1], na.rm = TRUE) # will be used for sliding windows without data1 in it
+        if( ! is.null(data2)){
+            y.outside.data2.dot.nb <- integer() # vector that will contain the selected 1D coordinates (i.e., dots) of data2 that are upper or lower than the data1 frame
+            y.inside.data2.dot.nb <- integer() # vector that will contain the 1D coordinates (i.e., dots) of data2 that are not upper or lower than the data1 frame
+            y.unknown.data2.dot.nb <- integer() # vector that will contain the 1D coordinates (i.e., dots) of data2 that are problematic: data2 dots outside of the range of data1, or data2 dots in a sliding window without data1 dots
+            # recover data2 dots outside the range of data1
+            if(any(data2[, x2] < x.range[1])){
+                y.unknown.data2.dot.nb <- c(y.unknown.data2.dot.nb, data2$DOT_NB[data2[, x2] < x.range[1]])
+                #tempo.warn & indicate the interval
+            }
+            if(any(data2[, x2] > x.range[2])){
+                y.unknown.data2.dot.nb <- c(y.unknown.data2.dot.nb, data2$DOT_NB[data2[, x2] > x.range[2]])
+                #tempo.warn & indicate the interval
+            }
+            # end recover data2 dots outside the range of data1
+        }
+        # loop.ini.time <- as.numeric(Sys.time())
+        for(i1 in 0:(loop.nb + 1)){
+            min.pos <- x.range[1] + step * i1 # lower position of the sliding window in data1
+            max.pos <- min.pos + x.win.size # upper position of the sliding window in data1
+            x.data1.l <- c(x.data1.l, min.pos, min.pos + step) # min.pos + step to make the steps
+            x.data1.r <- c(x.data1.r, max.pos, max.pos + step) # max.pos + step to make the steps
+            x.data1.dot.here <- data1[, x1] >= min.pos & data1[, x1] < max.pos # is there data1 dot present in the sliding window, considering the x axis?
+            if( ! is.null(data2)){
+                x.data2.dot.here <- data2[, x2] >= min.pos & data2[, x2] < max.pos # is there data2 dot present in the sliding window, considering the x axis?
+            }
+            # recover the data1 dots outside the frame
+            if(any(x.data1.dot.here == TRUE)){
+                tempo.y.data1.top.limit <- quantile(data1[x.data1.dot.here, y1], probs = 1 - error, na.rm = TRUE)
+                tempo.y.data1.down.limit <- quantile(data1[x.data1.dot.here, y1], probs = 0 + error, na.rm = TRUE)
+                y.data1.top.limit.l <- c(y.data1.top.limit.l, tempo.y.data1.top.limit, tempo.y.data1.top.limit)
+                y.data1.down.limit.l <- c(y.data1.down.limit.l, tempo.y.data1.down.limit, tempo.y.data1.down.limit)
+                y.data1.top.limit.r <- c(y.data1.top.limit.r, tempo.y.data1.top.limit, tempo.y.data1.top.limit)
+                y.data1.down.limit.r <- c(y.data1.down.limit.r, tempo.y.data1.down.limit, tempo.y.data1.down.limit)
+                y.data1.dot.signif <- ( ! ((data1[, y1] <= tempo.y.data1.top.limit) & (data1[, y1] >= tempo.y.data1.down.limit))) & x.data1.dot.here # is there data1 dot present in the sliding window, above or below the data1 limits, considering the y axis?
+                y.data1.dot.not.signif <- x.data1.dot.here & ! y.data1.dot.signif
+                y.outside.data1.dot.nb <- c(y.outside.data1.dot.nb, data1$DOT_NB[y.data1.dot.signif]) # recover the row number of data1
+                y.outside.data1.dot.nb <- unique(y.outside.data1.dot.nb)
+                y.inside.data1.dot.nb <- c(y.inside.data1.dot.nb, data1$DOT_NB[y.data1.dot.not.signif])
+                y.inside.data1.dot.nb <- unique(y.inside.data1.dot.nb)
+            }else{
+                y.data1.top.limit.l <- c(y.data1.top.limit.l, y.data1.median, y.data1.median)
+                y.data1.down.limit.l <- c(y.data1.down.limit.l, y.data1.median, y.data1.median)
+                y.data1.top.limit.r <- c(y.data1.top.limit.r, y.data1.median, y.data1.median)
+                y.data1.down.limit.r <- c(y.data1.down.limit.r, y.data1.median, y.data1.median)
+            }
+            # end recover the data1 dots outside the frame
+            # recover the data2 dots outside the frame
+            if( ! is.null(data2)){
+                if(any(x.data1.dot.here == TRUE) & any(x.data2.dot.here == TRUE)){ 
+                    y.data2.dot.signif <- ( ! ((data2[, y2] <= tempo.y.data1.top.limit) & (data2[, y2] >= tempo.y.data1.down.limit))) & x.data2.dot.here # is there data2 dot present in the sliding window, above or below the data1 limits, considering the y axis?
+                    y.data2.dot.not.signif <- x.data2.dot.here & ! y.data2.dot.signif
+                    y.outside.data2.dot.nb <- c(y.outside.data2.dot.nb, data2$DOT_NB[y.data2.dot.signif])
+                    y.outside.data2.dot.nb <- unique(y.outside.data2.dot.nb)
+                    y.inside.data2.dot.nb <- c(y.inside.data2.dot.nb, data2$DOT_NB[y.data2.dot.not.signif])
+                    y.inside.data2.dot.nb <- unique(y.inside.data2.dot.nb)
+                }else if(any(x.data1.dot.here == FALSE) & any(x.data2.dot.here == TRUE)){ # problem: data2 dots in the the window but no data1 dots to generates the quantiles
+                    y.unknown.data2.dot.nb <- c(y.unknown.data2.dot.nb, data2$DOT_NB[x.data2.dot.here])
+                    y.unknown.data2.dot.nb <- unique(y.unknown.data2.dot.nb)
+                    #tempo.warn & indicate the interval
+                    
+                    
+                    
+                    
+                    # tempo.warn <- paste0("FROM FUNCTION ", function.name, ": THE [", round(min.pos, 3), " ; ", round(max.pos, 3), "] INTERVAL DOES NOT CONTAIN data1 X VALUES BUT CONTAINS data2 X VALUES WHICH CANNOT BE EVALUATED.\nTHE CONCERNED data2 ROW NUMBERS ARE:\n", paste(which(x.data1.dot.here == FALSE & x.data2.dot.here == TRUE), collapse = "\n"))
+                    # warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }
+            # end recover the data2 dots outside the frame
+            # if(any(i1 == seq(1, loop.nb, 500))){
+            # loop.fin.time <- as.numeric(Sys.time()) # time of process end
+            # cat(paste0("COMPUTATION TIME OF LOOP ", i1, " / ", loop.nb, ": ", as.character(lubridate::seconds_to_period(round(loop.fin.time - loop.ini.time))), "\n"))
+            # }
+        }
+        if(max.pos < x.range[2]){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": THE SLIDING WINDOW HAS NOT REACHED THE MAX VALUE OF data1 ON THE X-AXIS: ", max.pos, " VERSUS ", x.range[2])
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        y.incon.data1.dot.nb.final <- unique(c(y.outside.data1.dot.nb[y.outside.data1.dot.nb %in% y.inside.data1.dot.nb], y.inside.data1.dot.nb[y.inside.data1.dot.nb %in% y.outside.data1.dot.nb])) # inconsistent dots: if a row number of y.inside.data1.dot.nb is present in y.outside.data1.dot.nb (and vice versa), it means that during the sliding, a dot has been sometime inside, sometime outside -> removed from the outside list
+        y.outside.data1.dot.nb.final <- y.outside.data1.dot.nb[ ! (y.outside.data1.dot.nb %in% y.incon.data1.dot.nb.final)] # inconsistent dots removed from the outside list
+        y.inside.data1.dot.nb.final <- y.inside.data1.dot.nb[ ! (y.inside.data1.dot.nb %in% y.incon.data1.dot.nb.final)] # inconsistent dots removed from the inside list
+        if( ! is.null(data2)){
+            # if some unknown dots are also inside, and/or outside, they are put in the inside and/or outside. Ok, because then the intersection between inside and outside is treated -> inconsistent dots
+            tempo.unknown.out <- y.unknown.data2.dot.nb[y.unknown.data2.dot.nb %in% y.outside.data2.dot.nb]
+            y.outside.data2.dot.nb <- unique(c(y.outside.data2.dot.nb, tempo.unknown.out)) # if a row number of y.unknown.data2.dot.nb is present in y.outside.data2.dot.nb, it is put into outside
+            tempo.unknown.in <- y.unknown.data2.dot.nb[y.unknown.data2.dot.nb %in% y.inside.data2.dot.nb]
+            y.inside.data2.dot.nb <- unique(c(y.inside.data2.dot.nb, tempo.unknown.in)) # if a row number of y.unknown.data2.dot.nb is present in y.inside.data2.dot.nb, it is put into inside
+            y.unknown.data2.dot.nb.final <- y.unknown.data2.dot.nb[ ! (y.unknown.data2.dot.nb %in% c(y.outside.data2.dot.nb, y.inside.data2.dot.nb))] # then dots also in inside and outside are remove from unknown
+            y.incon.data2.dot.nb.final <- unique(c(y.outside.data2.dot.nb[y.outside.data2.dot.nb %in% y.inside.data2.dot.nb], y.inside.data2.dot.nb[y.inside.data2.dot.nb %in% y.outside.data2.dot.nb])) # inconsistent dots: if a row number of y.inside.data2.dot.nb is present in y.outside.data2.dot.nb (and vice versa), it means that during the sliding, a dot has been sometime inside, sometime outside -> removed from the outside list
+            y.outside.data2.dot.nb.final <- y.outside.data2.dot.nb[ ! (y.outside.data2.dot.nb %in% y.incon.data2.dot.nb.final)] # inconsistent dots removed from the outside list
+            y.inside.data2.dot.nb.final <- y.inside.data2.dot.nb[ ! (y.inside.data2.dot.nb %in% y.incon.data2.dot.nb.final)] # inconsistent dots removed from the inside list
+        }
+        # end x-axis sliding and y-axis limits of the data1 cloud -> y significant data2
+    }
+    # end Method using x unit interval 
+    
+    
+    
+    
+    # Method using y unit interval 
+    y.data1.d <- NULL # y coord of the x upper and lower limits defined on the data1 cloud for down step line
+    y.data1.t <- NULL # y coord of the x upper and lower limits defined on the data1 cloud for top step line
+    x.data1.left.limit.d <- NULL # left limit of the data1 cloud for down step line
+    x.data1.right.limit.d <- NULL # right limit of the data1 cloud for down step line
+    x.data1.left.limit.t <- NULL # left limit of the data1 cloud for top step line
+    x.data1.right.limit.t <- NULL # right limit of the data1 cloud for top step line
+    if( ! is.null(y.range.split)){
+        # data.frame ordering to slide the window from small to big values + sliding window definition
+        data1 <- data1[order(data1[, y1], na.last = TRUE), ]
+        if( ! is.null(data2)){
+            data2 <- data2[order(data2[, y2], na.last = TRUE), ]
+        }
+        y.win.size <- abs(diff(y.range) / y.range.split) # in unit of y-axis
+        step <- y.win.size / y.step.factor
+        # end data.frame ordering to slide the window from small to big values + sliding window definition
+        # y-axis sliding and x-axis limits of the data1 cloud -> x significant data2
+        loop.nb <- ceiling((diff(y.range) - y.win.size) / step) # y.win.size + n * step covers the y range if y.win.size + n * step >= diff(y.range), thus if n >= (diff(y.range) - y.win.size) / step 
+        x.outside.data1.dot.nb <- integer() # vector that will contain the selected rows numbers of data1 that are upper or lower than the frame
+        x.inside.data1.dot.nb <- integer() # vector that will contain the selected rows numbers of data1 that are not upper or lower than the frame
+        x.data1.median <- median(data1[, x1], na.rm = TRUE) # will be used for sliding window without data1 in it
+        if( ! is.null(data2)){
+            x.outside.data2.dot.nb <- integer() # vector that will contain the selected 1D coordinates (i.e., dots) of data2 that are upper or lower than the data1 frame
+            x.inside.data2.dot.nb <- integer() # vector that will contain the 1D coordinates (i.e., dots) of data2 that are not upper or lower than the data1 frame
+            x.unknown.data2.dot.nb <- integer() # vector that will contain the 1D coordinates (i.e., dots) of data2 that are problematic: data2 dots outside of the range of data1, or data2 dots in a sliding window without data1 dots
+            # recover data2 dots outside the range of data1
+            if(any(data2[, y2] < y.range[1])){
+                x.unknown.data2.dot.nb <- c(x.unknown.data2.dot.nb, data2$DOT_NB[data2[, y2] < y.range[1]])
+            }
+            if(any(data2[, y2] > y.range[2])){
+                x.unknown.data2.dot.nb <- c(x.unknown.data2.dot.nb, data2$DOT_NB[data2[, y2] > y.range[2]])
+            }
+            # end recover data2 dots outside the range of data1
+        }
+        # loop.ini.time <- as.numeric(Sys.time())
+        for(i1 in 0:(loop.nb + 1)){
+            min.pos <- y.range[1] + step * i1 # lower position of the sliding window in data1
+            max.pos <- min.pos + y.win.size # upper position of the sliding window in data1
+            y.data1.d <- c(y.data1.d, min.pos, min.pos + step) # min.pos + step to make the steps
+            y.data1.t <- c(y.data1.t, max.pos, max.pos + step) # max.pos + step to make the steps
+            y.data1.dot.here <- data1[, y1] >= min.pos & data1[, y1] < max.pos # is there data1 dot present in the sliding window, considering the y axis?
+            if( ! is.null(data2)){
+                y.data2.dot.here <- data2[, y2] >= min.pos & data2[, y2] < max.pos # is there data2 dot present in the sliding window, considering the y axis?
+            }
+            # recover the data1 dots outside the frame
+            if(any(y.data1.dot.here == TRUE)){
+                tempo.x.data1.right.limit <- quantile(data1[y.data1.dot.here, x1], probs = 1 - error, na.rm = TRUE)
+                tempo.x.data1.left.limit <- quantile(data1[y.data1.dot.here, x1], probs = 0 + error, na.rm = TRUE)
+                x.data1.right.limit.d <- c(x.data1.right.limit.d, tempo.x.data1.right.limit, tempo.x.data1.right.limit)
+                x.data1.left.limit.d <- c(x.data1.left.limit.d, tempo.x.data1.left.limit, tempo.x.data1.left.limit)
+                x.data1.right.limit.t <- c(x.data1.right.limit.t, tempo.x.data1.right.limit, tempo.x.data1.right.limit)
+                x.data1.left.limit.t <- c(x.data1.left.limit.t, tempo.x.data1.left.limit, tempo.x.data1.left.limit)
+                x.data1.dot.signif <- ( ! ((data1[, x1] <= tempo.x.data1.right.limit) & (data1[, x1] >= tempo.x.data1.left.limit))) & y.data1.dot.here # is there data2 dot present in the sliding window, above or below the data1 limits, considering the x axis?
+                x.data1.dot.not.signif <- y.data1.dot.here & ! x.data1.dot.signif
+                x.outside.data1.dot.nb <- c(x.outside.data1.dot.nb, data1$DOT_NB[x.data1.dot.signif]) # recover the row number of data1
+                x.outside.data1.dot.nb <- unique(x.outside.data1.dot.nb)
+                x.inside.data1.dot.nb <- c(x.inside.data1.dot.nb, data1$DOT_NB[x.data1.dot.not.signif])
+                x.inside.data1.dot.nb <- unique(x.inside.data1.dot.nb)
+            }else{
+                x.data1.right.limit.d <- c(x.data1.right.limit.d, x.data1.median, x.data1.median)
+                x.data1.left.limit.d <- c(x.data1.left.limit.d, x.data1.median, x.data1.median)
+                x.data1.right.limit.t <- c(x.data1.right.limit.t, x.data1.median, x.data1.median)
+                x.data1.left.limit.t <- c(x.data1.left.limit.t, x.data1.median, x.data1.median)
+            }
+            # end recover the data1 dots outside the frame
+            # recover the data2 dots outside the frame
+            if( ! is.null(data2)){
+                if(any(y.data1.dot.here == TRUE) & any(y.data2.dot.here == TRUE)){ 
+                    x.data2.dot.signif <- ( ! ((data2[, x2] <= tempo.x.data1.right.limit) & (data2[, x2] >= tempo.x.data1.left.limit))) & y.data2.dot.here # is there data2 dot present in the sliding window, above or below the data1 limits, considering the x axis?
+                    x.data2.dot.not.signif <- y.data2.dot.here & ! x.data2.dot.signif
+                    x.outside.data2.dot.nb <- c(x.outside.data2.dot.nb, data2$DOT_NB[x.data2.dot.signif])
+                    x.outside.data2.dot.nb <- unique(x.outside.data2.dot.nb)
+                    x.inside.data2.dot.nb <- c(x.inside.data2.dot.nb, data2$DOT_NB[x.data2.dot.not.signif])
+                    x.inside.data2.dot.nb <- unique(x.inside.data2.dot.nb)
+                }else if(any(y.data1.dot.here == FALSE) & any(y.data2.dot.here == TRUE)){ # recover the data2 dots outside the range of the data1 cloud
+                    x.unknown.data2.dot.nb <- c(x.unknown.data2.dot.nb, data2$DOT_NB[y.data2.dot.here])
+                    x.unknown.data2.dot.nb <- unique(x.unknown.data2.dot.nb)
+                    
+                    
+                    
+                    # tempo.warn <- paste0("FROM FUNCTION ", function.name, ": THE [", round(min.pos, 3), " ; ", round(max.pos, 3), "] INTERVAL DOES NOT CONTAIN data1 Y VALUES BUT CONTAINS data2 Y VALUES WHICH CANNOT BE EVALUATED.\nTHE CONCERNED data2 ROW NUMBERS ARE:\n", paste(which(y.data1.dot.here == FALSE & y.data2.dot.here == TRUE), collapse = "\n"))
+                    # warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }
+            # end recover the data2 dots outside the frame
+            # if(any(i1 == seq(1, loop.nb, 500))){
+            # loop.fin.time <- as.numeric(Sys.time()) # time of process end
+            # cat(paste0("COMPUTATION TIME OF LOOP ", i1, " / ", loop.nb, ": ", as.character(lubridate::seconds_to_period(round(loop.fin.time - loop.ini.time))), "\n"))
+            # }
+        }
+        if(max.pos < y.range[2]){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": THE SLIDING WINDOW HAS NOT REACHED THE MAX VALUE OF data1 ON THE Y-AXIS: ", max.pos, " VERSUS ", y.range[2])
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        x.incon.data1.dot.nb.final <- unique(c(x.outside.data1.dot.nb[x.outside.data1.dot.nb %in% x.inside.data1.dot.nb], x.inside.data1.dot.nb[x.inside.data1.dot.nb %in% x.outside.data1.dot.nb])) # inconsistent dots: if a row number of x.inside.data1.dot.nb is present in x.outside.data1.dot.nb (and vice versa), it means that during the sliding, a dot has been sometime inside, sometime outside -> removed from the outside list
+        x.outside.data1.dot.nb.final <- x.outside.data1.dot.nb[ ! (x.outside.data1.dot.nb %in% x.incon.data1.dot.nb.final)] # inconsistent dots removed from the outside list
+        x.inside.data1.dot.nb.final <- x.inside.data1.dot.nb[ ! (x.inside.data1.dot.nb %in% x.incon.data1.dot.nb.final)] # inconsistent dots removed from the inside list
+        if( ! is.null(data2)){
+            # if some unknown dots are also inside, and/or outside, they are put in the inside and/or outside. Ok, because then the intersection between inside and outside is treated -> inconsistent dots
+            tempo.unknown.out <- x.unknown.data2.dot.nb[x.unknown.data2.dot.nb %in% x.outside.data2.dot.nb]
+            x.outside.data2.dot.nb <- unique(c(x.outside.data2.dot.nb, tempo.unknown.out)) # if a row number of x.unknown.data2.dot.nb is present in x.outside.data2.dot.nb, it is put into outside
+            tempo.unknown.in <- x.unknown.data2.dot.nb[x.unknown.data2.dot.nb %in% x.inside.data2.dot.nb]
+            x.inside.data2.dot.nb <- unique(c(x.inside.data2.dot.nb, tempo.unknown.in)) # if a row number of x.unknown.data2.dot.nb is present in x.inside.data2.dot.nb, it is put into inside
+            x.unknown.data2.dot.nb.final <- x.unknown.data2.dot.nb[ ! (x.unknown.data2.dot.nb %in% c(x.outside.data2.dot.nb, x.inside.data2.dot.nb))] # then dots also in inside and outside are remove from unknown
+            x.incon.data2.dot.nb.final <- unique(c(x.outside.data2.dot.nb[x.outside.data2.dot.nb %in% x.inside.data2.dot.nb], x.inside.data2.dot.nb[x.inside.data2.dot.nb %in% x.outside.data2.dot.nb])) # inconsistent dots: if a row number of x.inside.data2.dot.nb is present in x.outside.data2.dot.nb (and vice versa), it means that during the sliding, a dot has been sometime inside, sometime outside -> removed from the outside list
+            x.outside.data2.dot.nb.final <- x.outside.data2.dot.nb[ ! (x.outside.data2.dot.nb %in% x.incon.data2.dot.nb.final)] # inconsistent dots removed from the outside list
+            x.inside.data2.dot.nb.final <- x.inside.data2.dot.nb[ ! (x.inside.data2.dot.nb %in% x.incon.data2.dot.nb.final)] # inconsistent dots removed from the inside list
+        }
+        # end y-axis sliding and x-axis limits of the data1 cloud -> x significant data2
+    }
+    # end Method using y unit interval 
+    
+    
+    
+    # recovering the frame coordinates
+    hframe = rbind(
+        data.frame(
+            x = if(is.null(x.data1.l)){NULL}else{x.data1.l}, 
+            y = if(is.null(x.data1.l)){NULL}else{y.data1.down.limit.l}, 
+            kind = if(is.null(x.data1.l)){NULL}else{"down.frame1"},
+            stringsAsFactors = TRUE
+        ), 
+        data.frame(
+            x = if(is.null(x.data1.r)){NULL}else{x.data1.r}, 
+            y = if(is.null(x.data1.r)){NULL}else{y.data1.down.limit.r}, 
+            kind = if(is.null(x.data1.r)){NULL}else{"down.frame2"},
+            stringsAsFactors = TRUE
+        ), 
+        data.frame(
+            x = if(is.null(x.data1.l)){NULL}else{x.data1.l}, 
+            y = if(is.null(x.data1.l)){NULL}else{y.data1.top.limit.l}, 
+            kind = if(is.null(x.data1.l)){NULL}else{"top.frame1"},
+            stringsAsFactors = TRUE
+        ), 
+        data.frame(
+            x = if(is.null(x.data1.r)){NULL}else{x.data1.r}, 
+            y = if(is.null(x.data1.r)){NULL}else{y.data1.top.limit.r}, 
+            kind = if(is.null(x.data1.r)){NULL}else{"top.frame2"},
+            stringsAsFactors = TRUE
+        ), 
+        stringsAsFactors = TRUE
+    )
+    vframe = rbind(
+        data.frame(
+            x = if(is.null(y.data1.d)){NULL}else{x.data1.left.limit.d}, 
+            y = if(is.null(y.data1.d)){NULL}else{y.data1.d}, 
+            kind = if(is.null(y.data1.d)){NULL}else{"left.frame1"},
+            stringsAsFactors = TRUE
+        ), 
+        data.frame(
+            x = if(is.null(y.data1.t)){NULL}else{x.data1.left.limit.t}, 
+            y = if(is.null(y.data1.t)){NULL}else{y.data1.t}, 
+            kind = if(is.null(y.data1.t)){NULL}else{"left.frame2"},
+            stringsAsFactors = TRUE
+        ), 
+        data.frame(
+            x = if(is.null(y.data1.d)){NULL}else{x.data1.right.limit.d}, 
+            y = if(is.null(y.data1.d)){NULL}else{y.data1.d}, 
+            kind = if(is.null(y.data1.d)){NULL}else{"right.frame1"},
+            stringsAsFactors = TRUE
+        ),
+        data.frame(
+            x = if(is.null(y.data1.t)){NULL}else{x.data1.right.limit.t}, 
+            y = if(is.null(y.data1.t)){NULL}else{y.data1.t}, 
+            kind = if(is.null(y.data1.t)){NULL}else{"right.frame2"},
+            stringsAsFactors = TRUE
+        ), 
+        stringsAsFactors = TRUE
+    )
+    # end recovering the frame coordinates
+    # recovering the dot coordinates
+    data1.signif.dot <- NULL
+    data1.non.signif.dot <- NULL
+    data1.incon.dot <- NULL
+    data2.signif.dot <- NULL
+    data2.non.signif.dot <- NULL
+    data2.unknown.dot <- NULL
+    data2.incon.dot <- NULL
+    if(( ! is.null(x.range.split)) & ( ! is.null(y.range.split))){
+        # inconsistent dots recovery 
+        if(length(unique(c(x.incon.data1.dot.nb.final, y.incon.data1.dot.nb.final))) > 0){
+            data1.incon.dot <- data1[data1$DOT_NB %in% unique(c(x.incon.data1.dot.nb.final, y.incon.data1.dot.nb.final)), ] # if a dot in inconsistent in x or y -> classified as inconsistent (so unique() used)
+            # removal of the inconsistent dot in the other classifications
+            x.inside.data1.dot.nb.final <- x.inside.data1.dot.nb.final[ ! x.inside.data1.dot.nb.final %in% data1.incon.dot$DOT_NB]
+            y.inside.data1.dot.nb.final <- y.inside.data1.dot.nb.final[ ! y.inside.data1.dot.nb.final %in% data1.incon.dot$DOT_NB]
+            x.outside.data1.dot.nb.final <- x.outside.data1.dot.nb.final[ ! x.outside.data1.dot.nb.final %in% data1.incon.dot$DOT_NB]
+            y.outside.data1.dot.nb.final <- y.outside.data1.dot.nb.final[ ! y.outside.data1.dot.nb.final %in% data1.incon.dot$DOT_NB]
+            x.unknown.data1.dot.nb.final <- x.unknown.data1.dot.nb.final[ ! x.unknown.data1.dot.nb.final %in% data1.incon.dot$DOT_NB]
+            y.unknown.data1.dot.nb.final <- y.unknown.data1.dot.nb.final[ ! y.unknown.data1.dot.nb.final %in% data1.incon.dot$DOT_NB]
+            # end removal of the inconsistent dot in the other classifications
+        }
+        if( ! is.null(data2)){
+            if(length(unique(c(x.incon.data2.dot.nb.final, y.incon.data2.dot.nb.final))) > 0){
+                data2.incon.dot <- data2[data2$DOT_NB %in% unique(c(x.incon.data2.dot.nb.final, y.incon.data2.dot.nb.final)), ]
+                # removal of the inconsistent dot in the other classifications
+                x.inside.data2.dot.nb.final <- x.inside.data2.dot.nb.final[ ! x.inside.data2.dot.nb.final %in% data2.incon.dot$DOT_NB]
+                y.inside.data2.dot.nb.final <- y.inside.data2.dot.nb.final[ ! y.inside.data2.dot.nb.final %in% data2.incon.dot$DOT_NB]
+                x.outside.data2.dot.nb.final <- x.outside.data2.dot.nb.final[ ! x.outside.data2.dot.nb.final %in% data2.incon.dot$DOT_NB]
+                y.outside.data2.dot.nb.final <- y.outside.data2.dot.nb.final[ ! y.outside.data2.dot.nb.final %in% data2.incon.dot$DOT_NB]
+                x.unknown.data2.dot.nb.final <- x.unknown.data2.dot.nb.final[ ! x.unknown.data2.dot.nb.final %in% data2.incon.dot$DOT_NB]
+                y.unknown.data2.dot.nb.final <- y.unknown.data2.dot.nb.final[ ! y.unknown.data2.dot.nb.final %in% data2.incon.dot$DOT_NB]
+                # end removal of the inconsistent dot in the other classifications
+            }
+        }
+        # end inconsistent dots recovery 
+        # unknown dots recovery 
+        if( ! is.null(data2)){
+            if(data2.pb.dot == "signif"){
+                x.outside.data2.dot.nb.final <- unique(c(x.outside.data2.dot.nb.final, x.unknown.data2.dot.nb.final))
+                x.inside.data2.dot.nb.final <- x.inside.data2.dot.nb.final[ ! x.inside.data2.dot.nb.final %in% x.unknown.data2.dot.nb.final] # remove x.unknown.data2.dot.nb.final from x.inside.data2.dot.nb.final
+                y.outside.data2.dot.nb.final <- unique(c(y.outside.data2.dot.nb.final, y.unknown.data2.dot.nb.final))
+                y.inside.data2.dot.nb.final <- y.inside.data2.dot.nb.final[ ! y.inside.data2.dot.nb.final %in% y.unknown.data2.dot.nb.final] # remove y.unknown.data2.dot.nb.final from y.inside.data2.dot.nb.final
+                x.unknown.data2.dot.nb.final <- NULL
+                y.unknown.data2.dot.nb.final <- NULL
+                data2.unknown.dot <- NULL
+            }else if(data2.pb.dot == "not.signif"){
+                x.inside.data2.dot.nb.final <- unique(c(x.inside.data2.dot.nb.final, x.unknown.data2.dot.nb.final))
+                x.outside.data2.dot.nb.final <- x.outside.data2.dot.nb.final[ ! x.outside.data2.dot.nb.final %in% x.unknown.data2.dot.nb.final] # remove x.unknown.data2.dot.nb.final from x.outside.data2.dot.nb.final
+                y.inside.data2.dot.nb.final <- unique(c(y.inside.data2.dot.nb.final, y.unknown.data2.dot.nb.final))
+                y.outside.data2.dot.nb.final <- y.outside.data2.dot.nb.final[ ! y.outside.data2.dot.nb.final %in% y.unknown.data2.dot.nb.final] # remove y.unknown.data2.dot.nb.final from y.outside.data2.dot.nb.final
+                x.unknown.data2.dot.nb.final <- NULL
+                y.unknown.data2.dot.nb.final <- NULL
+                data2.unknown.dot <- NULL
+            }else if(data2.pb.dot == "unknown"){
+                if(length(unique(c(x.unknown.data2.dot.nb.final, y.unknown.data2.dot.nb.final))) > 0){
+                    data2.unknown.dot <- data2[data2$DOT_NB %in% unique(c(x.unknown.data2.dot.nb.final, y.unknown.data2.dot.nb.final)), ] # if a dot in unknown in x or y -> classified as unknown (so unique() used)
+                    x.outside.data2.dot.nb.final <- x.outside.data2.dot.nb.final[ ! x.outside.data2.dot.nb.final %in% data2.unknown.dot$DOT_NB] # remove x.unknown.data2.dot.nb.final from x.outside.data2.dot.nb.final
+                    x.inside.data2.dot.nb.final <- x.inside.data2.dot.nb.final[ ! x.inside.data2.dot.nb.final %in% data2.unknown.dot$DOT_NB] # remove x.unknown.data2.dot.nb.final from x.inside.data2.dot.nb.final
+                    y.outside.data2.dot.nb.final <- y.outside.data2.dot.nb.final[ ! y.outside.data2.dot.nb.final %in% data2.unknown.dot$DOT_NB] # remove y.unknown.data2.dot.nb.final from y.outside.data2.dot.nb.final
+                    y.inside.data2.dot.nb.final <- y.inside.data2.dot.nb.final[ ! y.inside.data2.dot.nb.final %in% data2.unknown.dot$DOT_NB] # remove y.unknown.data2.dot.nb.final from y.inside.data2.dot.nb.final
+                }
+            }else{
+                tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 3")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+        }
+        # end unknown dots recovery 
+        # sign and non sign dot recovery
+        if(xy.cross.kind == "|"){ # here the problem is to deal with significant dots depending on x and y. Thus I start with that, recover dots finally non significant in outside and put them in inside (when &), and remove from inside the dots in outside
+            if(length(unique(c(x.outside.data1.dot.nb.final, y.outside.data1.dot.nb.final))) > 0){
+                tempo.outside <- unique(c(x.outside.data1.dot.nb.final, y.outside.data1.dot.nb.final)) # union so unique() used
+                tempo.inside <- unique(c(x.inside.data1.dot.nb.final, y.inside.data1.dot.nb.final))
+                tempo.inside <- tempo.inside[ ! tempo.inside %in% tempo.outside]
+                data1.signif.dot <- data1[data1$DOT_NB %in% tempo.outside, ]
+                data1.non.signif.dot <- data1[data1$DOT_NB %in% tempo.inside, ]
+            }else{
+                data1.non.signif.dot <- data1[unique(c(x.inside.data1.dot.nb.final, y.inside.data1.dot.nb.final)), ] # if no outside dots, I recover all the inside dots and that's it
+            }
+        }else if(xy.cross.kind == "&"){
+            if(sum(x.outside.data1.dot.nb.final %in% y.outside.data1.dot.nb.final) > 0){ # that is intersection
+                tempo.outside <- unique(x.outside.data1.dot.nb.final[x.outside.data1.dot.nb.final %in% y.outside.data1.dot.nb.final]) # intersection
+                tempo.outside.removed <- unique(c(x.outside.data1.dot.nb.final, y.outside.data1.dot.nb.final))[ ! unique(c(x.outside.data1.dot.nb.final, y.outside.data1.dot.nb.final)) %in% tempo.outside]
+                tempo.inside <- unique(c(x.inside.data1.dot.nb.final, y.inside.data1.dot.nb.final))
+                data1.signif.dot <- data1[data1$DOT_NB %in% tempo.outside, ]
+                data1.non.signif.dot <- data1[data1$DOT_NB %in% tempo.inside, ]
+            }else{
+                data1.non.signif.dot <- data1[unique(c(x.inside.data1.dot.nb.final, y.inside.data1.dot.nb.final)), ] # if no outside dots, I recover all the inside dots and that's it
+            }
+        }else{
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 4")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if( ! is.null(data2)){
+            if(xy.cross.kind == "|"){ # here the problem is to deal with significant dots depending on x and y. Thus I start with that, recover dots finally non significant in outside and put them in inside (when &), and remove from inside the dots in outside
+                if(length(unique(c(x.outside.data2.dot.nb.final, y.outside.data2.dot.nb.final))) > 0){
+                    tempo.outside <- unique(c(x.outside.data2.dot.nb.final, y.outside.data2.dot.nb.final)) # union so unique() used
+                    tempo.inside <- unique(c(x.inside.data2.dot.nb.final, y.inside.data2.dot.nb.final))
+                    tempo.inside <- tempo.inside[ ! tempo.inside %in% tempo.outside]
+                    data2.signif.dot <- data2[data2$DOT_NB %in% tempo.outside, ]
+                    data2.non.signif.dot <- data2[data2$DOT_NB %in% tempo.inside, ]
+                }else{
+                    data2.non.signif.dot <- data2[unique(c(x.inside.data2.dot.nb.final, y.inside.data2.dot.nb.final)), ] # if no outside dots, I recover all the inside dots and that's it
+                }
+            }else if(xy.cross.kind == "&"){
+                if(sum(x.outside.data2.dot.nb.final %in% y.outside.data2.dot.nb.final) > 0){ # that is intersection
+                    tempo.outside <- unique(x.outside.data2.dot.nb.final[x.outside.data2.dot.nb.final %in% y.outside.data2.dot.nb.final]) # intersection
+                    tempo.outside.removed <- unique(c(x.outside.data2.dot.nb.final, y.outside.data2.dot.nb.final))[ ! unique(c(x.outside.data2.dot.nb.final, y.outside.data2.dot.nb.final)) %in% tempo.outside]
+                    tempo.inside <- unique(c(x.inside.data2.dot.nb.final, y.inside.data2.dot.nb.final))
+                    data2.signif.dot <- data2[data2$DOT_NB %in% tempo.outside, ]
+                    data2.non.signif.dot <- data2[data2$DOT_NB %in% tempo.inside, ]
+                }else{
+                    data2.non.signif.dot <- data2[unique(c(x.inside.data2.dot.nb.final, y.inside.data2.dot.nb.final)), ] # if no outside dots, I recover all the inside dots and that's it
+                }
+            }else{
+                tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 5")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+        }
+        # end sign and non sign dot recovery
+    }else if(( ! is.null(x.range.split)) & is.null(y.range.split)){
+        # inconsistent dots recovery 
+        if(length(y.incon.data1.dot.nb.final) > 0){
+            data1.incon.dot <- data1[data1$DOT_NB %in% y.incon.data1.dot.nb.final, ]
+        }
+        if( ! is.null(data2)){
+            if(length(y.incon.data2.dot.nb.final) > 0){
+                data2.incon.dot <- data2[data2$DOT_NB %in% y.incon.data2.dot.nb.final, ]
+            }
+        }# end inconsistent dots recovery 
+        # unknown dots recovery 
+        if( ! is.null(data2)){
+            if(data2.pb.dot == "signif"){
+                y.outside.data2.dot.nb.final <- unique(c(y.outside.data2.dot.nb.final, y.unknown.data2.dot.nb.final))
+            }else if(data2.pb.dot == "not.signif"){
+                y.inside.data2.dot.nb.final <- unique(c(y.inside.data2.dot.nb.final, y.unknown.data2.dot.nb.final))
+            }else if(data2.pb.dot == "unknown"){
+                if(length(y.unknown.data2.dot.nb.final) > 0){
+                    data2.unknown.dot <- data2[data2$DOT_NB %in% y.unknown.data2.dot.nb.final, ]
+                }
+            }else{
+                tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 6")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+        }
+        # end unknown dots recovery 
+        # sign and non sign dot recovery
+        if(length(y.outside.data1.dot.nb.final) > 0){
+            data1.signif.dot <- data1[data1$DOT_NB %in% y.outside.data1.dot.nb.final, ]
+        }
+        if(length(y.inside.data1.dot.nb.final) > 0){
+            data1.non.signif.dot <- data1[data1$DOT_NB %in% y.inside.data1.dot.nb.final, ]
+        }
+        if( ! is.null(data2)){
+            if(length(y.outside.data2.dot.nb.final) > 0){
+                data2.signif.dot <- data2[data2$DOT_NB %in% y.outside.data2.dot.nb.final, ]
+            }
+            if(length(y.inside.data2.dot.nb.final) > 0){
+                data2.non.signif.dot <- data2[data2$DOT_NB %in% y.inside.data2.dot.nb.final, ]
+            }
+        }
+        # end sign and non sign dot recovery
+    }else if(is.null(x.range.split) & ( ! is.null(y.range.split))){
+        # inconsistent dots recovery 
+        if(length(x.incon.data1.dot.nb.final) > 0){
+            data1.incon.dot <- data1[data1$DOT_NB %in% x.incon.data1.dot.nb.final, ]
+        }
+        if( ! is.null(data2)){
+            if(length(x.incon.data2.dot.nb.final) > 0){
+                data2.incon.dot <- data2[data2$DOT_NB %in% x.incon.data2.dot.nb.final, ]
+            }
+        }# end inconsistent dots recovery 
+        # unknown dots recovery 
+        if( ! is.null(data2)){
+            if(data2.pb.dot == "signif"){
+                x.outside.data2.dot.nb.final <- unique(c(x.outside.data2.dot.nb.final, x.unknown.data2.dot.nb.final))
+            }else if(data2.pb.dot == "not.signif"){
+                x.inside.data2.dot.nb.final <- unique(c(x.inside.data2.dot.nb.final, x.unknown.data2.dot.nb.final))
+            }else if(data2.pb.dot == "unknown"){
+                if(length(x.unknown.data2.dot.nb.final) > 0){
+                    data2.unknown.dot <- data2[data2$DOT_NB %in% x.unknown.data2.dot.nb.final, ]
+                }
+            }else{
+                tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 7")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+        }
+        # end unknown dots recovery 
+        # sign and non sign dot recovery
+        if(length(x.outside.data1.dot.nb.final) > 0){
+            data1.signif.dot <- data1[data1$DOT_NB %in% x.outside.data1.dot.nb.final, ]
+        }
+        if(length(x.inside.data1.dot.nb.final) > 0){
+            data1.non.signif.dot <- data1[data1$DOT_NB %in% x.inside.data1.dot.nb.final, ]
+        }
+        if( ! is.null(data2)){
+            if(length(x.outside.data2.dot.nb.final) > 0){
+                data2.signif.dot <- data2[data2$DOT_NB %in% x.outside.data2.dot.nb.final, ]
+            }
+            if(length(x.inside.data2.dot.nb.final) > 0){
+                data2.non.signif.dot <- data2[data2$DOT_NB %in% x.inside.data2.dot.nb.final, ]
+            }
+        }
+        # end sign and non sign dot recovery
+    }
+    # end recovering the dot coordinates
+    # verif
+    if(any(data1.signif.dot$DOT_NB %in% data1.non.signif.dot$DOT_NB)){
+        tempo.cat <- paste0("ERROR IN ", FUNCTION.NAME, ": CODE INCONSISTENCY 8")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(any(data1.non.signif.dot$DOT_NB %in% data1.signif.dot$DOT_NB)){
+        tempo.cat <- paste0("ERROR IN ", FUNCTION.NAME, ": CODE INCONSISTENCY 9")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(any(data1.signif.dot$DOT_NB %in% data1.incon.dot$DOT_NB)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 10")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(any(data1.incon.dot$DOT_NB %in% data1.signif.dot$DOT_NB)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 11")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(any(data1.non.signif.dot$DOT_NB %in% data1.incon.dot$DOT_NB)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 12")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(any(data1.incon.dot$DOT_NB %in% data1.non.signif.dot$DOT_NB)){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 13")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! is.null(data2)){
+        if(any(data2.signif.dot$DOT_NB %in% data2.non.signif.dot$DOT_NB)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 14")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(data2.non.signif.dot$DOT_NB %in% data2.signif.dot$DOT_NB)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 15")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(data2.signif.dot$DOT_NB %in% data2.unknown.dot$DOT_NB)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 16")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(data2.unknown.dot$DOT_NB %in% data2.signif.dot$DOT_NB)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 17")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(data2.signif.dot$DOT_NB %in% data2.incon.dot$DOT_NB)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 18")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(data2.incon.dot$DOT_NB %in% data2.signif.dot$DOT_NB)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 19")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(data2.non.signif.dot$DOT_NB %in% data2.unknown.dot$DOT_NB)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 20")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(data2.unknown.dot$DOT_NB %in% data2.non.signif.dot$DOT_NB)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 21")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(data2.non.signif.dot$DOT_NB %in% data2.incon.dot$DOT_NB)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 22")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(data2.incon.dot$DOT_NB %in% data2.non.signif.dot$DOT_NB)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 23")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(data2.unknown.dot$DOT_NB %in% data2.incon.dot$DOT_NB)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 24")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(data2.incon.dot$DOT_NB %in% data2.unknown.dot$DOT_NB)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 25")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # end verif
+    # plot
+    # recovering the axes data whatever plot or not
+    if(is.null(data2)){
+        axes <- fun_gg_scatter(data1 = list(data1), x = list(x1), y = list(y1), categ = list(NULL), color = list(fun_gg_palette(2)[2]), geom = list("geom_point"), alpha = list(0.5), x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, plot = FALSE, return = TRUE)$axes
+    }else{
+        axes <- fun_gg_scatter(data1 = list(data1, data2), x = list(x1, x2), y = list(y1, y2), categ = list(NULL, NULL), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1]), geom = list("geom_point", "geom_point"), alpha = list(0.5, 0.5), x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, plot = FALSE, return = TRUE)$axes
+    }
+    # end recovering the axes data whatever plot or not
+    if(plot == TRUE){
+        # add a categ for plot legend
+        tempo.df.name <- c("data1", "data1.signif.dot", "data1.incon.dot", "data2", "data2.signif.dot", "data2.unknown.dot", "data2.incon.dot")
+        tempo.class.name <- c("data1", "data1", "data1", "data2", "data2", "data2", "data2")
+        for(i2 in 1:length(tempo.df.name)){
+            if( ! is.null(get(tempo.df.name[i2], env = sys.nframe(), inherit = FALSE))){
+                assign(tempo.df.name[i2], data.frame(get(tempo.df.name[i2], env = sys.nframe(), inherit = FALSE), kind = tempo.class.name[i2]),
+                       stringsAsFactors = TRUE)
+            }
+        }
+        # end add a categ for plot legend
+        if(( ! is.null(x.range.split)) & ( ! is.null(y.range.split))){
+            if(graph.in.file == FALSE){
+                fun_open(pdf = FALSE)
+            }
+            tempo.graph <- fun_gg_scatter(data1 = list(data1, hframe, vframe), x = list(x1, "x", "x"), y = list(y1, "y", "y"), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "HORIZ FRAME" , "VERT FRAME"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_path", "geom_path"), alpha = list(0.5, 0.5, 0.5), title = "DATA1", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+            if( ! is.null(tempo.graph$warn)){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+            if( ! is.null(data1.signif.dot)){
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                tempo.graph <- fun_gg_scatter(data1 = list(data1, hframe, vframe, data1.signif.dot), x = list(x1, "x", "x", x1), y = list(y1, "y", "y", y1), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "HORIZ FRAME" , "VERT FRAME", "SIGNIF DOTS"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2), "black"), geom = list("geom_point", "geom_path", "geom_path", "geom_point"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA1 SIGNIFICANT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                if( ! is.null(tempo.graph$warn)){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }else{
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA1 DOTS\nOUTSIDE THE FRAMES", text.size = 8, title = "DATA1 + DATA1 SIGNIFICANT DOTS")
+            }
+            if( ! is.null(data1.incon.dot)){
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                tempo.graph <- fun_gg_scatter(data1 = list(data1, hframe, vframe, data1.incon.dot), x = list(x1, "x", "x", x1), y = list(y1, "y", "y", y1), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "HORIZ FRAME" , "VERT FRAME", "INCONSISTENT DOTS"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2), fun_gg_palette(7)[6]), geom = list("geom_point", "geom_path", "geom_path", "geom_point"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA1 INCONSISTENT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                if( ! is.null(tempo.graph$warn)){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }else{
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA1\nINCONSISTENT DOTS", text.size = 8, title = "DATA1 + DATA1 INCONSISTENT DOTS")
+            }
+            if( ! is.null(data2)){
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, hframe , vframe), x = list(x1, x2, "x", "x"), y = list(y1, y2, "y", "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "HORIZ FRAME" , "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_path", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                if( ! is.null(tempo.graph$warn)){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+                if( ! is.null(data2.signif.dot)){
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.signif.dot, hframe , vframe), x = list(x1, x2, x2, "x", "x"), y = list(y1, y2, y2, "y", "y"), categ = list("kind", "kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "SIGNIF DOTS", "HORIZ FRAME" , "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], "black", rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 SIGNIFICANT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                    if( ! is.null(tempo.graph$warn)){
+                        warn.count <- warn.count + 1
+                        tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    }
+                }else{
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2 DOTS\nOUTSIDE THE FRAMES", text.size = 8, title = "DATA1 + DATA2 + DATA2 SIGNIFICANT DOTS")
+                }
+                if( ! is.null(data2.incon.dot)){
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.incon.dot, hframe , vframe), x = list(x1, x2, x2, "x", "x"), y = list(y1, y2, y2, "y", "y"), categ = list("kind", "kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "INCONSISTENT DOTS", "HORIZ FRAME" , "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], fun_gg_palette(7)[6], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 INCONSISTENT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                    if( ! is.null(tempo.graph$warn)){
+                        warn.count <- warn.count + 1
+                        tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    }
+                }else{
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2\nINCONSISTENT DOTS", text.size = 8, title = "DATA2 + DATA2 INCONSISTENT DOTS")
+                }
+                if( ! is.null(data2.unknown.dot)){
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.unknown.dot, hframe , vframe), x = list(x1, x2, x2, "x", "x"), y = list(y1, y2, y2, "y", "y"), categ = list("kind", "kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "UNKNOWN DOTS", "HORIZ FRAME" , "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], fun_gg_palette(7)[5], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 UNKNOWN DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                    
+                    if( ! is.null(tempo.graph$warn)){
+                        warn.count <- warn.count + 1
+                        tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    }
+                }else{
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2\nUNKNOWN DOTS", text.size = 12, title = "DATA2 + DATA2 UNKNOWN DOTS")
+                }
+            }
+        }else if(( ! is.null(x.range.split)) & is.null(y.range.split)){
+            if(graph.in.file == FALSE){
+                fun_open(pdf = FALSE)
+            }
+            tempo.graph <- fun_gg_scatter(data1 = list(data1, hframe), x = list(x1, "x"), y = list(y1, "y"), categ = list("kind", "kind"), legend.name = list("DATASET", "HORIZ FRAME"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2)), geom = list("geom_point", "geom_path"), alpha = list(0.5, 0.5), title = "DATA1", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+            if( ! is.null(tempo.graph$warn)){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+            if( ! is.null(data1.signif.dot)){
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                tempo.graph <- fun_gg_scatter(data1 = list(data1, hframe, data1.signif.dot), x = list(x1, "x", x1), y = list(y1, "y", y1), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "HORIZ FRAME", "SIGNIF DOTS"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), "black"), geom = list("geom_point", "geom_path", "geom_point"), alpha = list(0.5, 0.5, 0.5), title = "DATA1 + DATA1 SIGNIFICANT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                if( ! is.null(tempo.graph$warn)){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }else{
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA1 DOTS\nOUTSIDE THE FRAMES", text.size = 8, title = "DATA1 + DATA1 SIGNIFICANT DOTS")
+            }
+            if( ! is.null(data1.incon.dot)){
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                tempo.graph <- fun_gg_scatter(data1 = list(data1, hframe, data1.incon.dot), x = list(x1, "x", x1), y = list(y1, "y", y1), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "HORIZ FRAME", "INCONSISTENT DOTS"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2), fun_gg_palette(7)[6]), geom = list("geom_point", "geom_path", "geom_point"), alpha = list(0.5, 0.5, 0.5), title = "DATA1 + DATA1 INCONSISTENT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                if( ! is.null(tempo.graph$warn)){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }else{
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA1\nINCONSISTENT DOTS", text.size = 8, title = "DATA1 + DATA1 INCONSISTENT DOTS")
+            }
+            if( ! is.null(data2)){
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, hframe), x = list(x1, x2, "x"), y = list(y1, y2, "y"), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "HORIZ FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2)), geom = list("geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5), title = "DATA1 + DATA2", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                if( ! is.null(tempo.graph$warn)){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+                if( ! is.null(data2.signif.dot)){
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.signif.dot, hframe), x = list(x1, x2, x2, "x"), y = list(y1, y2, y2, "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "SIGNIF DOTS", "HORIZ FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], "black", rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 SIGNIFICANT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                    if( ! is.null(tempo.graph$warn)){
+                        warn.count <- warn.count + 1
+                        tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    }
+                }else{
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2 DOTS\nOUTSIDE THE FRAMES", text.size = 8, title = "DATA1 + DATA2 + DATA2 SIGNIFICANT DOTS")
+                }
+                if( ! is.null(data2.incon.dot)){
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.incon.dot, hframe), x = list(x1, x2, x2, "x"), y = list(y1, y2, y2, "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "INCONSISTENT DOTS", "HORIZ FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], fun_gg_palette(7)[6], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 INCONSISTENT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                    if( ! is.null(tempo.graph$warn)){
+                        warn.count <- warn.count + 1
+                        tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    }
+                }else{
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2\nINCONSISTENT DOTS", text.size = 8, title = "DATA2 + DATA2 INCONSISTENT DOTS")
+                }
+                if( ! is.null(data2.unknown.dot)){
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.unknown.dot, hframe), x = list(x1, x2, x2, "x"), y = list(y1, y2, y2, "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "UNKNOWN DOTS", "HORIZ FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], fun_gg_palette(7)[5], rep(hsv(h = c(0.1, 0.15), v = c(0.75, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 UNKNOWN DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                    if( ! is.null(tempo.graph$warn)){
+                        warn.count <- warn.count + 1
+                        tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    }
+                }else{
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2\nUNKNOWN DOTS", text.size = 8, title = "DATA2 + DATA2 UNKNOWN DOTS")
+                }
+            }
+        }else if(is.null(x.range.split) & ( ! is.null(y.range.split))){
+            if(graph.in.file == FALSE){
+                fun_open(pdf = FALSE)
+            }
+            tempo.graph <- fun_gg_scatter(data1 = list(data1, vframe), x = list(x1, "x"), y = list(y1, "y"), categ = list("kind", "kind"), legend.name = list("DATASET", "VERT FRAME"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_path"), alpha = list(0.5, 0.5), title = "DATA1", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+            if( ! is.null(tempo.graph$warn)){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+            if( ! is.null(data1.signif.dot)){
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                tempo.graph <- fun_gg_scatter(data1 = list(data1, vframe, data1.signif.dot), x = list(x1, "x", x1), y = list(y1, "y", y1), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "VERT FRAME", "SIGNIF DOTS"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2), "black"), geom = list("geom_point", "geom_path", "geom_point"), alpha = list(0.5, 0.5, 0.5), title = "DATA1 + DATA1 SIGNIFICANT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                if( ! is.null(tempo.graph$warn)){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }else{
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA1 DOTS\nOUTSIDE THE FRAMES", text.size = 8, title = "DATA1 + DATA1 SIGNIFICANT DOTS")
+            }
+            if( ! is.null(data1.incon.dot)){
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                tempo.graph <- fun_gg_scatter(data1 = list(data1, vframe, data1.incon.dot), x = list(x1, "x", x1), y = list(y1, "y", y1), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "VERT FRAME", "INCONSISTENT DOTS"), color = list(fun_gg_palette(2)[2], rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2), fun_gg_palette(7)[6]), geom = list("geom_point", "geom_path", "geom_point"), alpha = list(0.5, 0.5, 0.5), title = "DATA1 + DATA1 INCONSISTENT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                if( ! is.null(tempo.graph$warn)){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }else{
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA1\nINCONSISTENT DOTS", text.size = 8, title = "DATA1 + DATA1 INCONSISTENT DOTS")
+            }
+            if( ! is.null(data2)){
+                if(graph.in.file == FALSE){
+                    fun_open(pdf = FALSE)
+                }
+                tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, vframe), x = list(x1, x2, "x"), y = list(y1, y2, "y"), categ = list("kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5), title = "DATA1 + DATA2", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                if( ! is.null(tempo.graph$warn)){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+                if( ! is.null(data2.signif.dot)){
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.signif.dot, vframe), x = list(x1, x2, x2, "x"), y = list(y1, y2, y2, "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "SIGNIF DOTS", "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], "black", rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 SIGNIFICANT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                    if( ! is.null(tempo.graph$warn)){
+                        warn.count <- warn.count + 1
+                        tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    }
+                }else{
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2 DOTS\nOUTSIDE THE FRAMES", text.size = 8, title = "DATA1 + DATA2 + DATA2 SIGNIFICANT DOTS")
+                }
+                if( ! is.null(data2.incon.dot)){
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.incon.dot, vframe), x = list(x1, x2, x2, "x"), y = list(y1, y2, y2, "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "INCONSISTENT DOTS", "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], fun_gg_palette(7)[6], rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 INCONSISTENT DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                    if( ! is.null(tempo.graph$warn)){
+                        warn.count <- warn.count + 1
+                        tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    }
+                }else{
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2\nINCONSISTENT DOTS", text.size = 8, title = "DATA2 + DATA2 INCONSISTENT DOTS")
+                }
+                if( ! is.null(data2.unknown.dot)){
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    tempo.graph <- fun_gg_scatter(data1 = list(data1, data2, data2.unknown.dot, vframe), x = list(x1, x2, x2, "x"), y = list(y1, y2, y2, "y"), categ = list("kind", "kind", "kind", "kind"), legend.name = list("DATASET", "DATASET", "UNKNOWN DOTS", "VERT FRAME"), color = list(fun_gg_palette(2)[2], fun_gg_palette(2)[1], fun_gg_palette(7)[5], rep(hsv(h = c(0.5, 0.6), v = c(0.9, 1)), 2)), geom = list("geom_point", "geom_point", "geom_point", "geom_path"), alpha = list(0.5, 0.5, 0.5, 0.5), title = "DATA1 + DATA2 + DATA2 UNKNOWN DOTS", x.lim = x.range.plot, y.lim = y.range.plot, raster = raster, return = TRUE)
+                    if( ! is.null(tempo.graph$warn)){
+                        warn.count <- warn.count + 1
+                        tempo.warn <- paste0("(", warn.count,") FROM fun_gg_scatter():\n", tempo.graph$warn)
+                        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    }
+                }else{
+                    if(graph.in.file == FALSE){
+                        fun_open(pdf = FALSE)
+                    }
+                    fun_gg_empty_graph(text = "NO PLOT\nBECAUSE\nNO DATA2\nUNKNOWN DOTS", text.size = 8, title = "DATA2 + DATA2 UNKNOWN DOTS")
+                }
+            }
+        }
+    }
+    # end plot
+    if(warn.print == TRUE & ! is.null(warn)){
+        options(warning.length = 8170)
+        on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
+    }
+    on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
+    tempo.list <- list(data1.removed.row.nb = data1.removed.row.nb, data1.removed.rows = data1.removed.rows, data2.removed.row.nb = data2.removed.row.nb, data2.removed.rows = data2.removed.rows, hframe = hframe, vframe = vframe, data1.signif.dot = data1.signif.dot, data1.non.signif.dot = data1.non.signif.dot, data1.inconsistent.dot = data1.incon.dot, data2.signif.dot = data2.signif.dot, data2.non.signif.dot = data2.non.signif.dot, data2.unknown.dot = data2.unknown.dot, data2.inconsistent.dot = data2.incon.dot, axes = axes, warn = warn)
+    return(tempo.list)
 }
-if(line.count== 3L){
-fin.lg.disp[[6]] <- legend.disp[[point.count + line.count]]
-lg.order[[6]] <- point.count + line.count
-lg.color[[6]] <- color[[i1]] # if color == NULL -> NULL
-lg.line.size[[6]] <- line.size[[i1]]
-lg.line.type[[6]] <- line.type[[i1]]
-if(plot == TRUE & fin.lg.disp[[6]] == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list())== 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE LINES (LINE LAYER NUMBER ", line.count, ") IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-lg.alpha[[6]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
-}else{
-lg.alpha[[6]] <- alpha[[i1]]
+
+
+################ Import
+
+
+######## fun_pack() #### check if R packages are present and import into the working environment
+
+
+fun_pack <- function(
+    req.package, 
+    load = FALSE, 
+    lib.path = NULL
+){
+    # AIM
+    # check if the specified R packages are present in the computer and import them into the working environment
+    # ARGUMENTS
+    # req.package: character vector of package names to import
+    # load: logical. Load the package into the environement (using library())? Interesting if packages are not in default folders or for checking the functions names of packages using search()
+    # lib.path: optional character vector specifying the absolute pathways of the directories containing some of the listed packages in the req.package argument, if not in the default directories. Ignored if NULL
+    # RETURN
+    # nothing
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # fun_pack(req.package = "nopackage")
+    # fun_pack(req.package = "ggplot2")
+    # fun_pack(req.package = "ggplot2", lib.path = "blablabla")
+    # DEBUGGING
+    # req.package = "ggplot2" ; lib.path = "C:/Program Files/R/R-3.5.1/library"
+    # req.package = "serpentine" ; lib.path = "C:/users/gael/appdata/roaming/python/python36/site-packages"
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = req.package, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = load, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(lib.path)){
+        tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
+                tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    if(is.null(lib.path)){
+        lib.path <- .libPaths() # .libPaths(new = lib.path) # or .libPaths(new = c(.libPaths(), lib.path))
+    }else{
+        .libPaths(new = sub(x = lib.path, pattern = "/$|\\\\$", replacement = "")) # .libPaths(new = ) add path to default path. BEWARE: .libPaths() does not support / at the end of a submitted path. Thus check and replace last / or \\ in path
+        lib.path <- .libPaths()
+    }
+    tempo <- NULL
+    for(i1 in 1:length(req.package)){
+        if( ! req.package[i1] %in% rownames(utils::installed.packages(lib.loc = lib.path))){
+            tempo <- c(tempo, req.package[i1])
+        }
+    }
+    if( ! is.null(tempo)){
+        tempo.cat <- paste0(
+            "ERROR IN ", 
+            function.name, 
+            ": PACKAGE", 
+            ifelse(length(tempo) == 1L, paste0("\n\n", tempo, "\n\n"), paste0("S\n", paste(tempo, collapse = "\n"), "\n")), 
+            "MUST BE INSTALLED IN", 
+            ifelse(length(lib.path) == 1L, "", " ONE OF THESE FOLDERS"), 
+            ":\n", 
+            paste(lib.path, collapse = "\n")
+        )
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else if(load == TRUE){
+        for(i2 in 1:length(req.package)){
+            suppressMessages(suppressWarnings(suppressPackageStartupMessages(library(req.package[i2], lib.loc = lib.path, quietly = TRUE, character.only = TRUE))))
+        }
+    }
 }
-class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
-for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
-tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::", # no CR here te0("ggpl
-ifelse(geom[[i1]] == 'geom_stick', 'geom_segment', geom[[i1]]), # geom_segment because geom_stick converted to geom_segment for plotting
-"(data = tempo.data.frame, mapping = ggplot2::aes(x = ", 
-x[[i1]], 
-ifelse(geom[[i1]] == 'geom_stick', ", yend = ", ", y = "), 
-y[[i1]], 
-if(geom[[i1]] == 'geom_stick'){paste0(', xend = ', x[[i1]], ', y = ', ifelse(is.null(geom.stick.base), y.lim[1], geom.stick.base[[i1]]))}, 
-", size = ", 
-categ[[i1]], 
-"), color = \"", 
-color[[i1]][i5], 
-"\", linetype = ", 
-ifelse(is.numeric(line.type[[i1]]), "", "\""), 
-line.type[[i1]], 
-ifelse(is.numeric(line.type[[i1]]), "", "\""), 
-ifelse(geom[[i1]] == 'geom_path', ', lineend = \"round\"', ''), 
-ifelse(geom[[i1]] == 'geom_step', paste0(', direction = \"', geom.step.dir[[i1]], '\"'), ''), 
-", alpha = ", 
-alpha[[i1]], 
-", show.legend = FALSE)"
-)))) # WARNING: a single color allowed for color argument outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.). Used here to avoid multiple layers of legend which corrupt transparency
-coord.names <- c(coord.names, paste0(geom[[i1]], ".", class.categ[i5]))
+
+
+######## fun_python_pack() #### check if python packages are present
+
+
+fun_python_pack <- function(
+    req.package, 
+    python.exec.path = NULL, 
+    lib.path = NULL, 
+    R.lib.path = NULL
+){
+    # AIM
+    # check if the specified python packages are present in the computer (no import)
+    # WARNINGS
+    # for python 3.7. Previous versions return an error "Error in sys$stdout$flush() : attempt to apply non-function"
+    # ARGUMENTS
+    # req.package: character vector of package names to import
+    # python.exec.path: optional character vector specifying the absolute pathways of the executable python file to use (associated to the packages to use). If NULL, the reticulate::import_from_path() function used in fun_python_pack() seeks for an available version of python.exe, and then uses python_config(python_version, required_module, python_versions). But might not be the correct one for the lib.path parameter specified. Thus, it is recommanded to do not leave NULL, notably when using computing clusters
+    # lib.path: optional character vector specifying the absolute pathways of the directories containing some of the listed packages in the req.package argument, if not in the default directories
+    # R.lib.path: absolute path of the reticulate packages, if not in the default folders
+    # RETURN
+    # nothing
+    # REQUIRED PACKAGES
+    # reticulate
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # fun_pack()
+    # EXAMPLES
+    # example of error message
+    # fun_python_pack(req.package = "nopackage")
+    # example without error message (require the installation of the python serpentine package from https://github.com/koszullab/serpentine
+    # fun_python_pack(req.package = "serpentine", python.exec.path = "C:/ProgramData/Anaconda3/python.exe", lib.path = "c:/programdata/anaconda3/lib/site-packages/")
+    # another example of error message
+    # fun_python_pack(req.package = "serpentine", lib.path = "blablabla")
+    # DEBUGGING
+    # req.package = "serpentine" ; python.exec.path = "C:/ProgramData/Anaconda3/python.exe" ; lib.path = "c:/programdata/anaconda3/lib/site-packages/" ; R.lib.path = NULL
+    # req.package = "bad" ; lib.path = NULL ; R.lib.path = NULL
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(length(utils::find("fun_pack", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = req.package, class = "character", fun.name = function.name) ; eval(ee)
+    if( ! is.null(python.exec.path)){
+        tempo <- fun_check(data = python.exec.path, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if( ! all(file.exists(python.exec.path))){ # separation to avoid the problem of tempo$problem == FALSE and python.exec.path == NA
+                tempo.cat <- paste0("ERROR IN ", function.name, ": FILE PATH INDICATED IN THE python.exec.path ARGUMENT DOES NOT EXISTS:\n", paste(python.exec.path, collapse = "\n"))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }
+    if( ! is.null(lib.path)){
+        tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
+                tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }
+    if( ! is.null(R.lib.path)){
+        tempo <- fun_check(data = R.lib.path, class = "character", fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if( ! all(dir.exists(R.lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and R.lib.path == NA
+                tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE R.lib.path ARGUMENT DOES NOT EXISTS:\n", paste(R.lib.path, collapse = "\n"))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # package checking
+    fun_pack(req.package = "reticulate", lib.path = R.lib.path)
+    # end package checking
+    # main code
+    if(is.null(python.exec.path)){
+        python.exec.path <- reticulate::py_run_string("
+import sys ;
+path_lib = sys.path
+") # python string
+        python.exec.path <- python.exec.path$path_lib
+    }
+    if(is.null(lib.path)){
+        lib.path <- reticulate::py_run_string("
+import sys ;
+path_lib = sys.path
+") # python string
+        lib.path <- lib.path$path_lib
+    }
+    reticulate::use_python(Sys.which(python.exec.path), required = TRUE) # required to avoid the use of erratic python exec by reticulate::import_from_path()
+    for(i1 in 1:length(req.package)){
+        tempo.try <- vector("list", length = length(lib.path))
+        for(i2 in 1:length(lib.path)){
+            tempo.try[[i2]] <- suppressWarnings(try(reticulate::import_from_path(req.package[i1], path = lib.path[i2]), silent = TRUE))
+            tempo.try[[i2]] <- suppressWarnings(try(reticulate::import_from_path(req.package[i1], path = lib.path[i2]), silent = TRUE)) # done twice to avoid the error message  about flushing present the first time but not the second time. see https://stackoverflow.com/questions/57357001/reticulate-1-13-error-in-sysstdoutflush-attempt-to-apply-non-function
+        }
+        if(all(sapply(tempo.try, FUN = grepl, pattern = "[Ee]rror"))){
+            print(tempo.try)
+            tempo.cat <- paste0("ERROR IN ", function.name, ": PACKAGE ", req.package[i1], " MUST BE INSTALLED IN THE MENTIONNED DIRECTORY:\n", paste(lib.path, collapse = "\n"))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+        } # else{
+        # suppressMessages(suppressWarnings(suppressPackageStartupMessages(assign(req.package[i1], reticulate::import(req.package[i1]))))) # not required because try() already evaluates
+        # }
+    }
 }
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "size", name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(line.size[[i1]], length(color[[i1]])), breaks = class.categ)) # values are the values of linetype. 1 means solid. Regarding the alpha bug, I have tried different things without success: alpha in guide alone, in geom alone, in both, breaks reorder the classes according to class.categ in the legend
+
+
+################ Print / Exporting results (text & tables)
+
+
+######## fun_report() #### print string or data object into output file
+
+
+fun_report <- function(
+    data, 
+    output = "results.txt", 
+    path = "C:/Users/Gael/Desktop/", 
+    overwrite = FALSE, 
+    rownames.kept = FALSE, 
+    vector.cat = FALSE, 
+    noquote = TRUE, 
+    sep = 2
+){
+    # AIM
+    # log file function: print a character string or a data object into a same output file
+    # ARGUMENTS
+    # data: object to print in the output file. If NULL, nothing is done, with no warning
+    # output: name of the output file
+    # path: location of the output file
+    # overwrite: (logical) if output file already exists, defines if the printing is appended (default FALSE) or if the output file content is erased before printing (TRUE)
+    # rownames.kept: (logical) defines whether row names have to be removed or not in small tables (less than length.rows rows)
+    # vector.cat (logical). If TRUE print a vector of length > 1 using cat() instead of capture.output(). Otherwise (default FALSE) the opposite
+    # noquote: (logical). If TRUE no quote are present for the characters
+    # sep: number of separating lines after printed data (must be integer)
+    # RETURN
+    # nothing
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # fun_report()
+    # fun_report(data = 1:3, output = "results.txt", path = "C:/Users/Gael/Desktop", overwrite = TRUE, rownames.kept = FALSE, vector.cat = FALSE, noquote = FALSE, sep = 2)
+    # DEBUGGING
+    # data = 1:3 ; output = "results.txt" ; path = "C:/Users/Gael/Desktop" ; overwrite = TRUE ; rownames.kept = FALSE ; vector.cat = FALSE ; noquote = FALSE ; sep = 2 # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # argument checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = output, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE & output == ""){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": output ARGUMENT AS \"\" DOES NOT CORRESPOND TO A VALID FILE NAME")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    tempo <- fun_check(data = path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE){
+        if( ! all(dir.exists(path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
+            tempo.cat <- paste0("ERROR IN ", function.name, ": path ARGUMENT DOES NOT CORRESPOND TO EXISTING DIRECTORY\n", paste(path, collapse = "\n"))
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }
+    tempo <- fun_check(data = overwrite, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = rownames.kept, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = vector.cat, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = noquote, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = sep, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end argument checking
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # the 4 next lines are inactivated but kept because at a time, I might have a problem with data (solved with data = NULL). These 4 lines are just to know how to detect a missing argument. Important here because if data is not provided, print the code of the data function
+    # arg.user.list <- as.list(match.call(expand.dots = FALSE))[-1] # recover all the arguments provided by the function user (excluding the argument with defaults values not provided by the user. Thus, it is really the list indicated by the user)
+    # default.arg.list <- formals(fun = sys.function(sys.parent())) # list of all the arguments of the function with their default values (not the values of the user !). It seems that ls() as first line of the function provide the names of the arguments (empty, called, etc., or not)
+    # arg.without.default.value <- sapply(default.arg.list, is.symbol) & sapply(sapply(default.arg.list, as.character), identical, "") # logical to detect argument without default values (these are typeof "symbol" and class "name" and empty character
+    # if( ! all(names(default.arg.list)[arg.without.default.value] %in% names(arg.user.list))){ # test that the arguments with no null values are provided by the user
+    # tempo.cat <- paste0("ERROR IN ", function.name, ": VALUE REQUIRED FOR THESE ARGUMENTS WITH NO DEFAULTS VALUES: ", paste(names(default.arg.list)[arg.without.default.value][ ! names(default.arg.list)[arg.without.default.value] %in% names(arg.user.list)], collapse = " "))
+    # stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    # }
+    # end argument checking
+    # main code
+    if( ! is.null(data)){
+        if(all(class(data) == "data.frame") | all(class(data) == "table") | all(class(data) %in% c("matrix", "array"))){ # before R4.0.0, it was  all(class(data) %in% c("matrix", "data.frame", "table"))
+            if(rownames.kept == FALSE & all(class(data) == "data.frame") & nrow(data) != 0 & nrow(data) <= 4){ # for data frames with nrows <= 4
+                rownames.output.tables <- ""
+                length.rows <- nrow(data)
+                for(i in 1:length.rows){ # replace the rownames of the first 4 rows by increasing number of spaces (because identical row names not allowed in data frames). This method cannot be extended to more rows as the printed data frame is shifted on the right because of "big empty rownames"
+                    rownames.output.tables <- c(rownames.output.tables, paste0(rownames.output.tables[i]," ", collapse=""))
+                }
+                row.names(data) <- rownames.output.tables[1:length.rows]
+            }else if(rownames.kept == FALSE & (all(class(data) == "table") | all(class(data) %in% c("matrix", "array")))){ # before R4.0.0, it was  & all(class(data) %in% c("matrix", "table"))
+                rownames(data) <- rep("", nrow(data)) # identical row names allowed in matrices and tables
+            }
+            if(noquote == TRUE){
+                utils::capture.output(noquote(data), file=paste0(path, "/", output), append = ! overwrite)
+            }else{
+                utils::capture.output(data, file=paste0(path, "/", output), append = ! overwrite)
+            }
+        }else if(is.vector(data) & all(class(data) != "list") & (length(data) == 1L | vector.cat == TRUE)){
+            if(noquote == TRUE){
+                cat(noquote(data), file= paste0(path, "/", output), append = ! overwrite)
+            }else{
+                cat(data, file= paste0(path, "/", output), append = ! overwrite)
+            }
+        }else if(all(base::mode(data) == "character")){ # characters (array, list, factor or vector with vector.cat = FALSE)
+            if(noquote == TRUE){
+                utils::capture.output(noquote(data), file=paste0(path, "/", output), append = ! overwrite)
+            }else{
+                utils::capture.output(data, file=paste0(path, "/", output), append = ! overwrite)
+            }
+        }else{ # other object (S4 for instance, which do not like noquote()
+            utils::capture.output(data, file=paste0(path, "/", output), append = ! overwrite)
+        }
+        sep.final <- paste0(rep("\n", sep), collapse = "")
+        write(sep.final, file= paste0(path, "/", output), append = TRUE) # add a sep
+    }
 }
+
+
+######## fun_get_message() #### return error/warning/other messages of an expression (that can be exported)
+
+
+fun_get_message <- function(
+    data, 
+    kind = "error", 
+    header = TRUE, 
+    print.no = FALSE, 
+    text = NULL, 
+    env = NULL
+){
+    # AIM
+    # evaluate an instruction written between "" and return the first of the error, or warning or standard (non error non warning) messages if ever exist
+    # using argument print.no = FALSE, return NULL if no message, which is convenient in some cases
+    # WARNINGS
+    # Only the first message is returned
+    # Always use the env argument when fun_get_message() is used inside functions
+    # The function does not prevent printing if print() is used inside the instruction tested. To prevent that, use tempo <- capture.output(error <- fun_get_message(data = "fun_check(data = 'a', class = mean, neg.values = FALSE, print = TRUE)")). The return of fun_get_message() is assigned into error and the printed messages are captured by capture.output() and assigned into tempo. See the examples
+    # ARGUMENTS
+    # data: character string to evaluate
+    # kind: character string. Either "error" to get error messages, or "warning" to get warning messages, or "message" to get non error and non warning messages
+    # header: logical. Add a header in the returned message?
+    # print.no: logical. Print a message saying that no message reported?
+    # text: character string added to the output message (even if no message exists and print.no is TRUE). Inactivated if header is FALSE
+    # env: the name of an existing environment. NULL if not required
+    # RETURN
+    # the message or NULL if no message and print.no is FALSE
+    # REQUIRED PACKAGES
+    # none
+    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
+    # fun_check()
+    # EXAMPLES
+    # fun_get_message(data = "wilcox.test(c(1,1,3), c(1, 2, 4), paired = TRUE)", kind = "error", print.no = TRUE, text = "IN A")
+    # fun_get_message(data = "wilcox.test(c(1,1,3), c(1, 2, 4), paired = TRUE)", kind = "warning", print.no = TRUE, text = "IN A")
+    # fun_get_message(data = "wilcox.test(c(1,1,3), c(1, 2, 4), paired = TRUE)", kind = "message", print.no = TRUE, text = "IN A")
+    # fun_get_message(data = "wilcox.test()", kind = "error", print.no = TRUE, text = "IN A")
+    # fun_get_message(data = "sum(1)", kind = "error", print.no = TRUE, text = "IN A")
+    # fun_get_message(data = "message('ahah')", kind = "error", print.no = TRUE, text = "IN A")
+    # fun_get_message(data = "message('ahah')", kind = "message", print.no = TRUE, text = "IN A")
+    # fun_get_message(data = "ggplot2::ggplot(data = data.frame(X = 1:10, stringsAsFactors = TRUE), mapping = ggplot2::aes(x = X)) + ggplot2::geom_histogram()", kind = "message", print.no = TRUE, text = "IN FUNCTION 1")
+    # set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; fun_get_message(data = 'fun_gg_boxplot(data = obs1, y = "Time", categ = "Group1")', kind = "message", print.no = TRUE, text = "IN FUNCTION 1")
+    # DEBUGGING
+    # data = "wilcox.test(c(1,1,3), c(1, 2, 4), paired = TRUE)" ; kind = "warning" ; header = TRUE ; print.no = FALSE ; text = NULL ; env = NULL # for function debugging
+    # data = "sum(1)" ; kind = "warning" ; header = TRUE ; print.no = FALSE ; text = NULL ; env = NULL  # for function debugging
+    # set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Group1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; data = 'fun_gg_boxplot(data1 = obs1, y = "Time", categ = "Group1")' ; kind = "warning" ; header = TRUE ; print.no = FALSE ; text = NULL ; env = NULL  # for function debugging
+    # data = "message('ahah')" ; kind = "error" ; header = TRUE ; print.no = TRUE ; text = "IN A" ; env = NULL 
+    # data = 'ggplot2::ggplot(data = data.frame(X = "a", stringsAsFactors = TRUE), mapping = ggplot2::aes(x = X)) + ggplot2::geom_histogram()' ; kind = "message" ; header = TRUE ; print.no = FALSE ; text = NULL # for function debugging
+    # data = 'ggplot2::ggplot(data = data.frame(X = "a", stringsAsFactors = TRUE), mapping = ggplot2::aes(x = X)) + ggplot2::geom_histogram()' ; kind = "warning" ; header = TRUE ; print.no = FALSE ; text = NULL # for function debugging
+    # data = "emmeans::emmeans(object = emm.rg, specs = contrast.var)" ; kind = "message" ; header = TRUE ; print.no = FALSE ; text = NULL ; env = NULL # for function debugging
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    # end function name
+    # required function checking
+    if(length(utils::find("fun_check", mode = "function")) == 0L){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # no need to use reserved words to avoid bugs, because it is local, and  exists("tempo.warning", inherit = FALSE), never use the scope
+    # argument checking
+    # argument checking with fun_check()
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = data, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = kind, options = c("error", "warning", "message"), length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = print.no, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = header, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(text)){
+        tempo <- fun_check(data = text, class = "character", length = 1, fun.name = function.name) ; eval(ee)
+    }
+    if( ! is.null(env)){
+        tempo <- fun_check(data = env, class = "environment", fun.name = function.name) ; eval(ee) #
+    }
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # end argument checking with fun_check()
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument checking
+    # main code
+    pdf(file = NULL) # send plots into a NULL file, no pdf file created
+    window.nb <- dev.cur()
+    invisible(dev.set(window.nb))
+    # last warning cannot be used because suppressWarnings() does not modify last.warning present in the base evironment (created at first warning in a new R session), or warnings() # to reset the warning history : unlockBinding("last.warning", baseenv()) ; assign("last.warning", NULL, envir = baseenv())
+    output <- NULL
+    tempo.error <- try(suppressMessages(suppressWarnings(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env}))), silent = TRUE) # get error message, not warning or messages
+    if(any(class(tempo.error) %in% c("gg", "ggplot"))){
+        tempo.error <- try(suppressMessages(suppressWarnings(ggplot2::ggplot_build(tempo.error))), silent = TRUE)[1]
+    }
+    if(exists("tempo.error", inherit = FALSE) == TRUE){ # inherit = FALSE avoid the portee lexical and thus the declared word
+        if( ! all(class(tempo.error) == "try-error")){ # deal with NULL and S4 objects. Old code:  ! (all(class(tempo.error) == "try-error") & any(grepl(x = tempo.error, pattern = "^Error|^error|^ERROR"))) but problem with S4 objects. Old code : if((length(tempo.error) > 0 & ! any(grepl(x = tempo.error, pattern = "^Error|^error|^ERROR"))) | (length(tempo.error) == 0) ){ but problem when tempo.error is a list but added this did not work: | ! all(class(tempo.error) == "character")
+            tempo.error <- NULL
+        }
+    }else{
+        tempo.error <- NULL
+    }
+    if(kind == "error" & ! is.null(tempo.error)){ # 
+        if(header == TRUE){
+            tempo.error[1] <- gsub(x = tempo.error[1], pattern = "^Error i|^error i|^ERROR I", replacement = "I")
+            output <- paste0("ERROR MESSAGE REPORTED", ifelse(is.null(text), "", " "), text, ":\n", tempo.error[1]) #
+        }else{
+            output <- tempo.error[1] #
+        }
+    }else if(kind == "error" & is.null(tempo.error) & print.no == TRUE){
+        output <- paste0("NO ERROR MESSAGE REPORTED", ifelse(is.null(text), "", " "), text)
+    }else if(kind != "error" & ( ! is.null(tempo.error)) & print.no == TRUE){
+        output <- paste0("NO ", ifelse(kind == "warning", "WARNING", "STANDARD (NON ERROR AND NON WARNING)"), " MESSAGE BECAUSE OF ERROR MESSAGE REPORTED", ifelse(is.null(text), "", " "), text)
+    }else if(is.null(tempo.error)){
+        fun.warning.capture <- function(expr){
+            # from demo(error.catching) typed in the R console, coming from ?tryCatch
+            # see also http://mazamascience.com/WorkingWithData/?p=912
+            # return a character string or NULL
+            # expr <- wilcox.test.default(c(1, 1, 3), c(1, 2, 4), paired = TRUE)
+            W <- NULL
+            w.handler <- function(w){ # warning handler
+                W <<- w # send to the above env, i.e., the inside of the fun.warning.capture function
+                invokeRestart("muffleWarning") # here w.handler() muffles all the warnings. See http://romainfrancois.blog.free.fr/index.php?post/2009/05/20/Disable-specific-warnings to muffle specific warnings and print others
+            }
+            output <- list(
+                value = suppressMessages(withCallingHandlers(tryCatch(expr, error = function(e){e}), warning = w.handler)), # BEWARE: w.handler is a function written without (), like in other functions with FUN argument
+                warning = W # processed by w.handler()
+            )
+            return(if(is.null(output$warning)){NULL}else{as.character(output$warning)})
+        }
+        tempo.warn <- fun.warning.capture(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env}))
+        # warn.options.ini <- options()$warn ; options(warn = 1) ; tempo.warn <- utils::capture.output({tempo <- suppressMessages(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env}))}, type = "message") ; options(warn = warn.options.ini) # this recover warnings not messages and not errors but does not work in all enviroments
+        tempo.message <- utils::capture.output({
+            tempo <- suppressMessages(suppressWarnings(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env})))
+            if(any(class(tempo) %in% c("gg", "ggplot"))){
+                tempo <- ggplot2::ggplot_build(tempo)
+            }else{
+                tempo <- suppressWarnings(eval(parse(text = data), envir = if(is.null(env)){parent.frame()}else{env}))
+            }
+        }, type = "message") # recover messages not warnings and not errors
+        if(kind == "warning" & ! is.null(tempo.warn)){
+            if(length(tempo.warn) > 0){ # to avoid character(0)
+                if( ! any(sapply(tempo.warn, FUN = "grepl", pattern = "() FUNCTION:$"))){
+                    tempo.warn <- paste(unique(tempo.warn), collapse = "\n") # if FALSE, means that the tested data is a special function. If TRUE, means that the data is a standard function. In that case, the output of capture.output() is two strings per warning messages: if several warning messages -> identical first string, which is removed in next messages by unique()
+                }else{
+                    tempo.warn <- paste(tempo.warn, collapse = "\n")
+                }
+                if(header == TRUE){
+                    if(any(grepl(x = tempo.warn[[1]], pattern = "^simpleWarning i"))){
+                        tempo.warn[[1]] <- gsub(x = tempo.warn[[1]], pattern = "^Warning i", replacement = "I")
+                    }
+                    if(any(grepl(x = tempo.warn[[1]], pattern = "^Warning i"))){
+                        tempo.warn[[1]] <- gsub(x = tempo.warn[[1]], pattern = "^Warning i", replacement = "I")
+                    }
+                    output <- paste0("WARNING MESSAGE REPORTED", ifelse(is.null(text), "", " "), text, ":\n", tempo.warn) #
+                }else{
+                    output <- tempo.warn #
+                }
+            }else{
+                if(print.no == TRUE){
+                    output <- paste0("NO WARNING MESSAGE REPORTED", ifelse(is.null(text), "", " "), text)
+                } # no need else{} here because output is already NULL at first
+            }
+        }else if(kind == "warning" & is.null(tempo.warn) & print.no == TRUE){
+            output <- paste0("NO WARNING MESSAGE REPORTED", ifelse(is.null(text), "", " "), text)
+        }else if(kind == "message" & exists("tempo.message", inherit = FALSE) == TRUE){ # inherit = FALSE avoid the portee lexical and thus the declared word
+            if(length(tempo.message) > 0){ # if something is returned by capture.ouptput() (only in this env) with a length more than 1
+                if(header == TRUE){
+                    output <- paste0("STANDARD (NON ERROR AND NON WARNING) MESSAGE REPORTED", ifelse(is.null(text), "", " "), text, ":\n", tempo.message) #
+                }else{
+                    output <- tempo.message #
+                }
+            }else{
+                if(print.no == TRUE){
+                    output <- paste0("NO STANDARD (NON ERROR AND NON WARNING) MESSAGE REPORTED", ifelse(is.null(text), "", " "), text)
+                } # no need else{} here because output is already NULL at first
+            }
+        }else if(kind == "message" & exists("tempo.message", inherit = FALSE) == FALSE & print.no == TRUE){
+            output <- paste0("NO STANDARD (NON ERROR AND NON WARNING) MESSAGE REPORTED", ifelse(is.null(text), "", " "), text)
+        } # no need else{} here because output is already NULL at first
+    } # no need else{} here because output is already NULL at first
+    invisible(dev.off(window.nb)) # end send plots into a NULL file
+    return(output) # do not use cat() because the idea is to reuse the message
 }
+
+
+
+
+
+# Error: class order not good when a class is removed due to NA
+# Error: line 136 in check 20201126 with add argument
+# Solve this: sometimes error messages can be more than the max display (8170). Thus, check every paste0("ERROR IN ", function.name, and trunck the message if to big. In addition, add at the begining of the warning message that it is too long and see the $warn output for complete message. Add also this into fun_scatter
+# add dot.shape ? See with available aesthetic layers
+# rasterise: https://cran.r-project.org/web/packages/ggrastr/vignettes/Raster_geoms.html
+# add horizontal argument and deal any conflict with vertical argument. Start with horizontal = NULL as default. If ! is.null() -> convert vertical if required
+
+fun_gg_boxplot <- function(
+    data1, 
+    y, 
+    categ, 
+    categ.class.order = NULL, 
+    categ.color = NULL, 
+    box.legend.name = NULL, 
+    box.fill = FALSE, 
+    box.width = 0.5, 
+    box.space = 0.1, 
+    box.line.size = 0.75, 
+    box.notch = FALSE, 
+    box.alpha = 1, 
+    box.mean = TRUE, 
+    box.whisker.kind = "std", 
+    box.whisker.width = 0, 
+    dot.color = grey(0.25), 
+    dot.categ = NULL, 
+    dot.categ.class.order = NULL, 
+    dot.legend.name = NULL, 
+    dot.tidy = FALSE, 
+    dot.tidy.bin.nb = 50, 
+    dot.jitter = 0.5, 
+    dot.seed = 2, 
+    dot.size = 3, 
+    dot.alpha = 0.5, 
+    dot.border.size = 0.5, 
+    dot.border.color = NULL, 
+    x.lab = NULL, 
+    x.angle = 0, 
+    y.lab = NULL, 
+    y.lim = NULL, 
+    y.log = "no", 
+    y.tick.nb = NULL, 
+    y.second.tick.nb = 1, 
+    y.include.zero = FALSE, 
+    y.top.extra.margin = 0.05, 
+    y.bottom.extra.margin = 0.05, 
+    stat.pos = "top", 
+    stat.mean = FALSE, 
+    stat.size = 4, 
+    stat.dist = 5, 
+    stat.angle = 0, 
+    vertical = TRUE, 
+    text.size = 12, 
+    title = "", 
+    title.text.size = 8, 
+    legend.show = TRUE, 
+    legend.width = 0.5, 
+    article = TRUE, 
+    grid = FALSE, 
+    add = NULL, 
+    return = FALSE, 
+    return.ggplot = FALSE,
+    return.gtable = TRUE,
+    plot = TRUE, 
+    warn.print = FALSE, 
+    lib.path = NULL
+){
+    # AIM
+    # Plot ggplot2 boxplots + dots + means
+    # For ggplot2 specifications, see: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html
+    # WARNINGS
+    # Rows containing NA in data1[, c(y, categ)] will be removed before processing, with a warning (see below)
+    # Hinges are not computed like in the classical boxplot() function of R. See https://ggplot2.tidyverse.org/reference/geom_boxplot.html
+    # To have a single box, please create a factor column with a single class and specify the name of this column in the categ argument. For a single set of grouped boxes, create a factor column with a single class and specify this column in categ argument as first element (i.e., as categ1, knowing that categ2 must also be specified in this situation). See categ argument below
+    # The dot.alpha argument can alter the display of the color boxes when using pdf output
+    # Size arguments (box.line.size, dot.size, dot.border.size, stat.size, text.size and title.text.size) are in mm. See Hadley comment in https://stackoverflow.com/questions/17311917/ggplot2-the-unit-of-size. See also http://sape.inf.usi.ch/quick-reference/ggplot2/size). Unit object are not accepted, but conversion can be used (e.g., grid::convertUnit(grid::unit(0.2, "inches"), "mm", valueOnly = TRUE))
+    # Display seems to be done twice on Windows devices (like a blink). However, no double plots on pdf devices. Thus, the blink remains mysterious
+    # To remove boxes and have only dots, use box.alpha = 0
+    # ARGUMENTS
+    # data1: data frame containing one column of quantitative values (see the y argument below) and one or two columns of categories (see the categ argument below). Duplicated column names are not allowed
+    # y: character string of the data1 column name for y-axis (column containing numeric values). Numeric values will be split according to the classes of the column names indicated in the categ argument to generate the boxes and will also be used to plot the dots
+    # categ: vector of character strings of the data1 column name for categories (column of characters or factors). Must be either one or two column names. If a single column name (further referred to as categ1), then one box per class of categ1. If two column names (further referred to as categ1 and categ2), then one box per class of categ2, which form a group of boxes in each class of categ1. WARNING: no empty classes allowed. To have a single box, create a factor column with a single class and specify the name of this column in the categ argument (here, no categ2 in categ argument). For a single set of grouped boxes, create a factor column with a single class and specify this column in categ argument as first element (i.e., as categ1), in addition to the already used category (as categ2 in this situation)
+    # categ.class.order: list indicating the order of the classes of categ1 and categ2 represented on the boxplot (the first compartment for categ1 and and the second for categ2). If categ.class.order == NULL, classes are represented according to the alphabetical order. Some compartments can be NULL and others not. See the categ argument for categ1 and categ2 description
+    # categ.color: vector of color character string for box frames (see the categ argument for categ1 and categ2 description)
+    # If categ.color == NULL, default colors of ggplot2, whatever categ1 and categ2
+    # If categ.color is non-null and only categ1 in categ argument, categ.color can be either:
+    # (1) a single color string. All the boxes will have this color, whatever the number of classes of categ1
+    # (2) a vector of string colors, one for each class of categ1. Each color will be associated according to categ.class.order of categ1
+    # (3) a vector or factor of string colors, like if it was one of the column of data1 data frame. WARNING: a single color per class of categ1 and a single class of categ1 per color must be respected
+    # Color functions, like grey(), hsv(), etc., are also accepted
+    # Positive integers are also accepted instead of character strings, as long as above rules about length are respected. Integers will be processed by fun_gg_palette() using the maximal integer value among all the integers in categ.color (see fun_gg_palette())
+    # If categ.color is non-null and categ1 and categ2 are specified, all the rules described above will apply to categ2 instead of categ1 (colors will be determined for boxes inside a group of boxes)
+    # box.legend.name: character string of the legend title. If box.legend.name is NULL, then box.legend.name <- categ1 if only categ1 is present, and box.legend.name <- categ2 if categ1 and categ2 are present in the categ argument. Write "" if no legend required. See the categ argument for categ1 and categ2 description
+    # box.fill: logical. Fill the box? If TRUE, the categ.color argument will be used to generate filled boxplots (the box frames being black) as well as filled outlier dots (the dot border being controlled by the dot.border.color argument). If all the dots are plotted (argument dot.color other than NULL), they will be over the boxes. If FALSE, the categ.color argument will be used to color the box frames and the outlier dot borders. If all the dots are plotted, they will be beneath the boxes
+    # box.width: single numeric value (from 0 to 1) of width of either boxes or group of boxes
+    # When categ argument has a single categ1 element (i.e., separate boxes. See the categ argument for categ1 and categ2 description), then each class of categ1 is represented by a single box. In that case, box.width argument defines each box width, from 0 (no box width) to 1 (max box width), but also the space between boxes (the code uses 1 - box.width for the box spaces). Of note, xmin and xmax of the fun_gg_boxplot() output report the box boundaries (around x-axis unit 1, 2, 3, etc., for each box)
+    # When categ argument has a two categ1 and categ2 elements (i.e., grouped boxes), box.width argument defines the width allocated for each set of grouped boxes, from 0 (no group width) to 1 (max group width), but also the space between grouped boxes (the code uses 1 - box.width for the spaces). Of note, xmin and xmax of the fun_gg_boxplot() output report the box boundaries (around x-axis unit 1, 2, 3, etc., for each set of grouped box)
+    # box.space: single numeric value (from 0 to 1) indicating the box separation inside grouped boxes, when categ argument has a two categ1 and categ2 elements. 0 means no space and 1 means boxes shrunk to a vertical line. Ignored if categ argument has a single categ1 element
+    # box.line.size: single numeric value of line width of boxes and whiskers in mm
+    # box.notch: logical. Notched boxplot? It TRUE, display notched boxplot, notches corresponding approximately to the 95% confidence interval of the median (the notch interval is exactly 1.58 x Inter Quartile Range (IQR) / sqrt(n), with n the number of values that made the box). If notch intervals between two boxes do not overlap, it can be interpreted as significant median differences
+    # box.alpha: single numeric value (from 0 to 1) of box transparency (full transparent to full opaque, respectively). To remove boxplots, use box.alpha = 0
+    # box.mean: logical. Add mean value? If TRUE, a diamond-shaped dot, with the horizontal diagonal corresponding to the mean value, is displayed over each boxplot
+    # box.whisker.kind: range of the whiskers. Either "no" (no whiskers), or "std" (length of each whisker equal to 1.5 x Inter Quartile Range (IQR)), or "max" (length of the whiskers up or down to the most distant dot)
+    # box.whisker.width: single numeric value (from 0 to 1) of the whisker width, with 0 meaning no whiskers and 1 meaning a width equal to the box width
+    # dot.color: vector of color character string ruling the dot colors and the dot display. See the example section below for easier understanding of the rules described here
+    # If NULL, no dots plotted
+    # If "same", the dots will have the same colors as the respective boxplots
+    # Otherwise, as in the rule (1), (2) or (3) described in the categ.color argument, except that in the possibility (3), the rule "a single color per class of categ and a single class of categ per color", does not have to be respected (for instance, each dot can have a different color). Colors will also depend on the dot.categ argument. If dot.categ is NULL, then colors will be applied to each class of the last column name specified in categ. If dot.categ is non-NULL, colors will be applied to each class of the column name specified in dot.categ. See examples
+    # dot.categ: optional single character string of a column name (further referred to as categ3) of the data1 argument. This column of data1 will be used to generate a legend for dots, in addition to the legend for boxes. See the dot.color argument for details about the way the legend is built using the two dot.categ and dot.color arguments. If NULL, no legend created and the colors of dots will depend on dot.color and categ arguments (as explained in the dot.color argument)
+    # dot.categ.class.order: optional vector of character strings indicating the order of the classes of categ3 (see the dot.categ argument). If dot.categ is non-NULL and dot.categ.class.order is NULL, classes are displayed in the legend according to the alphabetical order. Ignored if dot.categ is NULL
+    # dot.legend.name: optional character string of the legend title for categ3 (see the dot.categ argument). If dot.legend.name == NULL, dot.categ value is used (name of the column in data1). Write "" if no legend required. Ignored if dot.categ is NULL
+    # dot.tidy: logical. Nice dot spreading? If TRUE, use the geom_dotplot() function for a nice representation. WARNING: change the true quantitative coordinates of dots (i.e., y-axis values for vertical display) because of binning. Thus, the gain in aestheticism is associated with a loss in precision that can be very important. If FALSE, dots are randomly spread on the qualitative axis, using the dot.jitter argument (see below) keeping the true quantitative coordinates
+    # dot.tidy.bin.nb: positive integer indicating the number of bins (i.e., nb of separations) of the y.lim range. Each dot will then be put in one of the bin, with a diameter of the width of the bin. In other words, increase the number of bins to have smaller dots. Not considered if dot.tidy is FALSE
+    # dot.jitter: numeric value (from 0 to 1) of random dot horizontal dispersion (for vertical display), with 0 meaning no dispersion and 1 meaning dispersion in the corresponding box width interval. Not considered if dot.tidy is TRUE
+    # dot.seed: integer value that set the random seed. Using the same number will generate the same dot jittering. Write NULL to have different jittering each time the same instruction is run. Ignored if dot.tidy is TRUE
+    # dot.size: numeric value of dot diameter in mm. Not considered if dot.tidy is TRUE
+    # dot.alpha: numeric value (from 0 to 1) of dot transparency (full transparent to full opaque, respectively)
+    # dot.border.size: numeric value of border dot width in mm. Write zero for no dot border. If dot.tidy is TRUE, value 0 remove the border and other values leave the border without size control (geom_doplot() feature)
+    # dot.border.color: single character color string defining the color of the dot border (same color for all the dots, whatever their categories). If dot.border.color == NULL, the border color will be the same as the dot color. A single integer is also accepted instead of a character string, that will be processed by fun_gg_palette()
+    # x.lab: a character string or expression for x-axis legend. If NULL, character string of categ1 (see the categ argument for categ1 and categ2 description)
+    # x.angle: integer value of the text angle for the x-axis numbers, using the same rules as in ggplot2. Positive values for counterclockwise rotation: 0 for horizontal, 90 for vertical, 180 for upside down etc. Negative values for clockwise rotation: 0 for horizontal, -90 for vertical, -180 for upside down etc.
+    # y.lab: a character string or expression for y-axis legend. If NULL, character string of the y argument
+    # y.lim: 2 numeric values indicating the range of the y-axis. Order matters (for inverted axis). If NULL, the range of the x column name of data1 will be used. 
+    # y.log: either "no", "log2" (values in the y argument column of the data1 data frame will be log2 transformed and y-axis will be log2 scaled) or "log10" (values in the y argument column of the data1 data frame will be log10 transformed and y-axis will be log10 scaled). WARNING: not possible to have horizontal boxes with a log axis, due to a bug in ggplot2 (see https://github.com/tidyverse/ggplot2/issues/881)
+    # y.tick.nb: approximate number of desired values labeling the y-axis (i.e., main ticks, see the n argument of the the cute::fun_scale() function). If NULL and if y.log is "no", then the number of labeling values is set by ggplot2. If NULL and if y.log is "log2" or "log10", then the number of labeling values corresponds to all the exposant integers in the y.lim range (e.g., 10^1, 10^2 and 10^3, meaning 3 main ticks for y.lim = c(9, 1200)). WARNING: if non-NULL and if y.log is "log2" or "log10", labeling can be difficult to read (e.g., ..., 10^2, 10^2.5, 10^3, ...)
+    # y.second.tick.nb: number of desired secondary ticks between main ticks. Ignored if y.log is other than "no" (log scale plotted). Use argument return = TRUE and see $plot$y.second.tick.values to have the values associated to secondary ticks. IF NULL, no secondary ticks
+    # y.include.zero: logical. Does y.lim range include 0? Ignored if y.log is "log2" or "log10"
+    # y.top.extra.margin: single proportion (between 0 and 1) indicating if extra margins must be added to y.lim. If different from 0, add the range of the axis multiplied by y.top.extra.margin (e.g., abs(y.lim[2] - y.lim[1]) * y.top.extra.margin) to the top of y-axis
+    # y.bottom.extra.margin: idem as y.top.extra.margin but to the bottom of y-axis
+    # stat.pos: add the median number above the corresponding box. Either NULL (no number shown), "top" (at the top of the plot region) or "above" (above each box)
+    # stat.mean: logical. Display mean numbers instead of median numbers? Ignored if stat.pos is NULL
+    # stat.size: numeric value of the stat font size in mm. Ignored if stat.pos is NULL
+    # stat.dist: numeric value of the stat distance in percentage of the y-axis range (stat.dist = 5 means move the number displayed at 5% of the y-axis range). Ignored if stat.pos is NULL or "top"
+    # stat.angle: integer value of the angle of stat, using the same rules as in ggplot2. Positive values for counterclockwise rotation: 0 for horizontal, 90 for vertical, 180 for upside down etc. Negative values for clockwise rotation: 0 for horizontal, -90 for vertical, -180 for upside down etc.
+    # vertical: logical. Vertical boxes? WARNING: will be automatically set to TRUE if y.log argument is other than "no". Indeed, not possible to have horizontal boxes with a log axis, due to a bug in ggplot2 (see https://github.com/tidyverse/ggplot2/issues/881)
+    # text.size: numeric value of the font size of the (1) axis numbers, (2) axis labels and (3) texts in the graphic legend (in mm)
+    # title: character string of the graph title
+    # title.text.size: numeric value of the title font size in mm
+    # legend.show: logical. Show legend? Not considered if categ argument is NULL, because this already generate no legend, excepted if legend.width argument is non-NULL. In that specific case (categ is NULL, legend.show is TRUE and legend.width is non-NULL), an empty legend space is created. This can be useful when desiring graphs of exactly the same width, whatever they have legends or not
+    # legend.width: single proportion (between 0 and 1) indicating the relative width of the legend sector (on the right of the plot) relative to the width of the plot. Value 1 means that the window device width is split in 2, half for the plot and half for the legend. Value 0 means no room for the legend, which will overlay the plot region. Write NULL to inactivate the legend sector. In such case, ggplot2 will manage the room required for the legend display, meaning that the width of the plotting region can vary between graphs, depending on the text in the legend
+    # article: logical. If TRUE, use an article theme (article like). If FALSE, use a classic related ggplot theme. Use the add argument (e.g., add = "+ggplot2::theme_classic()" for the exact classic ggplot theme
+    # grid: logical. Draw lines in the background to better read the box values? Not considered if article == FALSE (grid systematically present)
+    # add: character string allowing to add more ggplot2 features (dots, lines, themes, facet, etc.). Ignored if NULL
+    # WARNING: (1) the string must start with "+", (2) the string must finish with ")" and (3) each function must be preceded by "ggplot2::". Example: "+ ggplot2::coord_flip() + ggplot2::theme_bw()"
+    # If the character string contains the "ggplot2::theme" string, then the article argument of fun_gg_boxplot() (see above) is ignored with a warning. In addition, some arguments can be overwritten, like x.angle (check all the arguments)
+    # Handle the add argument with caution since added functions can create conflicts with the preexisting internal ggplot2 functions
+    # WARNING: the call of objects inside the quotes of add can lead to an error if the name of these objects are some of the fun_gg_boxplot() arguments. Indeed, the function will use the internal argument instead of the global environment object. Example article <- "a" in the working environment and add = '+ ggplot2::ggtitle(article)'. The risk here is to have TRUE as title. To solve this, use add = '+ ggplot2::ggtitle(get("article", envir = .GlobalEnv))'
+    # return: logical. Return the graph parameters?
+    # return.ggplot: logical. Return the ggplot object in the output list? Ignored if return argument is FALSE. WARNING: always assign the fun_gg_boxplot() function (e.g., a <- fun_gg_boxplot()) if return.ggplot argument is TRUE, otherwise, double plotting is performed. See $ggplot in the RETURN section below for more details
+    # return.gtable: logical. Return the ggplot object as gtable of grobs in the output list? Ignored if plot argument is FALSE. Indeed, the graph must be plotted to get the grobs dispositions. See $gtable in the RETURN section below for more details
+    # plot: logical. Plot the graphic? If FALSE and return argument is TRUE, graphical parameters and associated warnings are provided without plotting
+    # warn.print: logical. Print warnings at the end of the execution? ? If FALSE, warning messages are never printed, but can still be recovered in the returned list. Some of the warning messages (those delivered by the internal ggplot2 functions) are not apparent when using the argument plot = FALSE
+    # lib.path: character string indicating the absolute path of the required packages (see below). if NULL, the function will use the R library default folders
+    # RETURN
+    # A boxplot if plot argument is TRUE
+    # A list of the graph info if return argument is TRUE:
+    # $data: the initial data with graphic information added
+    # $stat: the graphic statistics (mostly equivalent to ggplot_build()$data[[2]])
+    # $removed.row.nb: which rows have been removed due to NA/Inf detection in y and categ columns (NULL if no row removed)
+    # $removed.rows: removed rows (NULL if no row removed)
+    # $plot: the graphic box and dot coordinates
+    # $dots: dot coordinates
+    # $main.box: coordinates of boxes
+    # $median: median coordinates
+    # $sup.whisker: coordinates of top whiskers (y for base and y.end for extremities)
+    # $inf.whisker: coordinates of bottom whiskers (y for base and y.end for extremities)
+    # $sup.whisker.edge: coordinates of top whisker edges (x and xend)
+    # $inf.whisker.edge: coordinates of bottom whisker edges(x and xend)
+    # $mean: diamond mean coordinates (only if box.mean argument is TRUE)
+    # $stat.pos: coordinates of stat numbers (only if stat.pos argument is not NULL)
+    # y.second.tick.positions: coordinates of secondary ticks (only if y.second.tick.nb argument is non-NULL or if y.log argument is different from "no")
+    # y.second.tick.values: values of secondary ticks. NULL except if y.second.tick.nb argument is non-NULL or if y.log argument is different from "no")
+    # $panel: the variable names used for the panels (NULL if no panels). WARNING: NA can be present according to ggplot2 upgrade to v3.3.0
+    # $axes: the x-axis and y-axis info
+    # $warn: the warning messages. Use cat() for proper display. NULL if no warning. WARNING: warning messages delivered by the internal ggplot2 functions are not apparent when using the argument plot = FALSE
+    # $ggplot: ggplot object that can be used for reprint (use print(...$ggplot) or update (use ...$ggplot + ggplot2::...). NULL if return.ggplot argument is FALSE. Of note, a non-NULL $ggplot in the output list is sometimes annoying as the manipulation of this list prints the plot
+    # $gtable: gtable object that can be used for reprint (use gridExtra::grid.arrange(...$ggplot) or with additionnal grobs (see the grob decomposition in the examples). NULL if return.ggplot argument is FALSE. Contrary to $ggplot, a non-NULL $gtable in the output list is not annoying as the manipulation of this list does not print the plot
+    # REQUIRED PACKAGES
+    # ggplot2
+    # gridExtra
+    # lemon (in case of use in the add argument)
+    # scales
+    # REQUIRED FUNCTIONS FROM THE cute PACKAGE
+    # fun_check()
+    # fun_comp_1d()
+    # fun_comp_2d()
+    # fun_gg_just()
+    # fun_gg_palette()
+    # fun_inter_ticks()
+    # fun_name_change()
+    # fun_pack()
+    # fun_round()
+    # fun_scale()
+    # EXAMPLE
+    # set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(20, 100, 10), rnorm(20, 200, 50), rnorm(20, 500, 60), rnorm(20, 100, 50)), Categ1 = rep(c("CAT", "DOG"), times = 40), Categ2 = rep(c("A", "B", "C", "D"), each = 20), Color1 = rep(c("coral", "lightblue"), times = 40), Color2 = rep(c("#9F2108", "#306100", "#007479", "#8500C0"), each = 20), stringsAsFactors = TRUE) ; set.seed(NULL) ; fun_gg_boxplot(data1 = obs1, y = "Time", categ = "Categ1")
+    # see http
+    # DEBUGGING
+    # set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Categ1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; set.seed(NULL) ; obs1$Time[1:10] <- NA ; data1 = obs1 ; y = "Time" ; categ = c("Categ1") ; categ.class.order = NULL ; categ.color = NULL ; box.legend.name = NULL ; box.fill = FALSE ; box.width = 0.5 ; box.space = 0.1 ; box.line.size = 0.75 ; box.notch = FALSE ; box.alpha = 1 ; box.mean = TRUE ; box.whisker.kind = "std" ; box.whisker.width = 0 ; dot.color = grey(0.25) ; dot.categ = NULL ; dot.categ.class.order = NULL ; dot.legend.name = NULL ; dot.tidy = FALSE ; dot.tidy.bin.nb = 50 ; dot.jitter = 0.5 ; dot.seed = 2 ; dot.size = 3 ; dot.alpha = 0.5 ; dot.border.size = 0.5 ; dot.border.color = NULL ; x.lab = NULL ; x.angle = 0 ; y.lab = NULL ; y.lim = NULL ; y.log = "no" ; y.tick.nb = NULL ; y.second.tick.nb = 1 ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0.05 ; stat.pos = "top" ; stat.mean = FALSE ; stat.size = 4 ; stat.dist = 5 ; stat.angle = 0 ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; legend.show = TRUE ; legend.width = 0.5 ; article = TRUE ; grid = FALSE ; add = NULL ; return = FALSE ; return.ggplot = FALSE ; return.gtable = TRUE ; plot = TRUE ; warn.print = FALSE ; lib.path = NULL
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
+    arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
+    arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
+    # end function name
+    # required function checking
+    req.function <- c(
+        "fun_comp_2d", 
+        "fun_gg_just", 
+        "fun_gg_palette", 
+        "fun_name_change", 
+        "fun_pack", 
+        "fun_check", 
+        "fun_round", 
+        "fun_scale",
+        "fun_inter_ticks"
+    )
+    tempo <- NULL
+    for(i1 in req.function){
+        if(length(find(i1, mode = "function")) == 0L){
+            tempo <- c(tempo, i1)
+        }
+    }
+    if( ! is.null(tempo)){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # reserved words to avoid bugs (names of dataframe columns used in this function)
+    reserved.words <- c("categ.check", "categ.color", "dot.color", "dot.categ", "dot.max", "dot.min", "group", "PANEL", "group.check", "MEAN", "tempo.categ1", "tempo.categ2", "text.max.pos", "text.min.pos", "x", "x.y", "y", "y.check", "y_from.dot.max", "ymax", "tidy_group", "binwidth")
+    # end reserved words to avoid bugs (used in this function)
+    # arg with no default values
+    mandat.args <- c(
+        "data1", 
+        "y", 
+        "categ"
+    )
+    tempo <- eval(parse(text = paste0("missing(", paste0(mandat.args, collapse = ") | missing("), ")")))
+    if(any(tempo)){ # normally no NA for missing() output
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(length(mandat.args) > 1, "S HAVE", "HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args, collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end arg with no default values
+    # argument primary checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo <- fun_check(data = data1, class = "data.frame", na.contain = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = categ, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    if( ! is.null(categ.class.order)){
+        tempo <- fun_check(data = categ.class.order, class = "list", fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = categ.class.order, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(box.legend.name)){
+        tempo <- fun_check(data = box.legend.name, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = box.legend.name, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(categ.color)){
+        tempo1 <- fun_check(data = categ.color, class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name)
+        tempo2 <- fun_check(data = categ.color, class = "factor", na.contain = TRUE, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.check.color <- fun_check(data = categ.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, neg.values = FALSE, fun.name = function.name)$problem
+            if(tempo.check.color == TRUE){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg.color ARGUMENT MUST BE A FACTOR OR CHARACTER VECTOR OR POSITVE INTEGER VECTOR") # integer possible because dealt above
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }else if(any(categ.color == 0L, na.rm = TRUE)){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg.color ARGUMENT MUST BE A FACTOR OR CHARACTER VECTOR OR POSITVE INTEGER VECTOR") # integer possible because dealt above
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = categ.color, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = box.fill, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = box.width, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = box.space, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = box.line.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = box.notch, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = box.alpha, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = box.mean, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = box.whisker.kind, options = c("no", "std", "max"), length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = box.whisker.width, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(dot.color)){
+        tempo1 <- fun_check(data = dot.color, class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name)
+        tempo2 <- fun_check(data = dot.color, class = "factor", na.contain = TRUE, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.check.color <- fun_check(data = dot.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, neg.values = FALSE, fun.name = function.name)$problem
+            if(tempo.check.color == TRUE){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.color MUST BE A FACTOR OR CHARACTER VECTOR OR POSITVE INTEGER VECTOR") # integer possible because dealt above
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }else if(any(dot.color == 0L, na.rm = TRUE)){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.color ARGUMENT MUST BE A FACTOR OR CHARACTER VECTOR OR POSITVE INTEGER VECTOR") # integer possible because dealt above
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = dot.color, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(dot.categ)){
+        tempo <- fun_check(data = dot.categ, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = dot.categ, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(dot.categ.class.order)){
+        tempo <- fun_check(data = dot.categ.class.order, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = dot.categ.class.order, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(dot.legend.name)){
+        tempo <- fun_check(data = dot.legend.name, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = dot.legend.name, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = dot.tidy, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = dot.tidy.bin.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    if(tempo$problem == FALSE){
+        if(dot.tidy.bin.nb == 0L){ # length and NA checked above
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.tidy.bin.nb ARGUMENT MUST BE A NON-NULL AND POSITVE INTEGER VALUE") # integer possible because dealt above
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }
+    tempo <- fun_check(data = dot.jitter, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(dot.seed)){
+        tempo <- fun_check(data = dot.seed, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = TRUE, fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = dot.seed, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = dot.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = dot.alpha, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = dot.border.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    if( ! is.null(dot.border.color)){
+        tempo1 <- fun_check(data = dot.border.color, class = "vector", mode = "character", length = 1, fun.name = function.name)
+        tempo2 <- fun_check(data = dot.border.color, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.border.color ARGUMENT MUST BE (1) A HEXADECIMAL COLOR STRING STARTING BY #, OR (2) A COLOR NAME GIVEN BY colors(), OR (3) AN INTEGER VALUE")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }else if(tempo1$problem == FALSE & tempo2$problem == TRUE){
+            if( ! all(dot.border.color %in% colors() | grepl(pattern = "^#", dot.border.color), na.rm = TRUE)){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.border.color ARGUMENT MUST BE (1) A HEXADECIMAL COLOR STRING STARTING BY #, OR (2) A COLOR NAME GIVEN BY colors(), OR (3) AN INTEGER VALUE")
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = dot.border.color, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(x.lab)){
+        tempo1 <- fun_check(data = x.lab, class = "expression", length = 1, fun.name = function.name)
+        tempo2 <- fun_check(data = x.lab,  class = "vector", mode = "character", length = 1, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nx.lab ARGUMENT MUST BE A SINGLE CHARACTER STRING OR EXPRESSION")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = x.lab, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = x.angle, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, neg.values = TRUE, fun.name = function.name) ; eval(ee)
+    if( ! is.null(y.lab)){
+        tempo1 <- fun_check(data = y.lab, class = "expression", length = 1, fun.name = function.name)
+        tempo2 <- fun_check(data = y.lab,  class = "vector", mode = "character", length = 1, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lab ARGUMENT MUST BE A SINGLE CHARACTER STRING OR EXPRESSION")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = y.lab, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(y.lim)){
+        tempo <- fun_check(data = y.lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if(any(is.infinite(y.lim))){ # normally no NA for is.infinite() output
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = y.lim, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = y.log, options = c("no", "log2", "log10"), length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(y.tick.nb)){
+        tempo <- fun_check(data = y.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if(y.tick.nb < 0){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ny.tick.nb ARGUMENT MUST BE A NON NULL POSITIVE INTEGER")
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = y.tick.nb, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(y.second.tick.nb)){
+        tempo <- fun_check(data = y.second.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if(y.second.tick.nb <= 0){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ny.second.tick.nb ARGUMENT MUST BE A NON NULL POSITIVE INTEGER")
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = y.second.tick.nb, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = y.include.zero, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y.top.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y.bottom.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(stat.pos)){
+        tempo <- fun_check(data = stat.pos, options = c("top", "above"), length = 1, fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = stat.pos, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = stat.mean, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = stat.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = stat.dist, class = "vector", mode = "numeric", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = stat.angle, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, neg.values = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = vertical, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = title, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = title.text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = legend.show, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(legend.width)){
+        tempo <- fun_check(data = legend.width, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = legend.width, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = article, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = grid, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(add)){
+        tempo <- fun_check(data = add, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = add, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = return, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = return.ggplot, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = return.gtable, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = plot, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(lib.path)){
+        tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if( ! all(dir.exists(lib.path), na.rm = TRUE)){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
+                tempo.cat <- paste0("ERROR IN ", function.name, "\nDIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = lib.path, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if(any(arg.check) == TRUE){ # normally no NA
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between == #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument primary checking
+    # second round of checking and data preparation
+    # management of NA arguments
+    tempo.arg <- names(arg.user.setting) # values provided by the user
+    tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length) == 1L # no argument provided by the user can be just NA
+    if(any(tempo.log) == TRUE){ # normally no NA because is.na() used here
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT JUST BE NA")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NA arguments
+    # management of NULL arguments
+    tempo.arg <-c(
+        "data1", 
+        "y", 
+        "categ", 
+        "box.fill", 
+        "box.width", 
+        "box.space", 
+        "box.line.size", 
+        "box.notch", 
+        "box.alpha", 
+        "box.mean", 
+        "box.whisker.kind", 
+        "box.whisker.width", 
+        # "dot.color", # inactivated because can be null
+        "dot.tidy", 
+        "dot.tidy.bin.nb", 
+        "dot.jitter", 
+        # "dot.seed", # inactivated because can be null
+        "dot.size", 
+        "dot.alpha", 
+        "dot.border.size", 
+        "x.angle", 
+        "y.log", 
+        # "y.second.tick.nb", # inactivated because can be null
+        "y.include.zero", 
+        "y.top.extra.margin", 
+        "y.bottom.extra.margin", 
+        # "stat.pos", # inactivated because can be null
+        "stat.mean", 
+        "stat.size", 
+        "stat.dist", 
+        "stat.angle", 
+        "vertical", 
+        "text.size", 
+        "title", 
+        "title.text.size", 
+        "legend.show", 
+        # "legend.width", # inactivated because can be null
+        "article", 
+        "grid", 
+        "return", 
+        "return.ggplot", 
+        "return.gtable", 
+        "plot", 
+        "warn.print"
+    )
+    tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
+    if(any(tempo.log) == TRUE){# normally no NA with is.null()
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NULL arguments
+    # code that protects set.seed() in the global environment
+    # see also Protocol 100-rev0 Parallelization in R.docx
+    if(exists(".Random.seed", envir = .GlobalEnv)){ # if .Random.seed does not exists, it means that no random operation has been performed yet in any R environment
+        tempo.random.seed <- .Random.seed
+        on.exit(assign(".Random.seed", tempo.random.seed, env = .GlobalEnv))
+    }else{
+        on.exit(set.seed(NULL)) # inactivate seeding -> return to complete randomness
+    }
+    set.seed(dot.seed)
+    # end code that protects set.seed() in the global environment
+    # warning initiation
+    ini.warning.length <- options()$warning.length
+    options(warning.length = 8170)
+    warn <- NULL
+    warn.count <- 0
+    # end warning initiation
+    # other checkings
+    if(any(duplicated(names(data1)), na.rm = TRUE)){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nDUPLICATED COLUMN NAMES OF data1 ARGUMENT NOT ALLOWED:\n", paste(names(data1)[duplicated(names(data1))], collapse = " "))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! (y %in% names(data1))){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\ny ARGUMENT MUST BE A COLUMN NAME OF data1")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else{
+        tempo <- fun_check(data = data1[, y], data.name = "y COLUMN OF data1", class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name)
+        if(tempo$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ny ARGUMENT MUST BE NUMERIC COLUMN IN data1")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if(length(categ) > 2){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg ARGUMENT CANNOT HAVE MORE THAN 2 COLUMN NAMES OF data1")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else if( ! all(categ %in% names(data1))){ # all() without na.rm -> ok because categ cannot be NA (tested above)
+        tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg ARGUMENT MUST BE COLUMN NAMES OF data1. HERE IT IS:\n", paste(categ, collapse = " "))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(length(dot.categ) > 1){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ ARGUMENT CANNOT HAVE MORE THAN 1 COLUMN NAMES OF data1")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else if( ! all(dot.categ %in% names(data1))){ # all() without na.rm -> ok because dot.categ cannot be NA (tested above)
+        tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ ARGUMENT MUST BE COLUMN NAMES OF data1. HERE IT IS:\n", paste(dot.categ, collapse = " "))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # reserved word checking
+    if(any(names(data1) %in% reserved.words, na.rm = TRUE)){
+        if(any(duplicated(names(data1)), na.rm = TRUE)){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nDUPLICATED COLUMN NAMES OF data1 ARGUMENT NOT ALLOWED:\n", paste(names(data1)[duplicated(names(data1))], collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if( ! is.null(dot.categ)){
+            if(dot.categ %in% categ){
+                reserved.words <- c(reserved.words, paste0(dot.categ, "_DOT")) # paste0(dot.categ, "_DOT") is added to the reserved words because in such situation, a new column will be added to data1 that is named paste0(dot.categ, "_DOT")
+            }
+        }
+        tempo.output <- fun_name_change(names(data1), reserved.words)
+        for(i2 in 1:length(tempo.output$ini)){ # a loop to be sure to take the good ones
+            names(data1)[names(data1) == tempo.output$ini[i2]] <- tempo.output$post[i2]
+            if(any(y == tempo.output$ini[i2])){ # any() without na.rm -> ok because y cannot be NA (tested above)
+                y[y == tempo.output$ini[i2]] <- tempo.output$post[i2]
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") IN y ARGUMENT (COLUMN NAMES OF data1 ARGUMENT),\n", tempo.output$ini[i2], " HAS BEEN REPLACED BY ", tempo.output$post[i2], "\nBECAUSE RISK OF BUG AS SOME NAMES IN y ARGUMENT ARE RESERVED WORD USED BY THE ", function.name, " FUNCTION")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+            # WARNING: names of y argument potentially replaced
+            if(any(categ == tempo.output$ini[i2])){ # any() without na.rm -> ok because categ cannot be NA (tested above)
+                categ[categ == tempo.output$ini[i2]] <- tempo.output$post[i2]
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") IN categ ARGUMENT (COLUMN NAMES OF data1 ARGUMENT),\n", tempo.output$ini[i2], " HAS BEEN REPLACED BY ", tempo.output$post[i2], "\nBECAUSE RISK OF BUG AS SOME NAMES IN categ ARGUMENT ARE RESERVED WORD USED BY THE ", function.name, " FUNCTION")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+            # WARNING: names of categ argument potentially replaced
+            if( ! is.null(dot.categ)){
+                if(any(dot.categ == tempo.output$ini[i2])){ # any() without na.rm -> ok because dot.categ cannot be NA (tested above)
+                    dot.categ[dot.categ == tempo.output$ini[i2]] <- tempo.output$post[i2]
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") IN dot.categ ARGUMENT (COLUMN NAMES OF data1 ARGUMENT),\n", tempo.output$ini[i2], " HAS BEEN REPLACED BY ", tempo.output$post[i2], "\nBECAUSE RISK OF BUG AS SOME NAMES IN dot.categ ARGUMENT ARE RESERVED WORD USED BY THE ", function.name, " FUNCTION")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }
+            # WARNING: names of dot.categ argument potentially replaced
+        }
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") REGARDING COLUMN NAMES REPLACEMENT, THE NAMES\n", paste(tempo.output$ini, collapse = " "), "\nHAVE BEEN REPLACED BY\n", paste(tempo.output$post, collapse = " "))
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        if( ! (is.null(add) | is.null(tempo.output$ini))){
+            if(grepl(x = add, pattern = paste(tempo.output$ini, collapse = "|"))){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\nDETECTION OF COLUMN NAMES OF data1 IN THE add ARGUMENT STRING, THAT CORRESPOND TO RESERVED STRINGS FOR ", function.name, "\nCOLUMN NAMES HAVE TO BE CHANGED\nTHE PROBLEMATIC COLUMN NAMES ARE SOME OF THESE NAMES:\n", paste(tempo.output$ini, collapse = " "), "\nIN THE DATA FRAME OF data1 AND IN THE STRING OF add ARGUMENT, TRY TO REPLACE NAMES BY:\n", paste(tempo.output$post, collapse = " "), "\n\nFOR INFORMATION, THE RESERVED WORDS ARE:\n", paste(reserved.words, collapse = "\n"))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+        }
+    }
+    if( ! (is.null(add))){
+        if(any(sapply(X = arg.names, FUN = grepl, x = add), na.rm = TRUE)){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") NAMES OF ", function.name, " ARGUMENTS DETECTED IN THE add STRING:\n", paste(arg.names[sapply(X = arg.names, FUN = grepl, x = add)], collapse = "\n"), "\nRISK OF WRONG OBJECT USAGE INSIDE ", function.name)
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    # end reserved word checking
+    # verif of add
+    if( ! is.null(add)){
+        if( ! grepl(pattern = "^\\s*\\+", add)){ # check that the add string start by +
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nadd ARGUMENT MUST START WITH \"+\": ", paste(unique(add), collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else if( ! grepl(pattern = "(ggplot2|lemon)\\s*::", add)){ #
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nFOR EASIER FUNCTION DETECTION, add ARGUMENT MUST CONTAIN \"ggplot2::\" OR \"lemon::\" IN FRONT OF EACH GGPLOT2 FUNCTION: ", paste(unique(add), collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else if( ! grepl(pattern = ")\\s*$", add)){ # check that the add string finished by )
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nadd ARGUMENT MUST FINISH BY \")\": ", paste(unique(add), collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # end verif of add
+    # management of add containing facet
+    facet.categ <- NULL
+    if( ! is.null(add)){
+        facet.check <- TRUE
+        tempo <- unlist(strsplit(x = add, split = "\\s*\\+\\s*(ggplot2|lemon)\\s*::\\s*")) #
+        tempo <- sub(x = tempo, pattern = "^facet_wrap", replacement = "ggplot2::facet_wrap")
+        tempo <- sub(x = tempo, pattern = "^facet_grid", replacement = "ggplot2::facet_grid")
+        tempo <- sub(x = tempo, pattern = "^facet_rep", replacement = "lemon::facet_rep")
+        if(any(grepl(x = tempo, pattern = "ggplot2::facet_wrap|lemon::facet_rep_wrap"), na.rm = TRUE)){
+            tempo1 <- suppressWarnings(eval(parse(text = tempo[grepl(x = tempo, pattern = "ggplot2::facet_wrap|lemon::facet_rep_wrap")])))
+            facet.categ <- names(tempo1$params$facets)
+            tempo.text <- "facet_wrap OR facet_rep_wrap"
+            facet.check <- FALSE
+        }else if(grepl(x = add, pattern = "ggplot2::facet_grid|lemon::facet_rep_grid")){
+            tempo1 <- suppressWarnings(eval(parse(text = tempo[grepl(x = tempo, pattern = "ggplot2::facet_grid|lemon::facet_rep_grid")])))
+            facet.categ <- c(names(tempo1$params$rows), names(tempo1$params$cols))
+            tempo.text <- "facet_grid OR facet_rep_grid"
+            facet.check <- FALSE
+        }
+        if(facet.check == FALSE & ! all(facet.categ %in% names(data1))){ # WARNING: all(facet.categ %in% names(data1)) is TRUE when facet.categ is NULL # all() without na.rm -> ok because facet.categ cannot be NA (tested above)
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nDETECTION OF \"", tempo.text, "\" STRING IN THE add ARGUMENT BUT PROBLEM OF VARIABLE DETECTION (COLUMN NAMES OF data1)\nTHE DETECTED VARIABLES ARE:\n", paste(facet.categ, collapse = " "), "\nTHE data1 COLUMN NAMES ARE:\n", paste(names(data1), collapse = " "), "\nPLEASE REWRITE THE add STRING AND RERUN")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # end management of add containing facet
+    # conversion of categ columns in data1 into factors
+    for(i1 in 1:length(categ)){
+        tempo1 <- fun_check(data = data1[, categ[i1]], data.name = paste0("categ NUMBER ", i1, " OF data1"), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name)
+        tempo2 <- fun_check(data = data1[, categ[i1]], data.name = paste0("categ NUMBER ", i1, " OF data1"), class = "factor", na.contain = TRUE, fun.name = function.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\n", paste0("categ NUMBER ", i1, " OF data1"), " MUST BE A FACTOR OR CHARACTER VECTOR")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else if(tempo1$problem == FALSE){ # character vector
+            if(box.alpha != 0){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") IN categ NUMBER ", i1, " IN data1, THE CHARACTER COLUMN HAS BEEN CONVERTED TO FACTOR, WITH LEVELS ACCORDING TO THE ALPHABETICAL ORDER")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+        }
+        data1[, categ[i1]] <- factor(data1[, categ[i1]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
+    }
+    # OK: all the categ columns of data1 are factors from here
+    # end conversion of categ columns in data1 into factors
+    
+    
+    
+    # management of log scale and Inf removal
+    if(any(( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])))){ # is.finite also detects NA: ( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])) detects only Inf  # normally no NA with is.finite0() and is.na()
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") PRESENCE OF -Inf OR Inf VALUES IN THE ", y, " COLUMN OF THE data1 ARGUMENT AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
+    data1.ini <- data1 # strictly identical to data1 except that in data1 y is log converted if and only if y.log != "no"
+    if(y.log != "no"){
+        tempo1 <- ! is.finite(data1[, y]) # where are initial NA and Inf
+        data1[, y] <- suppressWarnings(get(y.log)(data1[, y]))# no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
+        if(any( ! (tempo1 | is.finite(data1[, y])))){ # normally no NA with is.finite
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") LOG CONVERSION INTRODUCED -Inf OR Inf OR NaN VALUES IN THE ", y, " COLUMN OF THE data1 ARGUMENT AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    # Inf removal
+    if(any(( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])))){ # is.finite also detects NA: ( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])) detects only Inf # normally no NA with is.finite
+        removed.row.nb <- which(( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])))
+        removed.rows <- data1.ini[removed.row.nb, ] # here data1.ini used to have the y = O rows that will be removed because of Inf creation after log transformation
+        data1 <- data1[-removed.row.nb, ] #
+        data1.ini <- data1.ini[-removed.row.nb, ] #
+    }else{
+        removed.row.nb <- NULL
+        removed.rows <- data.frame(stringsAsFactors = FALSE)
+    }
+    # From here, data1 and data.ini have no more Inf
+    # end Inf removal
+    if(y.log != "no" & ! is.null(y.lim)){
+        if(any(y.lim <= 0)){ # any() without na.rm -> ok because y.lim cannot be NA (tested above)
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT CANNOT HAVE ZERO OR NEGATIVE VALUES WITH THE y.log ARGUMENT SET TO ", y.log, ":\n", paste(y.lim, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else if(any( ! is.finite(if(y.log == "log10"){log10(y.lim)}else{log2(y.lim)}))){ # normally no NA with is.finite
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT RETURNS INF/NA WITH THE y.log ARGUMENT SET TO ", y.log, "\nAS SCALE COMPUTATION IS ", ifelse(y.log == "log10", "log10", "log2"), ":\n", paste(if(y.log == "log10"){log10(y.lim)}else{log2(y.lim)}, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if(y.log != "no" & y.include.zero == TRUE){
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") y.log ARGUMENT SET TO ", y.log, " AND y.include.zero ARGUMENT SET TO TRUE -> y.include.zero ARGUMENT RESET TO FALSE BECAUSE 0 VALUE CANNOT BE REPRESENTED IN LOG SCALE")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        y.include.zero <- FALSE
+    }
+    if(y.log != "no" & vertical == FALSE){
+        vertical <- TRUE
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") BECAUSE OF A BUG IN ggplot2, CANNOT FLIP BOXES HORIZONTALLY WITH A Y.LOG SCALE -> vertical ARGUMENT RESET TO TRUE")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
+    # end management of log scale and Inf removal
+    # na detection and removal (done now to be sure of the correct length of categ)
+    column.check <- unique(c(y, categ, if( ! is.null(dot.color) & ! is.null(dot.categ)){dot.categ}, if( ! is.null(facet.categ)){facet.categ})) # dot.categ because can be a 3rd column of data1, categ.color and dot.color will be tested later
+    if(any(is.na(data1[, column.check]))){ # data1 used here instead of data1.ini in case of new NaN created by log conversion (neg values) # normally no NA with is.na
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") NA DETECTED IN COLUMNS OF data1 AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        for(i2 in 1:length(column.check)){
+            if(any(is.na(data1[, column.check[i2]]))){ # normally no NA with is.na
+                tempo.warn <- paste0("NA REMOVAL DUE TO COLUMN ", column.check[i2], " OF data1")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n", tempo.warn)))
+            }
+        }
+        tempo <- unique(unlist(lapply(lapply(c(data1[column.check]), FUN = is.na), FUN = which)))
+        removed.row.nb <- c(removed.row.nb, tempo) # removed.row.nb created to remove Inf
+        removed.rows <- rbind(removed.rows, data1.ini[tempo, ], stringsAsFactors = FALSE) # here data1.ini used to have the non NA rows that will be removed because of NAN creation after log transformation (neg values for instance)
+        column.check <- column.check[ ! column.check == y] # remove y to keep quali columns
+        if(length(tempo) != 0){
+            data1 <- data1[-tempo, ] # WARNING tempo here and not removed.row.nb because the latter contain more numbers thant the former
+            data1.ini <- data1.ini[-tempo, ] # WARNING tempo here and not removed.row.nb because the latter contain more numbers than the former
+            for(i3 in 1:length(column.check)){
+                if(any( ! unique(removed.rows[, column.check[i3]]) %in% unique(data1[, column.check[i3]]), na.rm = TRUE)){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") IN COLUMN ", column.check[i3], " OF data1, THE FOLLOWING CLASSES HAVE DISAPPEARED AFTER NA/Inf REMOVAL (IF COLUMN USED IN THE PLOT, THIS CLASS WILL NOT BE DISPLAYED):\n", paste(unique(removed.rows[, column.check[i3]])[ ! unique(removed.rows[, column.check[i3]]) %in% unique(data1[, column.check[i3]])], collapse = " "))
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }
+        }
+        count.categ <- 0
+        for(i2 in 1:length(column.check)){
+            if(column.check[i2] %in% categ){
+                count.categ <- count.categ + 1
+            }
+            if(column.check[i2] == categ[count.categ]){
+                categ.class.order[count.categ] <- list(levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]])]) # remove the absent color in the character vector
+                data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = unique(categ.class.order[[count.categ]]))
+            }
+            if( ! is.null(dot.color) & ! is.null(dot.categ)){ # reminder : dot.categ cannot be a column name of categ anymore (because in that case dot.categ name is changed into "..._DOT"
+                if(column.check[i2] == dot.categ){
+                    dot.categ.class.order <- levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]])] # remove the absent color in the character vector
+                    data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = unique(dot.categ.class.order))
+                }
+            }
+            if(column.check[i2] %in% facet.categ){ # works if facet.categ == NULL this method should keep the order of levels when removing some levels
+                tempo.levels <- levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(as.character(data1[, column.check[i2]]))]
+                data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = tempo.levels)
+            }
+        }
+    }
+    # end na detection and removal (done now to be sure of the correct length of categ)
+    # From here, data1 and data.ini have no more NA or NaN in y, categ, dot.categ (if dot.color != NULL) and facet.categ
+    
+    
+    
+    if( ! is.null(categ.class.order)){
+        if(length(categ.class.order) != length(categ)){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg.class.order ARGUMENT MUST BE A LIST OF LENGTH EQUAL TO LENGTH OF categ\nHERE IT IS LENGTH: ", length(categ.class.order), " VERSUS ", length(categ))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            for(i3 in 1:length(categ.class.order)){
+                if(is.null(categ.class.order[[i3]])){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") THE categ.class.order COMPARTMENT ", i3, " IS NULL. ALPHABETICAL ORDER WILL BE APPLIED")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    data1[, categ[i3]] <- factor(as.character(data1[, categ[i3]])) # if already a factor, change nothing, if characters, levels according to alphabetical order
+                    categ.class.order[[i3]] <- levels(data1[, categ[i3]]) # character vector that will be used later
+                }else{
+                    tempo <- fun_check(data = categ.class.order[[i3]], data.name = paste0("COMPARTMENT ", i3 , " OF categ.class.order ARGUMENT"), class = "vector", mode = "character", length = length(levels(data1[, categ[i3]])), fun.name = function.name) # length(data1[, categ[i1]) -> if data1[, categ[i1] was initially character vector, then conversion as factor after the NA removal, thus class number ok. If data1[, categ[i1] was initially factor, no modification after the NA removal, thus class number ok
+                    if(tempo$problem == TRUE){
+                        stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+                    }
+                }
+                if(any(duplicated(categ.class.order[[i3]]), na.rm = TRUE)){
+                    tempo.cat <- paste0("ERROR IN ", function.name, "\nCOMPARTMENT ", i3, " OF categ.class.order ARGUMENT CANNOT HAVE DUPLICATED CLASSES: ", paste(categ.class.order[[i3]], collapse = " "))
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+                }else if( ! (all(categ.class.order[[i3]] %in% unique(data1[, categ[i3]]), na.rm = TRUE) & all(unique(data1[, categ[i3]]) %in% categ.class.order[[i3]], na.rm = TRUE))){
+                    tempo.cat <- paste0("ERROR IN ", function.name, "\nCOMPARTMENT ", i3, " OF categ.class.order ARGUMENT MUST BE CLASSES OF ELEMENT ", i3, " OF categ ARGUMENT\nHERE IT IS:\n", paste(categ.class.order[[i3]], collapse = " "), "\nFOR COMPARTMENT ", i3, " OF categ.class.order AND IT IS:\n", paste(unique(data1[, categ[i3]]), collapse = " "), "\nFOR COLUMN ", categ[i3], " OF data1")
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+                }else{
+                    data1[, categ[i3]] <- factor(data1[, categ[i3]], levels = categ.class.order[[i3]]) # reorder the factor
+                    
+                }
+                names(categ.class.order)[i3] <- categ[i3]
+            }
+        }
+    }else{
+        categ.class.order <- vector("list", length = length(categ))
+        tempo.categ.class.order <- NULL
+        for(i2 in 1:length(categ.class.order)){
+            categ.class.order[[i2]] <- levels(data1[, categ[i2]])
+            names(categ.class.order)[i2] <- categ[i2]
+            tempo.categ.class.order <- c(tempo.categ.class.order, ifelse(i2 != 1, "\n", ""), categ.class.order[[i2]])
+        }
+        if(box.alpha != 0){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") THE categ.class.order SETTING IS NULL. ALPHABETICAL ORDER WILL BE APPLIED FOR BOX ORDERING:\n", paste(tempo.categ.class.order, collapse = " "))
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    # categ.class.order not NULL anymore (list)
+    if(is.null(box.legend.name) & box.alpha != 0){
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") THE box.legend.name SETTING IS NULL. NAMES OF categ WILL BE USED: ", paste(categ, collapse = " "))
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        box.legend.name <- categ[length(categ)] # if only categ1, then legend name of categ1, if length(categ) == 2L, then legend name of categ2
+    }
+    # box.legend.name not NULL anymore (character string)
+    # management of categ.color
+    if( ! is.null(categ.color)){
+        # check the nature of color
+        # integer colors into gg_palette
+        tempo.check.color <- fun_check(data = categ.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name)$problem
+        if(tempo.check.color == FALSE){
+            # convert integers into colors
+            categ.color <- fun_gg_palette(max(categ.color, na.rm = TRUE))[categ.color]
+        }
+        # end integer colors into gg_palette
+        if( ! (all(categ.color %in% colors() | grepl(pattern = "^#", categ.color)))){ # check that all strings of low.color start by #, # all() without na.rm -> ok because categ.color cannot be NA (tested above)
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg.color ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors(): ", paste(unique(categ.color), collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(is.na(categ.color)) & box.alpha != 0){ # normally no NA with is.na
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") categ.color ARGUMENT CONTAINS NA")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+        # end check the nature of color
+        # check the length of color
+        categ.len <- length(categ) # if only categ1, then colors for classes of categ1, if length(categ) == 2L, then colors for classes of categ2
+        if(length(data1[, categ[categ.len]]) == length(levels(data1[, categ[categ.len]])) & length(categ.color) == length(data1[, categ[categ.len]])){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") THE NUMBER OF CLASSES OF THE COLUMN ", categ[categ.len], " THE NUMBER OF ROWS OF THIS COLUMN AND THE NUMBER OF COLORS OF THE categ.color ARGUMENT ARE ALL EQUAL. BOX COLORS WILL BE ATTRIBUTED ACCORDING THE LEVELS OF ", categ[categ.len], ", NOT ACCORDING TO THE ROWS OF ", categ[categ.len])
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+        if(length(categ.color) == length(levels(data1[, categ[categ.len]]))){ # here length(categ.color) is equal to the different number of categ
+            # data1[, categ[categ.len]] <- factor(data1[, categ[categ.len]]) # not required because sure that is is a factor
+            data1 <- data.frame(data1, categ.color = data1[, categ[categ.len]], stringsAsFactors = TRUE)  # no need stringsAsFactors here for stat.nolog as factors remain factors
+            data1$categ.color <- factor(data1$categ.color, labels = categ.color) # replace the characters of data1[, categ[categ.len]] put in the categ.color column by the categ.color (can be write like this because categ.color is length of levels of data1[, categ[categ.len]])
+            if(box.alpha != 0){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") IN ", categ[categ.len], " OF categ ARGUMENT, THE FOLLOWING COLORS:\n", paste(categ.color, collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(factor(data1[, categ[categ.len]])), collapse = " "))
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+        }else if(length(categ.color) == length(data1[, categ[categ.len]])){# here length(categ.color) is equal to nrow(data1) -> Modif to have length(categ.color) equal to the different number of categ (length(categ.color) == length(levels(data1[, categ[categ.len]])))
+            data1 <- data.frame(data1, categ.color = categ.color, stringsAsFactors = TRUE)
+            tempo.check <- unique(data1[ , c(categ[categ.len], "categ.color")])
+            if( ! (nrow(tempo.check) == length(unique(categ.color)) & nrow(tempo.check) == length(unique(data1[ , categ[categ.len]])))){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg.color ARGUMENT HAS THE LENGTH OF data1 ROW NUMBER\nBUT IS INCORRECTLY ASSOCIATED TO EACH CLASS OF categ ", categ[categ.len], ":\n", paste(unique(mapply(FUN = "paste", data1[ ,categ[categ.len]], data1[ ,"categ.color"])), collapse = "\n"))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }else{
+                # data1[, categ[categ.len]] <- factor(data1[, categ[categ.len]]) # not required because sure that is is a factor
+                categ.color <- unique(data1$categ.color[order(data1[, categ[categ.len]])]) # Modif to have length(categ.color) equal to the different number of categ (length(categ.color) == length(levels(data1[, categ[categ.len]])))
+                if(box.alpha != 0){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") categ.color ARGUMENT HAS THE LENGTH OF data1 ROW NUMBER\nCOLORS HAVE BEEN RESPECTIVELY ASSOCIATED TO EACH CLASS OF categ ", categ[categ.len], " AS:\n", paste(levels(factor(data1[, categ[categ.len]])), collapse = " "), "\n", paste(categ.color, collapse = " "))
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }
+        }else if(length(categ.color) == 1L){
+            # data1[, categ[categ.len]] <- factor(data1[, categ[categ.len]]) # not required because sure that is is a factor
+            data1 <- data.frame(data1, categ.color = categ.color, stringsAsFactors = TRUE)
+            categ.color <- rep(categ.color, length(levels(data1[, categ[categ.len]])))
+            if(box.alpha != 0){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") categ.color ARGUMENT HAS LENGTH 1, MEANING THAT ALL THE DIFFERENT CLASSES OF ", categ[categ.len], "\n", paste(levels(factor(data1[, categ[categ.len]])), collapse = " "), "\nWILL HAVE THE SAME COLOR\n", paste(categ.color, collapse = " "))
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+        }else{
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ncateg.color ARGUMENT MUST BE (1) LENGTH 1, OR (2) THE LENGTH OF data1 NROWS AFTER NA/Inf REMOVAL, OR (3) THE LENGTH OF THE CLASSES IN THE categ ", categ[categ.len], " COLUMN. HERE IT IS COLOR LENGTH ", length(categ.color), " VERSUS CATEG LENGTH ", length(data1[, categ[categ.len]]), " AND CATEG CLASS LENGTH ", length(unique(data1[, categ[categ.len]])), "\nPRESENCE OF NA/Inf COULD BE THE PROBLEM")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }else{
+        categ.len <- length(categ) # if only categ1, then colors for classes of categ1, if length(categ) == 2L, then colors for classes of categ2
+        # data1[, categ[categ.len]] <- factor(data1[, categ[categ.len]]) # not required because sure that is is a factor
+        categ.color <- fun_gg_palette(length(levels(data1[, categ[categ.len]])))
+        data1 <- data.frame(data1, categ.color = data1[, categ[categ.len]], stringsAsFactors = TRUE)
+        data1$categ.color <- factor(data1$categ.color, labels = categ.color)  # replace the characters of data1[, categ[categ.len]] put in the categ.color column by the categ.color (can be write like this because categ.color is length of levels of data1[, categ[categ.len]])
+        if(box.alpha != 0){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") NULL categ.color ARGUMENT -> COLORS RESPECTIVELY ATTRIBUTED TO EACH CLASS OF ", categ[categ.len], " IN data1:\n", paste(categ.color, collapse = " "), "\n", paste(levels(data1[, categ[categ.len]]), collapse = " "))
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    # categ.color not NULL anymore
+    categ.color <- as.character(categ.color)
+    # categ.color is a character string representing the diff classes
+    data1$categ.color <- factor(data1$categ.color, levels = unique(categ.color)) # ok because if categ.color is a character string, the order make class 1, class 2, etc. unique() because no duplicates allowed
+    # data1$categ.color is a factor with order of levels -> categ.color
+    # end management of categ.color
+    # management of dot.color
+    if( ! is.null(dot.color)){
+        # optional legend of dot colors
+        if( ! is.null(dot.categ)){
+            ini.dot.categ <- dot.categ
+            if( ! dot.categ %in% names(data1)){ # no need to use all() because length(dot.categ) = 1
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ ARGUMENT MUST BE A COLUMN NAME OF data1. HERE IT IS:\n", dot.categ)
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }else if(dot.categ %in% categ){ # no need to use all() because length(dot.categ) = 1. Do not use dot.categ %in% categ[length(categ)] -> error
+                # management of dot legend if dot.categ %in% categ (because legends with the same name are joined in ggplot2) 
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") THE COLUMN NAME OF data1 INDICATED IN THE dot.categ ARGUMENT (", dot.categ, ") HAS BEEN REPLACED BY ", paste0(dot.categ, "_DOT"), " TO AVOID MERGED LEGEND BY GGPLOT2")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                data1 <- data.frame(data1, dot.categ = data1[, dot.categ], stringsAsFactors = TRUE) # dot.categ is not a column name of data1 (checked above with reserved words)
+                dot.categ <- paste0(dot.categ, "_DOT")
+                names(data1)[names(data1) == "dot.categ"] <- dot.categ # paste0(dot.categ, "_DOT") is not a column name of data1 (checked above with reserved words)
+                # tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ ARGUMENT CANNOT BE A COLUMN NAME OF data1 ALREADY SPECIFIED IN THE categ ARGUMENT:\n", dot.categ, "\nINDEED, dot.categ ARGUMENT IS MADE TO HAVE MULTIPLE DOT COLORS NOT RELATED TO THE BOXPLOT CATEGORIES")
+                # stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            tempo1 <- fun_check(data = data1[, dot.categ], data.name = paste0(dot.categ, " COLUMN OF data1"), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name)
+            tempo2 <- fun_check(data = data1[, dot.categ], data.name = paste0(dot.categ, " COLUMN OF data1"), class = "factor", na.contain = TRUE, fun.name = function.name)
+            if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ COLUMN MUST BE A FACTOR OR CHARACTER VECTOR") #
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            data1[, dot.categ] <- factor(data1[, dot.categ]) # if already a factor, change nothing, if characters, levels according to alphabetical order
+            # dot.categ column of data1 is factor from here
+            if( ! is.null(dot.categ.class.order)){
+                if(any(duplicated(dot.categ.class.order), na.rm = TRUE)){
+                    tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ.class.order ARGUMENT CANNOT HAVE DUPLICATED CLASSES: ", paste(dot.categ.class.order, collapse = " "))
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+                }else if( ! (all(dot.categ.class.order %in% levels(data1[, dot.categ])) & all(levels(data1[, dot.categ]) %in% dot.categ.class.order, na.rm = TRUE))){
+                    tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.categ.class.order ARGUMENT MUST BE CLASSES OF dot.categ ARGUMENT\nHERE IT IS:\n", paste(dot.categ.class.order, collapse = " "), "\nFOR dot.categ.class.order AND IT IS:\n", paste(levels(data1[, dot.categ]), collapse = " "), "\nFOR dot.categ COLUMN (", ini.dot.categ, ") OF data1")
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+                }else{
+                    data1[, dot.categ] <- factor(data1[, dot.categ], levels = dot.categ.class.order) # reorder the factor
+                }
+            }else{
+                if(all(dot.color == "same") & length(dot.color)== 1L){ # all() without na.rm -> ok because dot.color cannot be NA (tested above)
+                    dot.categ.class.order <- unlist(categ.class.order[length(categ)])
+                    data1[, dot.categ] <- factor(data1[, dot.categ], levels = dot.categ.class.order) # reorder the factor
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") THE dot.categ.class.order SETTING IS NULL AND dot.color IS \"same\". ORDER OF categ.class.order WILL BE APPLIED FOR LEGEND DISPLAY: ", paste(dot.categ.class.order, collapse = " "))
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }else{
+                    dot.categ.class.order <- sort(levels(data1[, dot.categ]))
+                    data1[, dot.categ] <- factor(data1[, dot.categ], levels = dot.categ.class.order) # reorder the factor
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") THE dot.categ.class.order SETTING IS NULL. ALPHABETICAL ORDER WILL BE APPLIED FOR LEGEND DISPLAY: ", paste(dot.categ.class.order, collapse = " "))
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }
+            # dot.categ.class.order not NULL anymore (character string) if dot.categ is not NULL
+            if(all(dot.color == "same") & length(dot.color)== 1L){ # all() without na.rm -> ok because dot.color cannot be NA (tested above)
+                if( ! identical(ini.dot.categ, categ[length(categ)])){
+                    tempo.cat <- paste0("ERROR IN ", function.name, "\nWHEN dot.color ARGUMENT IS \"same\", THE COLUMN NAME IN dot.categ ARGUMENT MUST BE IDENTICAL TO THE LAST COLUMN NAME IN categ ARGUMENT. HERE IT IS:\ndot.categ: ", paste(ini.dot.categ, collapse = " "), "\ncateg: ", paste(categ, collapse = " "))
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+                }else if( ! fun_comp_1d(unlist(categ.class.order[length(categ)]), dot.categ.class.order)$identical.content){
+                    tempo.cat <- paste0("ERROR IN ", function.name, "\nWHEN dot.color ARGUMENT IS \"same\",\nLAST COMPARTMENT OF categ.class.order ARGUMENT AND dot.categ.class.order ARGUMENT CANNOT BE DIFFERENT:\nLAST COMPARTMENT OF categ.class.order: ", paste(unlist(categ.class.order[length(categ)]), collapse = " "), "\ndot.categ.class.order: ", paste(dot.categ.class.order, collapse = " "))
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+                }
+            }
+            for(i3 in 1:length(categ)){
+                if(identical(categ[i3], ini.dot.categ) & ! identical(unlist(categ.class.order[i3]), dot.categ.class.order) & identical(sort(unlist(categ.class.order[i3])), sort(dot.categ.class.order))){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") THE dot.categ ARGUMENT SETTING IS PRESENT IN THE categ ARGUMENT SETTING, BUT ORDER OF THE CLASSES IS NOT THE SAME:\ncateg.class.order: ", paste(unlist(categ.class.order[i3]), collapse = " "), "\ndot.categ.class.order: ", paste(dot.categ.class.order, collapse = " "), "\nNOTE THAT ORDER OF categ.class.order IS THE ONE USED FOR THE AXIS REPRESENTATION")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }
+            if(is.null(dot.legend.name)){
+                dot.legend.name <- if(ini.dot.categ %in% categ[length(categ)]){dot.categ}else{ini.dot.categ} #
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") THE dot.legend.name SETTING IS NULL -> ", dot.legend.name, " WILL BE USED AS LEGEND TITLE OF DOTS")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+            # dot.legend.name not NULL anymore (character string)
+        }else{
+            if( ! is.null(dot.categ.class.order)){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") THE dot.categ.class.order ARGUMENT IS NOT NULL, BUT IS THE dot.categ ARGUMENT\n-> dot.categ.class.order NOT CONSIDERED AS NO LEGEND WILL BE DRAWN")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+            # But dot.categ.class.order will be converted to NULL below (not now)
+        }
+        # end optional legend of dot colors
+        # check the nature of color
+        # integer colors into gg_palette
+        tempo.check.color <- fun_check(data = dot.color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name)$problem
+        if(tempo.check.color == FALSE){
+            # convert integers into colors
+            dot.color <- fun_gg_palette(max(dot.color, na.rm = TRUE))[dot.color]
+        }
+        # end integer colors into gg_palette
+        if(all(dot.color == "same") & length(dot.color)== 1L){# all() without na.rm -> ok because dot.color cannot be NA (tested above)
+            dot.color <- categ.color # same color of the dots as the corresponding box color
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") dot.color ARGUMENT HAS BEEN SET TO \"same\"\nTHUS, DOTS WILL HAVE THE SAME COLORS AS THE CORRESPONDING BOXPLOT")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }else if( ! (all(dot.color %in% colors() | grepl(pattern = "^#", dot.color)))){ # check that all strings of low.color start by #, # all() without na.rm -> ok because dot.color cannot be NA (tested above)
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.color ARGUMENT MUST BE (1) A HEXADECIMAL COLOR VECTOR STARTING BY #, OR (2) COLOR NAMES GIVEN BY colors(), OR (3) INTEGERS, OR THE STRING \"same\"\nHERE IT IS: ", paste(unique(dot.color), collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        if(any(is.na(dot.color))){ # normally no NA with is.finite
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") dot.color ARGUMENT CONTAINS NA")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+        # end check the nature of color
+        # check the length of color
+        if( ! is.null(dot.categ)){
+            # optional legend of dot colors
+            if(length(data1[, dot.categ]) == length(levels(data1[, dot.categ])) & length(dot.color) == length(data1[, dot.categ])){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") THE NUMBER OF CLASSES OF THE COLUMN ", dot.categ, " THE NUMBER OF ROWS OF THIS COLUMN AND THE NUMBER OF COLORS OF THE dot.color ARGUMENT ARE ALL EQUAL. DOT COLORS WILL BE ATTRIBUTED ACCORDING THE LEVELS OF ", dot.categ, ", NOT ACCORDING TO THE ROWS OF ", dot.categ)
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+            if(length(dot.color) > 1 & ! (length(dot.color) == length(unique(data1[, dot.categ])) | length(dot.color) == length(data1[, dot.categ]))){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\nWHEN LENGTH OF THE dot.color ARGUMENT IS MORE THAN 1, IT MUST BE EQUAL TO THE NUMBER OF 1) ROWS OR 2) LEVELS OF dot.categ COLUMN (", dot.categ, "):\ndot.color: ", paste(dot.color, collapse = " "), "\ndot.categ LEVELS: ", paste(levels(data1[, dot.categ]), collapse = " "))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }else if(length(dot.color) > 1 & length(dot.color) == length(unique(data1[, dot.categ]))){
+                data1 <- data.frame(data1, dot.color = data1[, dot.categ], stringsAsFactors = TRUE)
+                data1$dot.color <- factor(data1$dot.color, labels = dot.color) # do not use labels = unique(dot.color). Otherwise, we can have green1 green2 when dot.color is c("green", "green")
+            }else if(length(dot.color) > 1 & length(dot.color) == length(data1[, dot.categ])){
+                data1 <- data.frame(data1, dot.color = dot.color, stringsAsFactors = TRUE)
+            }else if(length(dot.color)== 1L){ # to deal with single color. Warning: & length(dot.categ.class.order) > 1 removed because otherwise, the data1 is not with dot.color column when length(dot.categ.class.order) == 1
+                data1 <- data.frame(data1, dot.color = dot.color, stringsAsFactors = TRUE)
+            }
+            dot.color <- as.character(unique(data1$dot.color[order(data1[, dot.categ])])) # reorder the dot.color character vector
+            if(length(dot.color)== 1L & length(dot.categ.class.order) > 1){ # to deal with single color
+                dot.color <- rep(dot.color, length(dot.categ.class.order))
+            }
+            tempo.check <- unique(data1[ , c(dot.categ, "dot.color")])
+            if(length(unique(data1[ , "dot.color"])) > 1 & ( ! (nrow(tempo.check) == length(unique(data1[ , "dot.color"])) & nrow(tempo.check) == length(unique(data1[ , dot.categ]))))){ # length(unique(data1[ , "dot.color"])) > 1 because if only one color, can be attributed to each class of dot.categ
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.color ARGUMENT IS INCORRECTLY ASSOCIATED TO EACH CLASS OF dot.categ (", dot.categ, ") COLUMN:\n", paste(unique(mapply(FUN = "paste", data1[ , dot.categ], data1[ ,"dot.color"])), collapse = "\n"))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }else{
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") IN dot.categ ARGUMENT (", ini.dot.categ, "), THE FOLLOWING COLORS OF DOTS:\n", paste(dot.color, collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(data1[, dot.categ]), collapse = " "))
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+            # dot.color is a character string representing the diff classes of dot.categ
+            # data1$dot.color is a factor with order of levels -> dot.categ
+            # end optional legend of dot colors
+        }else{
+            categ.len <- length(categ) # if only categ1, then colors for classes of categ1, if length(categ) == 2L, then colors for classes of categ2
+            if(length(dot.color) == length(levels(data1[, categ[categ.len]]))){ # here length(dot.color) is equal to the different number of categ
+                # data1[, categ[categ.len]] <- factor(data1[, categ[categ.len]]) # not required because sure that is is a factor
+                data1 <- data.frame(data1, dot.color = data1[, categ[categ.len]], stringsAsFactors = TRUE)
+                data1$dot.color <- factor(data1$dot.color, labels = dot.color)
+                if(box.alpha != 0){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") IN ", categ[categ.len], " OF categ ARGUMENT, THE FOLLOWING COLORS:\n", paste(dot.color, collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(factor(data1[, categ[categ.len]])), collapse = " "))
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }else if(length(dot.color) == length(data1[, categ[categ.len]])){# here length(dot.color) is equal to nrow(data1) -> Modif to have length(dot.color) equal to the different number of categ (length(dot.color) == length(levels(data1[, categ[categ.len]])))
+                data1 <- data.frame(data1, dot.color = dot.color, stringsAsFactors = TRUE)
+            }else if(length(dot.color)== 1L & ! all(dot.color == "same")){ # all() without na.rm -> ok because dot.color cannot be NA (tested above)
+                # data1[, categ[categ.len]] <- factor(data1[, categ[categ.len]]) # not required because sure that is is a factor
+                data1 <- data.frame(data1, dot.color = dot.color, stringsAsFactors = TRUE)
+                dot.color <- rep(dot.color, length(levels(data1[, categ[categ.len]])))
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") dot.color ARGUMENT HAS LENGTH 1, MEANING THAT ALL THE DIFFERENT CLASSES OF ", categ[categ.len], "\n", paste(levels(factor(data1[, categ[categ.len]])), collapse = " "), "\nWILL HAVE THE SAME COLOR\n", paste(dot.color, collapse = " "))
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }else{
+                tempo.cat <- paste0("ERROR IN ", function.name, "\ndot.color ARGUMENT MUST BE (1) LENGTH 1, OR (2) THE LENGTH OF data1 NROWS AFTER NA/Inf REMOVAL, OR (3) THE LENGTH OF THE CLASSES IN THE categ ", categ[categ.len], " COLUMN. HERE IT IS COLOR LENGTH ", length(dot.color), " VERSUS CATEG LENGTH ", length(data1[, categ[categ.len]]), " AND CATEG CLASS LENGTH ", length(unique(data1[, categ[categ.len]])), "\nPRESENCE OF NA/Inf COULD BE THE PROBLEM")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            # end check the length of color
+            dot.color <- as.character(dot.color)
+            # dot.color is a character string representing the diff classes
+            data1$dot.color <- factor(data1$dot.color, levels = unique(dot.color)) # ok because if dot.color is a character string, the order make class 1, class 2, etc. If dot.color is a column of data1, then levels will be created, without incidence, except if dot.categ specified (see below). unique() because no duplicates allowed
+            # data1$dot.color is a factor with order of levels -> dot.color
+        }
+        # end optional legend of dot colors
+    }else if(is.null(dot.color) & ! (is.null(dot.categ) & is.null(dot.categ.class.order) & is.null(dot.legend.name))){
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") dot.categ OR dot.categ.class.order OR dot.legend.name ARGUMENT HAS BEEN SPECIFIED BUT dot.color ARGUMENT IS NULL (NO DOT PLOTTED)")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
+    # dot.color either NULL (no dot plotted) or character string (potentially representing the diff classes of dot.categ)
+    # data1$dot.color is either NA or a factor (with order of levels -> depending on dot.categ or categ[length(categ)], or other
+    if(is.null(dot.categ)){
+        dot.categ.class.order <- NULL # because not used anyway
+    }
+    # dot.categ.class.order either NULL if dot.categ is NULL (no legend displayed) or character string (potentially representing the diff classes of dot.categ)
+    # end management of dot.color
+    if(is.null(dot.color) & box.fill == FALSE & dot.alpha <= 0.025){
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") THE FOLLOWING ARGUMENTS WERE SET AS:\ndot.color = NULL (NOT ALL DOTS BUT ONLY POTENTIAL OUTLIER DOTS DISPLAYED)\nbox.fill = FALSE (NO FILLING COLOR FOR BOTH BOXES AND POTENTIAL OUTLIER DOTS)\ndot.alpha = ", fun_round(dot.alpha, 4), "\n-> POTENTIAL OUTLIER DOTS MIGHT NOT BE VISIBLE BECAUSE ALMOST TRANSPARENT")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
+    if(is.null(dot.color) & box.fill == FALSE & dot.border.size == 0){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nTHE FOLLOWING ARGUMENTS WERE SET AS:\ndot.color = NULL (NOT ALL DOTS BUT ONLY POTENTIAL OUTLIER DOTS DISPLAYED)\nbox.fill = FALSE (NO FILLING COLOR FOR BOTH BOXES AND POTENTIAL OUTLIER DOTS)\ndot.border.size = 0 (NO BORDER FOR POTENTIAL OUTLIER DOTS)\n-> THESE SETTINGS ARE NOT ALLOWED BECAUSE THE POTENTIAL OUTLIER DOTS WILL NOT BE VISIBLE")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # integer dot.border.color into gg_palette
+    if( ! is.null(dot.border.color)){
+        tempo <- fun_check(data = dot.border.color, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name)
+        if(tempo$problem == FALSE){ # convert integers into colors
+            dot.border.color <- fun_gg_palette(max(dot.border.color, na.rm = TRUE))[dot.border.color]
+        }
+    }
+    # end integer dot.border.color into gg_palette
+    # na detection and removal (done now to be sure of the correct length of categ)
+    column.check <- c("categ.color", if( ! is.null(dot.color)){"dot.color"}) # 
+    if(any(is.na(data1[, column.check]))){ # data1 used here instead of data1.ini in case of new NaN created by log conversion (neg values) # normally no NA with is.na
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") NA DETECTED IN COLUMNS ", paste(column.check, collapse = " "), " OF data1 AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        for(i2 in 1:length(column.check)){
+            if(any(is.na(data1[, column.check[i2]]))){ # normally no NA with is.na
+                tempo.warn <- paste0("NA REMOVAL DUE TO COLUMN ", column.check[i2], " OF data1")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n", tempo.warn)))
+            }
+        }
+        tempo <- unique(unlist(lapply(lapply(c(data1[column.check]), FUN = is.na), FUN = which)))
+        removed.row.nb <- c(removed.row.nb, tempo)
+        removed.rows <- rbind(removed.rows, data1[tempo, ], stringsAsFactors = FALSE) # here data1 used because categorical columns tested
+        if(length(tempo) != 0){
+            data1 <- data1[-tempo, ] # WARNING tempo here and not removed.row.nb because the latter contain more numbers thant the former
+            data1.ini <- data1.ini[-tempo, ] # WARNING tempo here and not removed.row.nb because the latter contain more numbers thant the former
+            for(i3 in 1:length(column.check)){
+                if(any( ! unique(removed.rows[, column.check[i3]]) %in% unique(data1[, column.check[i3]]), na.rm = TRUE)){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") IN COLUMN ", column.check[i3], " OF data1, THE FOLLOWING CLASSES HAVE DISAPPEARED AFTER NA/Inf REMOVAL (IF COLUMN USED IN THE PLOT, THIS CLASS WILL NOT BE DISPLAYED):\n", paste(unique(removed.rows[, column.check[i3]])[ ! unique(removed.rows[, column.check[i3]]) %in% unique(data1[, column.check[i3]])], collapse = " "))
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }
+        }
+        for(i2 in 1:length(column.check)){
+            if(column.check[i2] == "categ.color"){
+                categ.color <- levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]])] # remove the absent color in the character vector
+                if(length(categ.color)== 1L & length(unlist(categ.class.order[length(categ)])) > 1){ # to deal with single color
+                    categ.color <- rep(categ.color, length(unlist(categ.class.order[length(categ)])))
+                }
+                data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = unique(categ.color))
+            }
+            if(column.check[i2] == "dot.color"){
+                dot.color <- levels(data1[, column.check[i2]])[levels(data1[, column.check[i2]]) %in% unique(data1[, column.check[i2]])] # remove the absent color in the character vector
+                if(length(dot.color)== 1L & length(dot.categ.class.order) > 1){ # to deal with single color. If dot.categ.class.order == NULL (which is systematically the case if dot.categ == NULL), no rep(dot.color, length(dot.categ.class.order)
+                    dot.color <- rep(dot.color, length(dot.categ.class.order))
+                }
+                data1[, column.check[i2]] <- factor(as.character(data1[, column.check[i2]]), levels = unique(dot.color))
+            }
+        }
+    }
+    # end na detection and removal (done now to be sure of the correct length of categ)
+    # From here, data1 and data.ini have no more NA or NaN
+    # end other checkings
+    # reserved word checking
+    #already done above
+    # end reserved word checking
+    # end second round of checking and data preparation
+    
+    
+    # package checking
+    fun_pack(req.package = c(
+        "ggplot2", 
+        "gridExtra", 
+        "lemon", 
+        "scales"
+    ), lib.path = lib.path)
+    # end package checking
+    
+    
+    
+    
+    
+    # main code
+    # y coordinates recovery (create ini.box.coord, dot.coord and modify data1)
+    if(length(categ)== 1L){
+        # width commputations
+        box.width2 <- box.width
+        box.space <- 0 # to inactivate the shrink that add space between grouped boxes, because no grouped boxes here
+        # end width commputations
+        # data1 check categ order for dots coordinates recovery
+        data1 <- data.frame(data1, categ.check = data1[, categ[1]], stringsAsFactors = TRUE)
+        data1$categ.check <- as.integer(data1$categ.check) # to check that data1[, categ[1]] and dot.coord$group are similar, during merging
+        # end data1 check categ order for dots coordinates recovery
+        # per box dots coordinates recovery
+        tempo.gg.name <- "gg.indiv.plot."
+        tempo.gg.count <- 0
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::ggplot()", if(is.null(add)){""}else{add})))) # add added here to have the facets
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, color = categ[1]), stroke = dot.border.size, size = dot.size, alpha = dot.alpha, shape = 21))
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "color", name = box.legend.name, values = if(is.null(categ.color)){rep(NA, length(unique(data1[, categ[1]])))}else if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[1]])))}else{categ.color})) # categ.color used for dot colors because at that stage, we do not care about colors
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, fill = categ[1]), coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf})) # fill because this is what is used with geom_box # to easily have the equivalent of the grouped boxes
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "fill", name = box.legend.name, values = if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[1]])))}else{categ.color}))
+        # end per box dots coordinates recovery
+    }else if(length(categ) == 2L){
+        # width commputations
+        box.width2 <- box.width / length(unique(data1[, categ[length(categ)]])) # real width of each box in x-axis unit, among the set of grouped box. Not relevant if no grouped boxes length(categ)== 1L
+        # end width commputations
+        # data1 check categ order for dots coordinates recovery
+        tempo.factor <- paste0(data1[order(data1[, categ[2]], data1[, categ[1]]), categ[2]], "_", data1[order(data1[, categ[2]], data1[, categ[1]]), categ[1]])
+        data1 <- data.frame(data1[order(data1[, categ[2]], data1[, categ[1]]), ], categ.check = factor(tempo.factor, levels = unique(tempo.factor)), stringsAsFactors = TRUE)
+        data1$categ.check <- as.integer(data1$categ.check)
+        # end data1 check categ order for dots coordinates recovery
+        # per box dots coordinates recovery
+        tempo.gg.name <- "gg.indiv.plot."
+        tempo.gg.count <- 0
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::ggplot()", if(is.null(add)){""}else{add})))) # add added here to have the facets
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, color = categ[2]), stroke = dot.border.size, size = dot.size, alpha = dot.alpha, shape = 21))
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "color", name = box.legend.name, values = if(is.null(categ.color)){rep(NA, length(unique(data1[, categ[2]])))}else if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[2]])))}else{categ.color})) # categ.color used for dot colors because at that stage, we do not care about colors
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, fill = categ[2]), coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf})) # fill because this is what is used with geom_box # to easily have the equivalent of the grouped boxes
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "fill", name = box.legend.name, values = if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[2]])))}else{categ.color}))
+        # end per box dots coordinates recovery
+    }else{
+        tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 1")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if( ! is.null(stat.pos)){
+        stat.just <- fun_gg_just(
+            angle = stat.angle, 
+            pos = ifelse(
+                vertical == TRUE, 
+                ifelse(stat.pos == "top", "bottom", "top"), # "bottom" because we want justification for text that are below the ref point which is the top of the graph. The opposite for "above"
+                ifelse(stat.pos == "top", "left", "right") # "left" because we want justification for text that are on the left of the ref point which is the right border of the graph. The opposite for "above"
+            ), 
+            kind = "text"
+        )
+    }
+    # has in fact no interest because ggplot2 does not create room for geom_text()
+    tempo.data.max <- data1[which.max(data1[, y]), ]
+    tempo.data.max <- data.frame(tempo.data.max, label = formatC(tempo.data.max[, y], digit = 2, drop0trailing = TRUE, format = "f"), stringsAsFactors = TRUE)
+    # end has in fact no interest because ggplot2 does not create room for geom_text()
+    tempo.graph.info.ini <- ggplot2::ggplot_build(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if( ! is.null(stat.pos)){' + ggplot2::geom_text(data = tempo.data.max, mapping = ggplot2::aes_string(x = 1, y = y, label = "label"), size = stat.size, color = "black", angle = stat.angle, hjust = stat.just$hjust, vjust = stat.just$vjust)'})))) # added here to have room for annotation
+    dot.coord <- tempo.graph.info.ini$data[[1]]
+    dot.coord$x <- as.numeric(dot.coord$x) # because weird class
+    dot.coord$PANEL <- as.numeric(dot.coord$PANEL) # because numbers as levels. But may be a problem is facet are reordered ?
+    tempo.mean <- aggregate(x = dot.coord$y, by = list(dot.coord$group, dot.coord$PANEL), FUN = mean, na.rm = TRUE)
+    names(tempo.mean)[names(tempo.mean) == "x"] <- "MEAN"
+    names(tempo.mean)[names(tempo.mean) == "Group.1"] <- "BOX"
+    names(tempo.mean)[names(tempo.mean) == "Group.2"] <- "PANEL"
+    dot.coord <- data.frame(
+        dot.coord[order(dot.coord$group, dot.coord$y), ], # dot.coord$PANEL deals below
+        y.check = as.double(data1[order(data1$categ.check, data1[, y]), y]), 
+        categ.check = data1[order(data1$categ.check, data1[, y]), "categ.check"], 
+        dot.color = if(is.null(dot.color)){NA}else{data1[order(data1$categ.check, data1[, y]), "dot.color"]}, 
+        data1[order(data1$categ.check, data1[, y]), ][categ], # avoid the renaming below
+        stringsAsFactors = TRUE
+    ) # y.check to be sure that the order is the same between the y of data1 and the y of dot.coord
+    # names(dot.coord)[names(dot.coord) == "tempo.categ1"] <- categ[1]
+    if( ! is.null(dot.categ)){
+        dot.coord <- data.frame(dot.coord, data1[order(data1$categ.check, data1[, y]), ][dot.categ], stringsAsFactors = TRUE) # avoid the renaming
+    }
+    if( ! is.null(facet.categ)){
+        dot.coord <- data.frame(dot.coord, data1[order(data1$categ.check, data1[, y]), ][facet.categ], stringsAsFactors = TRUE) # for facet panels
+        tempo.test <- NULL
+        for(i2 in 1:length(facet.categ)){
+            tempo.test <- paste0(tempo.test, ".", formatC(as.numeric(dot.coord[, facet.categ[i2]]), width = nchar(max(as.numeric(dot.coord[, facet.categ[i2]]), na.rm = TRUE)), flag = "0")) # convert factor into numeric with leading zero for proper ranking # merge the formatC() to create a new factor. The convertion to integer should recreate the correct group number. Here as.numeric is used and not as.integer in case of numeric in facet.categ (because comes from add and not checked by fun_check, contrary to categ)
+        }
+        tempo.test <- as.integer(factor(tempo.test))
+        if( ! identical(as.integer(dot.coord$PANEL), tempo.test)){
+            tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nas.integer(dot.coord$PANEL) AND tempo.test MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if(dot.tidy == TRUE){
+        if( ! is.null(dot.categ)){
+            dot.coord <- data.frame(dot.coord, tidy_group = data1[order(data1$categ.check, data1[, y]), ][, dot.categ], stringsAsFactors = TRUE) # avoid the renaming
+            # tidy_group_coord is to be able to fuse table when creating the table for dot coordinates
+            if(dot.categ %in% categ){
+                dot.coord <- data.frame(dot.coord, tidy_group_coord = dot.coord$group, stringsAsFactors = TRUE)
+            }else{
+                dot.coord <- data.frame(dot.coord, tidy_group_coord = as.integer(factor(paste0(
+                    formatC(as.integer(dot.coord[, categ[1]]), width = nchar(max(as.integer(dot.coord[, categ[1]]), na.rm = TRUE)), flag = "0"), # convert factor into numeric with leading zero for proper ranking
+                    ".", 
+                    if(length(categ) == 2L){formatC(as.integer(dot.coord[, categ[2]]), width = nchar(max(as.integer(dot.coord[, categ[2]]), na.rm = TRUE)), flag = "0")}, # convert factor into numeric with leading zero for proper ranking
+                    if(length(categ) == 2L){"."}, 
+                    formatC(as.integer(dot.coord[, dot.categ]), width = nchar(max(as.integer(dot.coord[, dot.categ]), na.rm = TRUE)), flag = "0") # convert factor into numeric with leading zero for proper ranking
+                )), stringsAsFactors = TRUE) # merge the 2 or 3 formatC() to create a new factor. The convertion to integer should recreate the correct group number
+                ) # for tidy dot plots
+            }
+        }else{
+            dot.coord <- data.frame(dot.coord, tidy_group = if(length(categ)== 1L){
+                dot.coord[, categ]}else{as.integer(factor(paste0(
+                    formatC(as.integer(dot.coord[, categ[1]]), width = nchar(max(as.integer(dot.coord[, categ[1]]), na.rm = TRUE)), flag = "0"), # convert factor into numeric with leading zero for proper ranking
+                    ".", 
+                    formatC(as.integer(dot.coord[, categ[2]]), width = nchar(max(as.integer(dot.coord[, categ[2]]), na.rm = TRUE)), flag = "0")# convert factor into numeric with leading zero for proper ranking
+                )), stringsAsFactors = TRUE) # merge the 2 formatC() to create a new factor. The convertion to integer should recreate the correct group number
+                }) # for tidy dot plots
+            # tidy_group_coord is to be able to fuse table when creating the table for dot coordinates
+            dot.coord <- data.frame(dot.coord, tidy_group_coord = dot.coord$group, stringsAsFactors = TRUE)
+        }
+    }
+    if( ! (identical(dot.coord$y, dot.coord$y.check) & identical(dot.coord$group, dot.coord$categ.check))){
+        tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\n(dot.coord$y AND dot.coord$y.check) AS WELL AS (dot.coord$group AND dot.coord$categ.check) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else{
+        if( ! identical(tempo.mean[order(tempo.mean$BOX, tempo.mean$PANEL), ]$BOX, unique(dot.coord[order(dot.coord$group, dot.coord$PANEL), c("group", "PANEL")])$group)){
+            tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\n(tempo.mean$BOX, tempo.mean$PANEL) AND (dot.coord$group, dot.coord$PANEL) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            tempo <- unique(dot.coord[order(dot.coord$group, dot.coord$PANEL), c(categ, if( ! is.null(dot.color) & ! is.null(dot.categ)){if(dot.categ != ini.dot.categ){dot.categ}}, if( ! is.null(facet.categ)){facet.categ}), drop = FALSE])
+            # names(tempo) <- paste0(names(tempo), ".mean")
+            tempo.mean <- data.frame(tempo.mean[order(tempo.mean$BOX, tempo.mean$PANEL), ], tempo, stringsAsFactors = TRUE)
+        }
+    }
+    # at that stage, categ color and dot color are correctly attributed in data1, box.coord and dot.coord
+    # end y dot coordinates recovery (create ini.box.coord, dot.coord and modify data1)
+    # ylim range
+    if(is.null(y.lim)){
+        y.lim <- tempo.graph.info.ini$layout$panel_params[[1]]$y.range # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+        if(any(( ! is.finite(y.lim)) | is.na(y.lim)) | length(y.lim) != 2){ # kept but normally no more Inf in data1 # normally no NA with is.finite, etc.
+            tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\ntempo.graph.info.ini$layout$panel_params[[1]]$y.range[1] CONTAINS NA OR Inf OR HAS LENGTH 1")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }else if(y.log != "no"){
+        y.lim <- get(y.log)(y.lim) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
+    }
+    if(y.log != "no"){
+        # normally this control is not necessary anymore
+        if(any( ! is.finite(y.lim))){ # normally no NA with is.finite
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT CANNOT HAVE ZERO OR NEGATIVE VALUES WITH THE y.log ARGUMENT SET TO ", y.log, ":\n", paste(y.lim, collapse = " "), "\nPLEASE, CHECK DATA VALUES (PRESENCE OF ZERO OR INF VALUES)")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    if(suppressWarnings(all(y.lim %in% c(Inf, -Inf)))){ # all() without na.rm -> ok because y.lim cannot be NA (tested above)
+        # normally this control is not necessary anymore
+        tempo.cat <- paste0("ERROR IN ", function.name, " y.lim CONTAINS Inf VALUES, MAYBE BECAUSE VALUES FROM data1 ARGUMENTS ARE NA OR Inf ONLY OR BECAUSE OF LOG SCALE REQUIREMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    if(suppressWarnings(any(is.na(y.lim)))){ # normally no NA with is.na
+        # normally this control is not necessary anymore
+        tempo.cat <- paste0("ERROR IN ", function.name, " y.lim CONTAINS NA OR NaN VALUES, MAYBE BECAUSE VALUES FROM data1 ARGUMENTS ARE NA OR Inf ONLY OR BECAUSE OF LOG SCALE REQUIREMENT")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    y.lim.order <- order(y.lim) # to deal with inverse axis
+    y.lim <- sort(y.lim)
+    y.lim[1] <- y.lim[1] - abs(y.lim[2] - y.lim[1]) * ifelse(diff(y.lim.order) > 0, y.bottom.extra.margin, y.top.extra.margin) # diff(y.lim.order) > 0 medians not inversed axis
+    y.lim[2] <- y.lim[2] + abs(y.lim[2] - y.lim[1]) * ifelse(diff(y.lim.order) > 0, y.top.extra.margin, y.bottom.extra.margin) # diff(y.lim.order) > 0 medians not inversed axis
+    if(y.include.zero == TRUE){ # no need to check y.log != "no" because done before
+        y.lim <- range(c(y.lim, 0), na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+    }
+    y.lim <- y.lim[y.lim.order]
+    if(any(is.na(y.lim))){ # normally no NA with is.na
+        tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 2")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end ylim range
+    
+    
+    
+    
+    
+    
+    # drawing
+    # constant part
+    tempo.gg.name <- "gg.indiv.plot."
+    tempo.gg.count <- 0
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::ggplot()", if(is.null(add)){""}else{add})))) # add is directly put here to deal with additional variable of data, like when using facet_grid. No problem if add is a theme, will be dealt below
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::xlab(if(is.null(x.lab)){categ[1]}else{x.lab}))
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ylab(if(is.null(y.lab)){y}else{y.lab}))
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggtitle(title))
+    # text angle management
+    axis.just <- fun_gg_just(angle = x.angle, pos = ifelse(vertical == TRUE, "bottom", "left"), kind = "axis")
+    # end text angle management
+    add.check <- TRUE
+    if( ! is.null(add)){ # if add is NULL, then = 0
+        if(grepl(pattern = "ggplot2\\s*::\\s*theme", add) == TRUE){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") \"ggplot2::theme\" STRING DETECTED IN THE add ARGUMENT\n-> INTERNAL GGPLOT2 THEME FUNCTIONS theme() AND theme_classic() HAVE BEEN INACTIVATED, TO BE USED BY THE USER\n-> article ARGUMENT WILL BE IGNORED")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            add.check <- FALSE
+        }
+    }
+    if(add.check == TRUE & article == TRUE){
+        # WARNING: not possible to add theme()several times. NO message but the last one overwrites the others
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::theme_classic(base_size = text.size))
+        if(grid == TRUE){
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
+                text = ggplot2::element_text(size = text.size), 
+                plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
+                line = ggplot2::element_line(size = 0.5), 
+                legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
+                axis.line.y.left = ggplot2::element_line(colour = "black"), # draw lines for the y axis
+                axis.line.x.bottom = ggplot2::element_line(colour = "black"), # draw lines for the x axis
+                panel.grid.major.x = if(vertical == TRUE){NULL}else{ggplot2::element_line(colour = "grey85", size = 0.75)},
+                panel.grid.major.y = if(vertical == TRUE){ggplot2::element_line(colour = "grey85", size = 0.75)}else{NULL},
+                panel.grid.minor.y = if(vertical == TRUE){ggplot2::element_line(colour = "grey90", size = 0.25)}else{NULL},
+                axis.text.x = if(vertical == TRUE){ggplot2::element_text(angle = axis.just$angle, hjust = axis.just$hjust, vjust = axis.just$vjust)}else{NULL},
+                axis.text.y = if(vertical == TRUE){NULL}else{ggplot2::element_text(angle = axis.just$angle, hjust = axis.just$hjust, vjust = axis.just$vjust)},
+                strip.background = ggplot2::element_rect(fill = NA, colour = NA) # for facet background
+            ))
+        }else{
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
+                text = ggplot2::element_text(size = text.size), 
+                plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
+                line = ggplot2::element_line(size = 0.5), 
+                legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
+                axis.line.y.left = ggplot2::element_line(colour = "black"), 
+                axis.line.x.bottom = ggplot2::element_line(colour = "black"),
+                axis.text.x = if(vertical == TRUE){ggplot2::element_text(angle = axis.just$angle, hjust = axis.just$hjust, vjust = axis.just$vjust)}else{NULL},
+                axis.text.y = if(vertical == TRUE){NULL}else{ggplot2::element_text(angle = axis.just$angle, hjust = axis.just$hjust, vjust = axis.just$vjust)},
+                strip.background = ggplot2::element_rect(fill = NA, colour = NA)
+            ))
+        }
+    }else if(add.check == TRUE & article == FALSE){
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
+            text = ggplot2::element_text(size = text.size), 
+            plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
+            line = ggplot2::element_line(size = 0.5), 
+            legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
+            panel.background = ggplot2::element_rect(fill = "grey95"), 
+            axis.line.y.left = ggplot2::element_line(colour = "black"), 
+            axis.line.x.bottom = ggplot2::element_line(colour = "black"), 
+            panel.grid.major.x = ggplot2::element_line(colour = "grey85", size = 0.75), 
+            panel.grid.major.y = ggplot2::element_line(colour = "grey85", size = 0.75), 
+            panel.grid.minor.x = ggplot2::element_blank(), 
+            panel.grid.minor.y = ggplot2::element_line(colour = "grey90", size = 0.25), 
+            strip.background = ggplot2::element_rect(fill = NA, colour = NA),
+            axis.text.x = if(vertical == TRUE){ggplot2::element_text(angle = axis.just$angle, hjust = axis.just$hjust, vjust = axis.just$vjust)}else{NULL},
+            axis.text.y = if(vertical == TRUE){NULL}else{ggplot2::element_text(angle = axis.just$angle, hjust = axis.just$hjust, vjust = axis.just$vjust)}
+        ))
+    }
+    # Contrary to fun_gg_bar(), cannot plot the boxplot right now, because I need the dots plotted first
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, group = categ[length(categ)]), position = ggplot2::position_dodge(width = NULL), color = NA, width = box.width, fill = NA)) # this is to set the graph (i.e., a blanck boxplot to be able to use x coordinates to plot dots before boxes)
+    # end constant part
+    
+    
+    
+    
+    # graphic info recovery (including means)
+    tempo.graph.info <- ggplot2::ggplot_build(eval(parse(text = paste0(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), ' + ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, fill = categ[length(categ)]), position = ggplot2::position_dodge(width = NULL), width = box.width, notch = box.notch, coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf}) + ggplot2::scale_discrete_manual(aesthetics = "fill", name = box.legend.name, values = if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[length(categ)]])))}else{categ.color})')))) # will be recovered later again, when ylim will be considered
+    tempo.yx.ratio <- (tempo.graph.info$layout$panel_params[[1]]$y.range[2] - tempo.graph.info$layout$panel_params[[1]]$y.range[1]) / (tempo.graph.info$layout$panel_params[[1]]$x.range[2] - tempo.graph.info$layout$panel_params[[1]]$x.range[1])
+    box.coord <- tempo.graph.info$data[[2]] # to have the summary statistics of the plot. Contrary to ini.box.plot, now integrates ylim Here because can be required for stat.pos when just box are plotted
+    box.coord$x <- as.numeric(box.coord$x) # because x is of special class that block comparison of values using identical
+    box.coord$PANEL <- as.numeric(box.coord$PANEL) # because numbers as levels. But may be a problem is facet are reordered ?
+    box.coord <- box.coord[order(box.coord$group, box.coord$PANEL), ]
+    if( ! (identical(tempo.mean$BOX, box.coord$group) & identical(tempo.mean$PANEL, box.coord$PANEL))){
+        tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nidentical(tempo.mean$BOX, box.coord$group) & identical(tempo.mean$PANEL, box.coord$PANEL) DO NOT HAVE THE SAME VALUE ORDER")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else{
+        # tempo <- c(categ, if( ! is.null(dot.color) & ! is.null(dot.categ)){if(dot.categ != ini.dot.categ){dot.categ}}, if( ! is.null(facet.categ)){facet.categ})
+        if(any(names(tempo.mean) %in% names(box.coord), na.rm = TRUE)){
+            names(tempo.mean)[names(tempo.mean) %in% names(box.coord)] <- paste0(names(tempo.mean)[names(tempo.mean) %in% names(box.coord)], ".mean")
+        }
+        box.coord <- data.frame(box.coord, tempo.mean, stringsAsFactors = TRUE)
+    }
+    # end graphic info recovery (including means)
+    
+    
+    
+    # stat output (will also serve for boxplot and mean display)
+    # x not added now (to do not have them in stat.nolog)
+    stat <- data.frame(
+        MIN = box.coord$ymin_final, 
+        QUART1 = box.coord$lower, 
+        MEDIAN = box.coord$middle, 
+        MEAN = box.coord$MEAN, 
+        QUART3 = box.coord$upper, 
+        MAX = box.coord$ymax_final, 
+        WHISK_INF = box.coord$ymin, 
+        BOX_INF = box.coord$lower, 
+        NOTCH_INF = box.coord$notchlower, 
+        NOTCH_SUP = box.coord$notchupper, 
+        BOX_SUP = box.coord$upper, 
+        WHISK_SUP = box.coord$ymax, 
+        OUTLIERS = box.coord["outliers"], 
+        tempo.mean[colnames(tempo.mean) != "MEAN"], 
+        COLOR = box.coord$fill, 
+        stringsAsFactors = TRUE
+    ) # box.coord["outliers"] written like this because it is a list. X coordinates not put now because several features to set
+    names(stat)[names(stat) == "outliers"] <- "OUTLIERS"
+    stat.nolog <- stat # stat.nolog ini will serve for outputs
+    if(y.log != "no"){
+        stat.nolog[c("MIN", "QUART1", "MEDIAN", "MEAN", "QUART3", "MAX", "WHISK_INF", "BOX_INF", "NOTCH_INF", "NOTCH_SUP", "BOX_SUP", "WHISK_SUP")] <- ifelse(y.log == "log2", 2, 10)^(stat.nolog[c("MIN", "QUART1", "MEDIAN", "MEAN", "QUART3", "MAX", "WHISK_INF", "BOX_INF", "NOTCH_INF", "NOTCH_SUP", "BOX_SUP", "WHISK_SUP")])
+        stat.nolog$OUTLIERS <- lapply(stat.nolog$OUTLIERS, FUN = function(X){ifelse(y.log == "log2", 2, 10)^X})
+    }
+    # end stat output (will also serve for boxplot and mean display)
+    
+    
+    
+    
+    
+    
+    # x coordinates management (for random plotting and for stat display)
+    # width commputations
+    width.ini <- c(box.coord$xmax - box.coord$xmin)[1] # all the box widths are equal here. Only the first one taken
+    width.correct <- width.ini * box.space / 2
+    if( ! (identical(stat$BOX, box.coord$group) & identical(stat$PANEL, box.coord$PANEL))){
+        tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nidentical(stat$BOX, box.coord$group) & identical(stat$PANEL, box.coord$PANEL) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else{
+        stat <- data.frame(
+            stat, 
+            X = box.coord$x, 
+            X_BOX_INF = box.coord$xmin + width.correct, 
+            X_BOX_SUP = box.coord$xmax - width.correct, 
+            X_NOTCH_INF = box.coord$x - (box.coord$x - (box.coord$xmin + width.correct)) / 2, 
+            X_NOTCH_SUP = box.coord$x + (box.coord$x - (box.coord$xmin + width.correct)) / 2, 
+            X_WHISK_INF = box.coord$x - (box.coord$x - (box.coord$xmin + width.correct)) * box.whisker.width, 
+            X_WHISK_SUP = box.coord$x + (box.coord$x - (box.coord$xmin + width.correct)) * box.whisker.width, 
+            # tempo.mean[colnames(tempo.mean) != "MEAN"], # already added above
+            stringsAsFactors = TRUE
+        )
+        stat$COLOR <- factor(stat$COLOR, levels = unique(categ.color))
+        if( ! all(stat$NOTCH_SUP < stat$BOX_SUP & stat$NOTCH_INF > stat$BOX_INF, na.rm = TRUE) & box.notch == TRUE){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") SOME NOTCHES ARE BEYOND BOX HINGES. TRY ARGUMENT box.notch = FALSE")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    dot.jitter <- c((box.coord$xmax - width.correct) - (box.coord$xmin + width.correct))[1] * dot.jitter # real dot.jitter. (box.coord$xmin + width.correct) - (box.coord$xmax - width.correct))[1] is the width of the box. Is equivalent to (box.coord$x - (box.coord$xmin + width.correct))[1] * 2
+    # end width commputations
+    if( ! is.null(dot.color)){
+        # random dots
+        if(dot.tidy == FALSE){
+            dot.coord.rd1 <- merge(dot.coord, box.coord[c("fill", "PANEL", "group", "x")], by = c("PANEL", "group"), sort = FALSE) # rd for random. Send the coord of the boxes into the coord data.frame of the dots (in the column x.y). WARNING: by = c("PANEL", "group") without fill column because PANEL & group columns are enough as only one value of x column per group number in box.coord. Thus, no need to consider fill column
+            if(nrow(dot.coord.rd1) != nrow(dot.coord)){
+                tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nTHE merge() FUNCTION DID NOT RETURN A CORRECT dot.coord.rd1 DATA FRAME. CODE HAS TO BE MODIFIED")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            sampled.dot.jitter <- if(nrow(dot.coord.rd1)== 1L){runif(n = nrow(dot.coord.rd1), min = - dot.jitter / 2, max = dot.jitter / 2)}else{sample(x = runif(n = nrow(dot.coord.rd1), min = - dot.jitter / 2, max = dot.jitter / 2), size = nrow(dot.coord.rd1), replace = FALSE)}
+            dot.coord.rd2 <- data.frame(dot.coord.rd1, dot.x = dot.coord.rd1$x.y + sampled.dot.jitter, stringsAsFactors = TRUE) # set the dot.jitter thanks to runif and dot.jitter range. Then, send the coord of the boxes into the coord data.frame of the dots (in the column x.y)
+            if(length(categ)== 1L){
+                tempo.data1 <- unique(data.frame(data1[categ[1]], group = as.integer(data1[, categ[1]]), stringsAsFactors = TRUE)) # categ[1] is factor
+                names(tempo.data1)[names(tempo.data1) == categ[1]] <- paste0(categ[1], ".check")
+                verif <- paste0(categ[1], ".check")
+            }else if(length(categ) == 2L){
+                tempo.data1 <- unique(
+                    data.frame(
+                        data1[c(categ[1], categ[2])], 
+                        group = as.integer(factor(paste0(
+                            formatC(as.integer(data1[, categ[2]]), width = nchar(max(as.integer(data1[, categ[2]]), na.rm = TRUE)), flag = "0"), # convert factor into numeric with leading zero for proper ranking
+                            ".", 
+                            formatC(as.integer(data1[, categ[1]]), width = nchar(max(as.integer(data1[, categ[1]]), na.rm = TRUE)), flag = "0")# convert factor into numeric with leading zero for proper ranking
+                        )), stringsAsFactors = TRUE) # merge the 2 formatC() to create a new factor. The convertion to integer should recreate the correct group number
+                    )
+                ) # categ[2] first if categ[2] is used to make the categories in ggplot and categ[1] is used to make the x-axis
+                names(tempo.data1)[names(tempo.data1) == categ[1]] <- paste0(categ[1], ".check")
+                names(tempo.data1)[names(tempo.data1) == categ[2]] <- paste0(categ[2], ".check")
+                verif <- c(paste0(categ[1], ".check"), paste0(categ[2], ".check"))
+            }else{
+                tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 3")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            dot.coord.rd3 <- merge(dot.coord.rd2, tempo.data1, by = intersect("group", "group"), sort = FALSE) # send the factors of data1 into coord. WARNING: I have replaced by = "group" by intersect("group", "group") because of an error due to wrong group group merging in dot.coord.rd3
+            if(nrow(dot.coord.rd3) != nrow(dot.coord) | ( ! fun_comp_2d(dot.coord.rd3[categ], dot.coord.rd3[verif])$identical.content)){
+                tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nTHE merge() FUNCTION DID NOT RETURN A CORRECT dot.coord.rd3 DATA FRAME. CODE HAS TO BE MODIFIED")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            # end random dots
+        }
+        # tidy dots
+        # coordinates are recovered during plotting (see dot.coord.tidy1 below)
+        # end tidy dots
+    }
+    # end x coordinates management (for random plotting and for stat display)
+    
+    
+    
+    
+    
+    # boxplot display before dot display if box.fill = TRUE
+    coord.names <- NULL
+    # creation of the data frame for (main box + legend) and data frame for means
+    if(box.notch == FALSE){
+        for(i3 in 1:length(categ)){
+            if(i3== 1L){
+                tempo.polygon <- data.frame(GROUPX = c(t(stat[, rep(categ[i3], 5)])), stringsAsFactors = TRUE)
+            }else{
+                tempo.polygon <- cbind(tempo.polygon, c(t(stat[, rep(categ[i3], 5)])), stringsAsFactors = TRUE)
+            }
+        }
+        names(tempo.polygon) <- categ
+        tempo.polygon <- data.frame(X = c(t(stat[, c("X_BOX_INF", "X_BOX_SUP", "X_BOX_SUP", "X_BOX_INF", "X_BOX_INF")])), Y = c(t(stat[, c("BOX_INF", "BOX_INF", "BOX_SUP", "BOX_SUP", "BOX_INF")])), COLOR = c(t(stat[, c("COLOR", "COLOR", "COLOR", "COLOR", "COLOR")])), BOX = as.character(c(t(stat[, c("BOX", "BOX", "BOX", "BOX", "BOX")]))), tempo.polygon, stringsAsFactors = TRUE)
+        if( ! is.null(facet.categ)){
+            for(i4 in 1:length(facet.categ)){
+                tempo.polygon <- data.frame(tempo.polygon, c(t(stat[, c(facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4])])), stringsAsFactors = TRUE)
+                names(tempo.polygon)[length(names(tempo.polygon))] <- facet.categ[i4]
+            }
+        }
+    }else{
+        for(i3 in 1:length(categ)){
+            if(i3== 1L){
+                tempo.polygon <- data.frame(GROUPX = c(t(stat[, rep(categ[i3], 11)])), stringsAsFactors = TRUE)
+            }else{
+                tempo.polygon <- cbind(tempo.polygon, c(t(stat[, rep(categ[i3], 11)])), stringsAsFactors = TRUE)
+            }
+        }
+        names(tempo.polygon) <- categ
+        tempo.polygon <- data.frame(X = c(t(stat[, c("X_BOX_INF", "X_BOX_SUP", "X_BOX_SUP", "X_NOTCH_SUP", "X_BOX_SUP", "X_BOX_SUP", "X_BOX_INF", "X_BOX_INF", "X_NOTCH_INF", "X_BOX_INF", "X_BOX_INF")])), Y = c(t(stat[, c("BOX_INF", "BOX_INF", "NOTCH_INF", "MEDIAN", "NOTCH_SUP", "BOX_SUP", "BOX_SUP", "NOTCH_SUP", "MEDIAN", "NOTCH_INF", "BOX_INF")])), COLOR = c(t(stat[, c("COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR", "COLOR")])), BOX = as.character(c(t(stat[, c("BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX", "BOX")]))), tempo.polygon, stringsAsFactors = TRUE)
+        if( ! is.null(facet.categ)){
+            for(i4 in 1:length(facet.categ)){
+                tempo.polygon <- data.frame(tempo.polygon, c(t(stat[, c(facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4], facet.categ[i4])])), stringsAsFactors = TRUE)
+                names(tempo.polygon)[length(names(tempo.polygon))] <- facet.categ[i4]
+            }
+        }
+    }
+    tempo.polygon$COLOR <- factor(tempo.polygon$COLOR, levels = unique(categ.color))
+    if( ! is.null(categ.class.order)){
+        for(i3 in 1:length(categ)){
+            tempo.polygon[, categ[i3]] <- factor(tempo.polygon[, categ[i3]], levels = categ.class.order[[i3]])
+        }
+    }
+    # modified name of dot.categ column (e.g., "Categ1_DOT") must be included for boxplot using ridy dots
+    if( ! is.null(dot.color) & ! is.null(dot.categ)){
+        if(dot.categ != ini.dot.categ){
+            tempo.polygon <- data.frame(tempo.polygon, GROUPX = tempo.polygon[, ini.dot.categ], stringsAsFactors = TRUE)
+            names(tempo.polygon)[names(tempo.polygon) == "GROUPX"] <- dot.categ
+            
+        }
+    }
+    tempo.diamon.mean <- data.frame(X = c(t(stat[, c("X", "X_NOTCH_INF", "X", "X_NOTCH_SUP", "X")])), Y = c(t(cbind(stat["MEAN"] - (stat[, "X"] - stat[, "X_NOTCH_INF"]) * tempo.yx.ratio, stat["MEAN"], stat["MEAN"] + (stat[, "X"] - stat[, "X_NOTCH_INF"]) * tempo.yx.ratio, stat["MEAN"], stat["MEAN"] - (stat[, "X"] - stat[, "X_NOTCH_INF"]) * tempo.yx.ratio, stringsAsFactors = TRUE))), COLOR = c(t(stat[, c("COLOR", "COLOR", "COLOR", "COLOR", "COLOR")])), GROUP = c(t(stat[, c("BOX", "BOX", "BOX", "BOX", "BOX")])), stringsAsFactors = TRUE) # stringsAsFactors = TRUE for cbind() because stat["MEAN"] is a data frame. Otherwise, stringsAsFactors is not an argument for cbind() on vectors
+    if( ! is.null(facet.categ)){
+        for(i3 in 1:length(facet.categ)){
+            tempo.diamon.mean <- data.frame(tempo.diamon.mean, c(t(stat[, c(facet.categ[i3], facet.categ[i3], facet.categ[i3], facet.categ[i3], facet.categ[i3])])), stringsAsFactors = TRUE)
+            names(tempo.diamon.mean)[length(names(tempo.diamon.mean))] <- facet.categ[i3]
+        }
+    }
+    tempo.diamon.mean$COLOR <- factor(tempo.diamon.mean$COLOR, levels = unique(categ.color))
+    # end creation of the data frame for (main box + legend) and data frame for means
+    if(box.fill == TRUE){
+        # assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, color = categ[length(categ)], fill = categ[length(categ)]), position = ggplot2::position_dodge(width = NULL), width = box.width, size = box.line.size, notch = box.notch, coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf}, alpha = box.alpha, outlier.shape = if( ! is.null(dot.color)){NA}else{21}, outlier.color = if( ! is.null(dot.color)){NA}else{dot.border.color}, outlier.fill = if( ! is.null(dot.color)){NA}else{NULL}, outlier.size = if( ! is.null(dot.color)){NA}else{dot.size}, outlier.stroke = if( ! is.null(dot.color)){NA}else{dot.border.size}, outlier.alpha = if( ! is.null(dot.color)){NA}else{dot.alpha})) # the color, size, etc. of the outliers are dealt here. outlier.color = NA to do not plot outliers when dots are already plotted. Finally, boxplot redrawn (see below)
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_polygon(
+            data = tempo.polygon, 
+            mapping = ggplot2::aes_string(x = "X", y = "Y", group = "BOX", fill = categ[length(categ)], color = categ[length(categ)]), 
+            size = box.line.size, 
+            alpha = box.alpha # works only for fill, not for color
+        ))
+        coord.names <- c(coord.names, "main.box")
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X, xend = X, y = BOX_SUP, yend = WHISK_SUP, group = categ[length(categ)]), color = "black", size = box.line.size, alpha = box.alpha)) # 
+        coord.names <- c(coord.names, "sup.whisker")
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X, xend = X, y = BOX_INF, yend = WHISK_INF, group = categ[length(categ)]), color = "black", size = box.line.size, alpha = box.alpha)) # 
+        coord.names <- c(coord.names, "inf.whisker")
+        if(box.whisker.width > 0){
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X_WHISK_INF, xend = X_WHISK_SUP, y = WHISK_SUP, yend = WHISK_SUP, group = categ[length(categ)]), color = "black", size = box.line.size, alpha = box.alpha, lineend = "round")) # 
+            coord.names <- c(coord.names, "sup.whisker.edge")
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X_WHISK_INF, xend = X_WHISK_SUP, y = WHISK_INF, yend = WHISK_INF, group = categ[length(categ)]), color = "black", size = box.line.size, alpha = box.alpha, lineend = "round")) # 
+            coord.names <- c(coord.names, "inf.whisker.edge")
+        }
+        if(box.mean == TRUE){
+            # assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(data = stat, mapping = ggplot2::aes_string(x = "X", y = "MEAN", group = categ[length(categ)]), shape = 23, stroke = box.line.size * 2, fill = stat$COLOR, size = box.mean.size, color = "black", alpha = box.alpha)) # group used in aesthetic to do not have it in the legend
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_polygon(
+                data = tempo.diamon.mean, 
+                mapping = ggplot2::aes(x = X, y = Y, group = GROUP), 
+                fill = tempo.diamon.mean[, "COLOR"], 
+                color = hsv(0, 0, 0, alpha = box.alpha), # outline of the polygon in black but with alpha
+                size = box.line.size, 
+                alpha = box.alpha
+            ))
+            coord.names <- c(coord.names, "mean")
+        }
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = if(box.notch == FALSE){X_BOX_INF}else{X_NOTCH_INF}, xend = if(box.notch == FALSE){X_BOX_SUP}else{X_NOTCH_SUP}, y = MEDIAN, yend = MEDIAN, group = categ[length(categ)]), color = "black", size = box.line.size * 2, alpha = box.alpha)) # 
+        coord.names <- c(coord.names, "median")
+    }
+    # end boxplot display before dot display if box.fill = TRUE
+    
+    
+    
+    
+    
+    
+    # dot display
+    if( ! is.null(dot.color)){
+        if(dot.tidy == FALSE){
+            if(is.null(dot.categ)){
+                if(dot.border.size == 0){
+                    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(
+                        data = dot.coord.rd3, 
+                        mapping = ggplot2::aes_string(x = "dot.x", y = "y", group = categ[length(categ)]), 
+                        size = dot.size, 
+                        shape = 19, 
+                        color = dot.coord.rd3$dot.color, 
+                        alpha = dot.alpha
+                    )) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
+                }else{
+                    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(
+                        data = dot.coord.rd3, 
+                        mapping = ggplot2::aes_string(x = "dot.x", y = "y", group = categ[length(categ)]), 
+                        shape = 21, 
+                        stroke = dot.border.size, 
+                        color = if(is.null(dot.border.color)){dot.coord.rd3$dot.color}else{rep(dot.border.color, nrow(dot.coord.rd3))}, 
+                        size = dot.size, 
+                        fill = dot.coord.rd3$dot.color, 
+                        alpha = dot.alpha
+                    )) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
+                }
+            }else{
+                if(dot.border.size == 0){
+                    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(
+                        data = dot.coord.rd3, 
+                        mapping = ggplot2::aes_string(x = "dot.x", y = "y", alpha = dot.categ), 
+                        size = dot.size, 
+                        shape = 19, 
+                        color = dot.coord.rd3$dot.color
+                    )) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
+                }else{
+                    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(
+                        data = dot.coord.rd3, 
+                        mapping = ggplot2::aes_string(x = "dot.x", y = "y", alpha = dot.categ), 
+                        size = dot.size, 
+                        shape = 21, 
+                        stroke = dot.border.size, 
+                        color = if(is.null(dot.border.color)){dot.coord.rd3$dot.color}else{rep(dot.border.color, nrow(dot.coord.rd3))}, 
+                        fill = dot.coord.rd3$dot.color
+                    )) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
+                }
+                assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "alpha", name = dot.legend.name, values = rep(dot.alpha, length(dot.categ.class.order)), guide = ggplot2::guide_legend(override.aes = list(fill = dot.color, color = if(is.null(dot.border.color)){dot.color}else{dot.border.color}, stroke = dot.border.size, alpha = dot.alpha)))) # values are the values of color (which is the border color in geom_box. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor
+            }
+            coord.names <- c(coord.names, "dots")
+        }else if(dot.tidy == TRUE){
+            # here plot using group -> no scale
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_dotplot(
+                data = dot.coord, 
+                mapping = ggplot2::aes_string(x = categ[1], y = "y", group = "group"), # not dot.categ here because the classes of dot.categ create new separations
+                position = ggplot2::position_dodge(width = box.width), 
+                binpositions = "all", 
+                binaxis = "y", 
+                stackdir = "center", 
+                alpha = dot.alpha, 
+                fill = dot.coord$dot.color, 
+                stroke = dot.border.size, 
+                color = if(is.null(dot.border.color)){dot.coord$dot.color}else{rep(dot.border.color, nrow(dot.coord))}, 
+                show.legend = FALSE, # WARNING: do not use show.legend = TRUE because it uses the arguments outside aes() as aesthetics (here color and fill). Thus I must find a way using ggplot2::scale_discrete_manual()
+                binwidth = (y.lim[2] - y.lim[1]) / dot.tidy.bin.nb
+            )) # geom_dotplot ggplot2 v3.3.0: I had to remove rev() in fill and color # very weird behavior of geom_dotplot ggplot2 v3.2.1, (1) because with aes group = (to avoid legend), the dot plotting is not good in term of coordinates, and (2) because data1 seems reorderer according to x = categ[1] before plotting. Thus, I have to use fill = dot.coord[rev(order(dot.coord[, categ[1]], decreasing = TRUE)), "dot.color"] to have the good corresponding colors # show.legend option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
+            coord.names <- c(coord.names, "dots")
+            if( ! is.null(dot.categ)){
+                assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_dotplot(
+                    data = dot.coord, 
+                    mapping = ggplot2::aes_string(x = categ[1], y = "y", alpha = dot.categ), # not dot.categ here because the classes of dot.categ create new separations
+                    position = ggplot2::position_dodge(width = box.width), 
+                    binpositions = "all", 
+                    binaxis = "y", 
+                    stackdir = "center", 
+                    fill = NA, 
+                    stroke = NA, 
+                    color = NA, 
+                    # WARNING: do not use show.legend = TRUE because it uses the arguments outside aes() as aesthetics (here color and fill). Thus I must find a way using ggplot2::scale_discrete_manual()
+                    binwidth = (y.lim[2] - y.lim[1]) / dot.tidy.bin.nb
+                )) # geom_dotplot ggplot2 v3.3.0: I had to remove rev() in fill and color # very weird behavior of geom_dotplot ggplot2 v3.2.1, (1) because with aes group = (to avoid legend), the dot plotting is not good in term of coordinates, and (2) because data1 seems reorderer according to x = categ[1] before plotting. Thus, I have to use fill = dot.coord[rev(order(dot.coord[, categ[1]], decreasing = TRUE)), "dot.color"] to have the good corresponding colors # show.legend option do not remove the legend, only the aesthetic of the legend (dot, line, etc.)
+                # assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "linetype", name = dot.legend.name, values = rep(1, length(categ.color)))) # values = rep("black", length(categ.color)) are the values of color (which is the border color of dots), and this modify the border color on the plot. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor
+                coord.names <- c(coord.names, "bad_remove")
+                assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "alpha", name = dot.legend.name, values = rep(dot.alpha, length(dot.categ.class.order)), labels = dot.categ.class.order, guide = ggplot2::guide_legend(title = if(ini.dot.categ == categ[length(categ)]){dot.categ}else{ini.dot.categ}, override.aes = list(fill = levels(dot.coord$dot.color), color = if(is.null(dot.border.color)){levels(dot.coord$dot.color)}else{dot.border.color}, stroke = dot.border.size, alpha = dot.alpha)))) # values are the values of color (which is the border color in geom_box. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor
+            }
+            # coordinates of tidy dots
+            tempo.coord <- ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "))))$data # to have the tidy dot coordinates
+            if(length(which(sapply(X = tempo.coord, FUN = function(X){any(names(X) == "binwidth", na.rm = TRUE)}))) != 1){ # detect the compartment of tempo.coord which is the binned data frame
+                # if(length(which(sapply(tempo.coord, FUN = nrow) == nrow(data1))) > if(is.null(dot.categ)){1}else{2}){ # this does not work if only one dot per class, thus replaced by above # if(is.null(dot.categ)){1}else{2} because 1 dotplot if dot.categ is NULL and 2 dotplots if not, with the second being a blank dotplot with wrong coordinates. Thus take the first in that situation
+                tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nEITHER MORE THAN 1 OR NO COMPARTMENT HAVING A DATA FRAME WITH binwidth AS COLUMN NAME IN THE tempo.coord LIST (FOR TIDY DOT COORDINATES). CODE HAS TO BE MODIFIED")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }else{
+                # dot.coord.tidy1 <- tempo.coord[[which(sapply(tempo.coord, FUN = nrow) == nrow(data1))[1]]] # this does not work if only one dot per class, thus replaced by above # the second being a blank dotplot with wrong coordinates. Thus take the first whatever situation
+                dot.coord.tidy1 <- tempo.coord[[which(sapply(X = tempo.coord, FUN = function(X){any(names(X) == "binwidth", na.rm = TRUE)}))]] # detect the compartment of tempo.coord which is the binned data frame
+                dot.coord.tidy1$x <- as.numeric(dot.coord.tidy1$x) # because weird class
+                dot.coord.tidy1$PANEL <- as.numeric(dot.coord.tidy1$PANEL) # because numbers as levels. But may be a problem is facet are reordered ?
+            }
+            # tempo.box.coord <- merge(box.coord, unique(dot.coord[, c("PANEL", "group", categ)]), by = c("PANEL", "group"), sort = FALSE) # not required anymore because box.coord already contains categ do not add dot.categ and tidy_group_coord here because the coordinates are for stats. Add the categ in box.coord. WARNING: by = c("PANEL", "group") without fill column because PANEL & group columns are enough as only one value of x column per group number in box.coord. Thus, no need to consider fill column
+            # below inactivated because not true when dealing with dot.categ different from categ
+            # if(nrow(tempo.box.coord) != nrow(box.coord)){
+            # tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nTHE merge() FUNCTION DID NOT RETURN A CORRECT tempo.box.coord DATA FRAME. CODE HAS TO BE MODIFIED")
+            # stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+            # }
+            dot.coord.tidy2 <- merge(dot.coord.tidy1, box.coord[c("fill", "PANEL", "group", "x", categ)], by = c("PANEL", "group"), sort = FALSE) # send the coord of the boxes into the coord data.frame of the dots (in the column x.y).WARNING: by = c("PANEL", "group") without fill column because PANEL & group columns are enough as only one value of x column per group number in tempo.box.coord. Thus, no need to consider fill colum # DANGER: from here the fill.y and x.y (from tempo.box.coord) are not good in dot.coord.tidy2. It is ok because Categ1 Categ2 from tempo.box.coord are ok with the group column from dot.coord.tidy1. This is due to the fact that dot.coord.tidy resulting from geom_dotplot does not make the same groups as the other functions
+            if(nrow(dot.coord.tidy2) != nrow(dot.coord)){
+                tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nTHE merge() FUNCTION DID NOT RETURN A CORRECT dot.coord.tidy2 DATA FRAME. CODE HAS TO BE MODIFIED")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            # From here, check for dot.coord.tidy3 which wil be important for stat over the plot. WARNING: dot.categ has nothing to do here for stat coordinates. Thus, not in tempo.data1
+            if(length(categ)== 1L){
+                tempo.data1 <- unique(data.frame(data1[categ[1]], group = as.integer(data1[, categ[1]]), stringsAsFactors = TRUE)) # categ[1] is factor
+                names(tempo.data1)[names(tempo.data1) == categ[1]] <- paste0(categ[1], ".check")
+                verif <- paste0(categ[1], ".check")
+            }else if(length(categ) == 2L){
+                tempo.data1 <- unique(
+                    data.frame(
+                        data1[c(categ[1], categ[2])], 
+                        group = as.integer(factor(paste0(
+                            formatC(as.integer(data1[, categ[2]]), width = nchar(max(as.integer(data1[, categ[2]]), na.rm = TRUE)), flag = "0"), # convert factor into numeric with leading zero for proper ranking
+                            ".", 
+                            formatC(as.integer(data1[, categ[1]]), width = nchar(max(as.integer(data1[, categ[1]]), na.rm = TRUE)), flag = "0")# convert factor into numeric with leading zero for proper ranking
+                        )), stringsAsFactors = TRUE) # merge the 2 formatC() to create a new factor. The convertion to integer should recreate the correct group number
+                    )
+                ) # categ[2] first if categ[2] is used to make the categories in ggplot and categ[1] is used to make the x-axis
+                names(tempo.data1)[names(tempo.data1) == categ[1]] <- paste0(categ[1], ".check")
+                names(tempo.data1)[names(tempo.data1) == categ[2]] <- paste0(categ[2], ".check")
+                verif <- c(paste0(categ[1], ".check"), paste0(categ[2], ".check"))
+            }else{
+                tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 4")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            dot.coord.tidy3 <- merge(dot.coord.tidy2, tempo.data1, by = intersect("group", "group"), sort = FALSE) # send the factors of data1 into coord. WARNING: I have tested intersect("group", "group") instead of by = "group". May be come back to by = "group" in case of error. But I did this because of an error in dot.coord.rd3 above
+            if(nrow(dot.coord.tidy3) != nrow(dot.coord) | ( ! fun_comp_2d(dot.coord.tidy3[categ], dot.coord.tidy3[verif])$identical.content)){
+                tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nTHE merge() FUNCTION DID NOT RETURN A CORRECT dot.coord.tidy3 DATA FRAME. CODE HAS TO BE MODIFIED")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+            }
+            # end coordinates of tidy dots
+        }
+    }
+    # end dot display
+    
+    
+    
+    # boxplot display (if box.fill = FALSE, otherwise, already plotted above)
+    if(box.fill == TRUE){
+        # overcome "work only for the filling of boxes, not for the frame. See https://github.com/tidyverse/ggplot2/issues/252"
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "fill", name = box.legend.name, values = if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[length(categ)]])))}else{categ.color}, guide = ggplot2::guide_legend(order = 1))) #, guide = ggplot2::guide_legend(override.aes = list(fill = levels(tempo.polygon$COLOR), color = "black")))) # values are the values of color (which is the border color in geom_box. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "color", name = box.legend.name, values = rep(hsv(0, 0, 0, alpha = box.alpha), length(unique(data1[, categ[length(categ)]]))), guide = ggplot2::guide_legend(order = 1))) # , guide = ggplot2::guide_legend(override.aes = list(color = "black", alpha = box.alpha)))) # values are the values of color (which is the border color in geom_box. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor # outline of the polygon in black but with alpha
+    }else{
+        # assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_boxplot(data = data1, mapping = ggplot2::aes_string(x = categ[1], y = y, color = categ[length(categ)], fill = categ[length(categ)]), position = ggplot2::position_dodge(width = NULL), width = box.width, size = box.line.size, notch = box.notch, alpha = box.alpha, coef = if(box.whisker.kind == "no"){0}else if(box.whisker.kind == "std"){1.5}else if(box.whisker.kind == "max"){Inf}, outlier.shape = if( ! is.null(dot.color)){NA}else{21}, outlier.color = if( ! is.null(dot.color)){NA}else{if(dot.border.size == 0){NA}else{dot.border.color}}, outlier.fill = if( ! is.null(dot.color)){NA}else{NULL}, outlier.size = if( ! is.null(dot.color)){NA}else{dot.size}, outlier.stroke = if( ! is.null(dot.color)){NA}else{dot.border.size}, outlier.alpha = if( ! is.null(dot.color)){NA}else{dot.alpha})) # the color, size, etc. of the outliers are dealt here. outlier.color = NA to do not plot outliers when dots are already plotted
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_path(
+            data = tempo.polygon, 
+            mapping = ggplot2::aes_string(x = "X", y = "Y", group = "BOX", color = categ[length(categ)]), 
+            size = box.line.size, 
+            alpha = box.alpha, 
+            lineend = "round", 
+            linejoin = "round"
+        ))
+        coord.names <- c(coord.names, "main.box")
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = if(box.notch == FALSE){X_BOX_INF}else{X_NOTCH_INF}, xend = if(box.notch == FALSE){X_BOX_SUP}else{X_NOTCH_SUP}, y = MEDIAN, yend = MEDIAN, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size * 2, alpha = box.alpha)) # 
+        coord.names <- c(coord.names, "median")
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X, xend = X, y = BOX_SUP, yend = WHISK_SUP, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size, alpha = box.alpha)) # 
+        coord.names <- c(coord.names, "sup.whisker")
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X, xend = X, y = BOX_INF, yend = WHISK_INF, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size, alpha = box.alpha)) # 
+        coord.names <- c(coord.names, "inf.whisker")
+        if(box.whisker.width > 0){
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X_WHISK_INF, xend = X_WHISK_SUP, y = WHISK_SUP, yend = WHISK_SUP, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size, alpha = box.alpha, lineend = "round")) # 
+            coord.names <- c(coord.names, "sup.whisker.edge")
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_segment(data = stat, mapping = ggplot2::aes(x = X_WHISK_INF, xend = X_WHISK_SUP, y = WHISK_INF, yend = WHISK_INF, group = categ[length(categ)]), color = stat$COLOR, size = box.line.size, alpha = box.alpha, lineend = "round")) # 
+            coord.names <- c(coord.names, "inf.whisker.edge")
+        }
+        if(box.mean == TRUE){
+            # assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_point(data = stat, mapping = ggplot2::aes_string(x = "X", y = "MEAN", group = categ[length(categ)]), shape = 23, stroke = box.line.size * 2, color = stat$COLOR, size = box.mean.size, fill = NA, alpha = box.alpha)) # group used in aesthetic to do not have it in the legend. Here ggplot2::scale_discrete_manual() cannot be used because of the group easthetic
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_path(
+                data = tempo.diamon.mean, 
+                mapping = ggplot2::aes(x = X, y = Y, group = GROUP), 
+                color = tempo.diamon.mean[, "COLOR"], 
+                size = box.line.size, 
+                alpha = box.alpha, 
+                lineend = "round", 
+                linejoin = "round"
+            ))
+            coord.names <- c(coord.names, "mean")
+        }
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "fill", name = box.legend.name, values = rep(NA, length(unique(data1[, categ[length(categ)]]))))) #, guide = ggplot2::guide_legend(override.aes = list(color = categ.color)))) # values are the values of color (which is the border color in geom_box. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "color", name = box.legend.name, values = if(length(categ.color)== 1L){rep(categ.color, length(unique(data1[, categ[length(categ)]])))}else{categ.color}, guide = ggplot2::guide_legend(override.aes = list(alpha = if(plot == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list()) == 0L & Sys.info()["sysname"] == "Windows"))){1}else{box.alpha})))) # , guide = ggplot2::guide_legend(override.aes = list(color = as.character(categ.color))))) # values are the values of color (which is the border color in geom_box. WARNING: values = categ.color takes the numbers to make the colors if categ.color is a factor
+        if(plot == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list()) == 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
+            # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE LINES IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    if(box.alpha == 0){ # remove box legend because no boxes drawn
+        # add this after the scale_xxx_manual() for boxplots
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::guides(fill = FALSE, color = FALSE)) # inactivate the legend
+    }
+    # end boxplot display (if box.fill = FALSE, otherwise, already plotted above)
+    
+    
+    
+    
+    # stat display
+    # layer after dots but ok, behind dots on the plot
+    if( ! is.null(stat.pos)){
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") NUMBERS DISPLAYED ARE ", ifelse(stat.mean == FALSE, "MEDIANS", "MEANS"))
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        if(stat.pos == "top"){
+            tempo.stat <- data.frame(stat, Y = y.lim[2], stringsAsFactors = TRUE) # I had to create a data frame for geom_tex() so that facet is taken into account, (ggplot2::annotate() does not deal with facet because no data and mapping arguments). Of note, facet.categ is in tempo.stat, via tempo.mean, via dot.coord
+            if(stat.mean == FALSE){tempo.stat$MEDIAN <- formatC(stat.nolog$MEDIAN, digit = 2, drop0trailing = TRUE, format = "f")}else{tempo.stat$MEAN <- formatC(stat.nolog$MEAN, digit = 2, drop0trailing = TRUE, format = "f")}
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_text(
+                data = tempo.stat, 
+                mapping = ggplot2::aes_string(x = "X", y = "Y", label = ifelse(stat.mean == FALSE, "MEDIAN", "MEAN")),
+                size = stat.size, 
+                color = "black", 
+                angle = stat.angle, 
+                hjust = stat.just$hjust, 
+                vjust = stat.just$vjust
+            )) # stat$X used here because identical to stat.nolog but has the X. WARNING: no need of order() for labels because box.coord$x set the order. For justification, see https://stackoverflow.com/questions/7263849/what-do-hjust-and-vjust-do-when-making-a-plot-using-ggplot
+            coord.names <- c(coord.names, "stat.pos")
+        }else if(stat.pos == "above"){
+            # stat coordinates
+            if( ! is.null(dot.color)){ # for text just above max dot
+                if(dot.tidy == FALSE){
+                    tempo.stat.ini <- dot.coord.rd3
+                }else if(dot.tidy == TRUE){
+                    tempo.stat.ini <- dot.coord.tidy3
+                    tempo.stat.ini$x.y <- tempo.stat.ini$x.x # this is just to be able to use tempo.stat.ini$x.y for untidy or tidy dots (remember that dot.coord.tidy3$x.y is not good, see above)
+                }
+                stat.coord1 <- aggregate(x = tempo.stat.ini["y"], by = {x.env <- if(length(categ)== 1L){list(tempo.stat.ini$group, tempo.stat.ini$PANEL, tempo.stat.ini$x.y, tempo.stat.ini[, categ[1]])}else if(length(categ) == 2L){list(tempo.stat.ini$group, tempo.stat.ini$PANEL, tempo.stat.ini$x.y, tempo.stat.ini[, categ[1]], tempo.stat.ini[, categ[2]])} ; names(x.env) <- if(length(categ)== 1L){c("group", "PANEL", "x.y", categ[1])}else if(length(categ) == 2L){c("group", "PANEL", "x.y", categ[1], categ[2])} ; x.env}, FUN = min, na.rm = TRUE)
+                names(stat.coord1)[names(stat.coord1) == "y"] <- "dot.min"
+                stat.coord2 <- aggregate(x = tempo.stat.ini["y"], by = {x.env <- if(length(categ)== 1L){list(tempo.stat.ini$group, tempo.stat.ini$PANEL, tempo.stat.ini$x.y, tempo.stat.ini[, categ[1]])}else if(length(categ) == 2L){list(tempo.stat.ini$group, tempo.stat.ini$PANEL, tempo.stat.ini$x.y, tempo.stat.ini[, categ[1]], tempo.stat.ini[, categ[2]])} ; names(x.env) <- if(length(categ)== 1L){c("group", "PANEL", "x.y", categ[1])}else if(length(categ) == 2L){c("group", "PANEL", "x.y", categ[1], categ[2])} ; x.env}, FUN = max, na.rm = TRUE)
+                names(stat.coord2) <- paste0(names(stat.coord2), "_from.dot.max")
+                names(stat.coord2)[names(stat.coord2) == "y_from.dot.max"] <- "dot.max"
+                stat.coord3 <- cbind(box.coord[order(box.coord$group, box.coord$PANEL), ], stat.coord1[order(stat.coord1$group, stat.coord1$x.y), ], stat.coord2[order(stat.coord2$group, stat.coord2$x.y), ], stringsAsFactors = TRUE) # 
+                if( ! all(identical(round(stat.coord3$x, 9), round(as.numeric(stat.coord3$x.y), 9)), na.rm = TRUE)){ # as.numeric() because stat.coord3$x is class "mapped_discrete" "numeric"
+                    tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nFUSION OF box.coord, stat.coord1 AND stat.coord2 ACCORDING TO box.coord$x, stat.coord1$x.y AND stat.coord2$x.y IS NOT CORRECT. CODE HAS TO BE MODIFIED")
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+                }
+                # text.coord <- stat.coord3[, c("x", "group", "dot.min", "dot.max")]
+                # names(text.coord)[names(text.coord) == "dot.min"] <- "text.min.pos"
+                #names(text.coord)[names(text.coord) == "dot.max"] <- "text.max.pos"
+                box.coord <- box.coord[order(box.coord$x, box.coord$group, box.coord$PANEL), ]
+                # text.coord <- text.coord[order(text.coord$x), ] # to be sure to have the two objects in the same order for x. WARNING: cannot add identical(as.integer(text.coord$group), as.integer(box.coord$group)) because with error, the correspondence between x and group is not the same
+                stat.coord3 <- stat.coord3[order(stat.coord3$x, stat.coord3$group, stat.coord3$PANEL), ] # to be sure to have the two objects in the same order for x. WARNING: cannot add identical(as.integer(text.coord$group), as.integer(box.coord$group)) because with error, the correspondence between x and group is not the same
+                if( ! (identical(box.coord$x, stat.coord3$x) & identical(box.coord$group, stat.coord3$group) & identical(box.coord$PANEL, stat.coord3$PANEL))){
+                    tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\ntext.coord AND box.coord DO NOT HAVE THE SAME x, group AND PANEL COLUMN CONTENT")
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+                }
+            }else{
+                stat.coord3 <- box.coord
+            }
+            stat.coord3 <- data.frame(
+                stat.coord3, 
+                Y = stat.coord3[, ifelse(
+                    is.null(dot.color), 
+                    ifelse(diff(y.lim) > 0, "ymax", "ymin"), 
+                    ifelse(diff(y.lim) > 0, "ymax_final", "ymin_final")
+                )], 
+                stringsAsFactors = TRUE
+            ) # ymax is top whisker, ymax_final is top dot
+            # stat.coord3 <- data.frame(stat.coord3, Y = vector("numeric", length = nrow(stat.coord3)), stringsAsFactors = TRUE)
+            # check.Y <- as.logical(stat.coord3$Y) # convert everything in Y into FALSE (because Y is full of zero)
+            # end stat coordinates
+            # stat display
+            # performed twice: first for y values >=0, then y values < 0, because only a single value allowed for hjust anf vjust
+            if(stat.mean == FALSE){
+                tempo.center.ref <- "middle"
+            }else{
+                tempo.center.ref <- "MEAN"
+            }
+            # if(is.null(dot.color)){
+            # tempo.low.ref <- "ymin"
+            # tempo.high.ref <- "ymax"
+            # }else{
+            # tempo.low.ref <- "ymin_final"
+            # tempo.high.ref <- "ymax_final"
+            # }
+            # tempo.log.high <- if(diff(y.lim) > 0){stat.coord3[, tempo.center.ref] >= 0}else{stat.coord3[, tempo.center.ref] < 0}
+            # tempo.log.low <- if(diff(y.lim) > 0){stat.coord3[, tempo.center.ref] < 0}else{stat.coord3[, tempo.center.ref] >= 0}
+            # stat.coord3$Y[tempo.log.high] <- stat.coord3[tempo.log.high, tempo.high.ref]
+            # stat.coord3$Y[tempo.log.low] <- stat.coord3[tempo.log.low, tempo.low.ref]
+            # add distance
+            stat.coord3$Y <- stat.coord3$Y + diff(y.lim) * stat.dist / 100
+            # end add distance
+            # correct median or mean text format
+            if(y.log != "no"){
+                stat.coord3[, tempo.center.ref] <- ifelse(y.log == "log2", 2, 10)^(stat.coord3[, tempo.center.ref])
+            }
+            stat.coord3[, tempo.center.ref] <- formatC(stat.coord3[, tempo.center.ref], digit = 2, drop0trailing = TRUE, format = "f")
+            # end correct median or mean text format
+            # if(any(tempo.log.high) == TRUE){
+            # tempo.stat <- stat.coord3[tempo.log.high,]
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_text(
+                data = stat.coord3, 
+                mapping = ggplot2::aes_string(x = "x", y = "Y", label = tempo.center.ref),
+                size = stat.size, 
+                color = "black", 
+                angle = stat.angle, 
+                hjust = stat.just$hjust, 
+                vjust = stat.just$vjust
+            )) # WARNING: no need of order() for labels because box.coord$x set the order
+            coord.names <- c(coord.names, "stat.pos")
+            # }
+            # if(any(tempo.log.low) == TRUE){
+            # tempo.stat <- stat.coord3[tempo.log.low,]
+            # assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::geom_text(
+            # data = tempo.stat, 
+            # mapping = ggplot2::aes_string(x = "x", y = "Y", label = tempo.center.ref),
+            # size = stat.size, 
+            # color = "black", 
+            # hjust = ifelse(vertical == TRUE, 0.5, 0.5 + stat.dist), 
+            # vjust = ifelse(vertical == TRUE, 0.5 + stat.dist, 0.5)
+            # )) # WARNING: no need of order() for labels because box.coord$x set the order
+            # coord.names <- c(coord.names, "stat.pos.negative")
+            # }
+            # end stat display
+        }else{
+            tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 5")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+    }
+    # end stat display
+    # legend management
+    if(legend.show == FALSE){ # must be here because must be before bef.final.plot <- 
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::guides(fill = FALSE, color = FALSE, alpha = FALSE)) # inactivate the initial legend
+    }
+    # end legend management
+    
+    
+    
+    # y scale management (cannot be before dot plot management)
+    # the rescaling aspect is complicated and not intuitive. See:
+    # explaination: https://github.com/tidyverse/ggplot2/issues/3948
+    # the oob argument of scale_y_continuous() https://ggplot2.tidyverse.org/reference/scale_continuous.html
+    # see also https://github.com/rstudio/cheatsheets/blob/master/data-visualization-2.1.pdf
+    # secondary ticks
+    bef.final.plot <- ggplot2::ggplot_build(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), ' + if(vertical == TRUE){ggplot2::scale_y_continuous(expand = c(0, 0), limits = sort(y.lim), oob = scales::rescale_none)}else{ggplot2::coord_flip(ylim = y.lim)}')))) # here I do not need the x-axis and y-axis orientation, I just need the number of main ticks and the legend. I DI NOT UNDERSTAND THE COMMENT HERE BECAUSE WE NEED COORD_FLiP
+    tempo.coord <- bef.final.plot$layout$panel_params[[1]]
+    # y.second.tick.positions: coordinates of secondary ticks (only if y.second.tick.nb argument is non NULL or if y.log argument is different from "no")
+    if(y.log != "no"){ # integer main ticks for log2 and log10
+        tempo.scale <- (as.integer(min(y.lim, na.rm = TRUE)) - 1):(as.integer(max(y.lim, na.rm = TRUE)) + 1)
+    }else{
+        tempo <- if(is.null(attributes(tempo.coord$y$breaks))){tempo.coord$y$breaks}else{unlist(attributes(tempo.coord$y$breaks))}
+        if(all(is.na(tempo))){# all() without na.rm -> ok because is.na() cannot be NA
+            tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nONLY NA IN tempo.coord$y$breaks")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }
+        tempo.scale <- fun_scale(lim = y.lim, n = ifelse(is.null(y.tick.nb), length(tempo[ ! is.na(tempo)]), y.tick.nb)) # in ggplot 3.3.0, tempo.coord$y.major_source replaced by tempo.coord$y$breaks. If fact: n = ifelse(is.null(y.tick.nb), length(tempo[ ! is.na(tempo)]), y.tick.nb)) replaced by n = ifelse(is.null(y.tick.nb), 4, y.tick.nb))
+    }
+    y.second.tick.values <- NULL
+    y.second.tick.pos <- NULL
+    if(y.log != "no"){
+        tempo <- fun_inter_ticks(lim = y.lim, log = y.log)
+        y.second.tick.values <- tempo$values
+        y.second.tick.pos <- tempo$coordinates
+        # if(vertical == TRUE){ # do not remove in case the bug is fixed
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", y = y.second.tick.pos, yend = y.second.tick.pos, x = tempo.coord$x.range[1], xend = tempo.coord$x.range[1] + diff(tempo.coord$x.range) / 80))
+        # }else{ # not working because of the ggplot2 bug
+        # assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", x = y.second.tick.pos, xend = y.second.tick.pos, y = tempo.coord$y.range[1], yend = tempo.coord$y.range[1] + diff(tempo.coord$y.range) / 80))
+        # }
+        coord.names <- c(coord.names, "y.second.tick.positions")
+    }else if(( ! is.null(y.second.tick.nb)) & y.log == "no"){
+        # if(y.second.tick.nb > 0){ #inactivated because already checked before
+        if(length(tempo.scale) < 2){
+            tempo.cat1 <- c("y.tick.nb", "y.second.tick.nb")
+            tempo.cat2 <- sapply(list(y.tick.nb, y.second.tick.nb), FUN = paste0, collapse = " ")
+            tempo.sep <- sapply(mapply(" ", max(nchar(tempo.cat1)) - nchar(tempo.cat1) + 3, FUN = rep, SIMPLIFY = FALSE), FUN = paste0, collapse = "")
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nTHE NUMBER OF GENERATED TICKS FOR THE Y-AXIS IS NOT CORRECT: ", length(tempo.scale), "\nUSING THESE ARGUMENT SETTINGS (NO DISPLAY MEANS NULL VALUE):\n", paste0(tempo.cat1, tempo.sep, tempo.cat2, collapse = "\n"), "\nPLEASE, TEST OTHER VALUES")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            tempo <- fun_inter_ticks(lim = y.lim, log = y.log, breaks = tempo.scale, n = y.second.tick.nb)
+        }
+        y.second.tick.values <- tempo$values
+        y.second.tick.pos <- tempo$coordinates
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
+            geom = "segment", 
+            y = y.second.tick.pos, 
+            yend = y.second.tick.pos, 
+            x = if(vertical == TRUE){tempo.coord$x.range[1]}else{tempo.coord$y.range[1]}, 
+            xend = if(vertical == TRUE){tempo.coord$x.range[1] + diff(tempo.coord$x.range) / 80}else{tempo.coord$y.range[1] + diff(tempo.coord$y.range) / 80}
+        ))
+        coord.names <- c(coord.names, "y.second.tick.positions")
+    }
+    # end y.second.tick.positions
+    # for the ggplot2 bug with y.log, this does not work: eval(parse(text = ifelse(vertical == FALSE & y.log == "log10", "ggplot2::scale_x_continuous", "ggplot2::scale_y_continuous")))
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_y_continuous(
+        breaks = tempo.scale, 
+        minor_breaks = y.second.tick.pos, 
+        labels = if(y.log == "log10"){scales::trans_format("identity", scales::math_format(10^.x))}else if(y.log == "log2"){scales::trans_format("identity", scales::math_format(2^.x))}else if(y.log == "no"){ggplot2::waiver()}else{tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 6") ; stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)}, # == in stop() to be able to add several messages between ==
+        expand = c(0, 0), # remove space after after axis limits
+        limits = sort(y.lim), # NA indicate that limits must correspond to data limits but ylim() already used
+        oob = scales::rescale_none, 
+        trans = ifelse(diff(y.lim) < 0, "reverse", "identity") # equivalent to ggplot2::scale_y_reverse() but create the problem of y-axis label disappearance with y.lim decreasing. Thus, do not use. Use ylim() below and after this
+    ))
+    if(vertical == TRUE){
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::coord_cartesian(ylim = y.lim)) # problem of ggplot2::ylim() is that it redraws new breaks # coord_cartesian(ylim = y.lim)) not used because bug -> y-axis label disappearance with y.lim decreasing I DO NOT UNDERSTAND THIS MESSAGE WHILE I USE COORD_CARTESIAN # clip = "off" to have secondary ticks outside plot region does not work
+    }else{
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::coord_flip(ylim = y.lim)) # clip = "off" to have secondary ticks outside plot region does not work # create the problem of y-axis label disappearance with y.lim decreasing. IDEM ABOVE
+        
+    }
+    # end y scale management (cannot be before dot plot management)
+    
+    
+    # legend management
+    if( ! is.null(legend.width)){
+        legend.final <- fun_gg_get_legend(ggplot_built = bef.final.plot, fun.name = function.name, lib.path = lib.path) # get legend
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::guides(fill = FALSE, color = FALSE, alpha = FALSE)) # inactivate the initial legend
+        if(is.null(legend.final) & plot == TRUE){ # even if any(unlist(legend.disp)) is TRUE
+            legend.final <- ggplot2::ggplot()+ggplot2::theme_void() # empty graph instead of legend
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") LEGEND REQUESTED (NON NULL categ ARGUMENT OR legend.show ARGUMENT SET TO TRUE)\nBUT IT SEEMS THAT THE PLOT HAS NO LEGEND -> EMPTY LEGEND SPACE CREATED BECAUSE OF THE NON NULL legend.width ARGUMENT\n")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    # end legend management
+    
+    
+    # drawing
+    fin.plot <- suppressMessages(suppressWarnings(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + ")))))
+    grob.save <- NULL
+    if(plot == TRUE){
+        # following lines inactivated because of problem in warn.recov and message.recov
+        # assign("env_fun_get_message", new.env())
+        # assign("tempo.gg.name", tempo.gg.name, envir = env_fun_get_message)
+        # assign("tempo.gg.count", tempo.gg.count, envir = env_fun_get_message)
+        # assign("add", add, envir = env_fun_get_message)
+        # two next line: for the moment, I cannot prevent the warning printing
+        # warn.recov <- fun_get_message(paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if(is.null(add)){NULL}else{add}), kind = "warning", header = FALSE, print.no = FALSE, env = env_fun_get_message) # for recovering warnings printed by ggplot() functions
+        # message.recov <- fun_get_message('print(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if(is.null(add)){NULL}else{add}))))', kind = "message", header = FALSE, print.no = FALSE, env = env_fun_get_message) # for recovering messages printed by ggplot() functions
+        # if( ! (return == TRUE & return.ggplot == TRUE)){ # because return() plots when return.ggplot is TRUE # finally not used -> see return.ggplot description
+        if(is.null(legend.width)){
+            grob.save <- suppressMessages(suppressWarnings(gridExtra::grid.arrange(fin.plot)))
+        }else{
+            grob.save <-suppressMessages(suppressWarnings(gridExtra::grid.arrange(fin.plot, legend.final, ncol=2, widths=c(1, legend.width))))
+        }
+        # }
+        # suppressMessages(suppressWarnings(print(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if(is.null(add)){NULL}else{add}))))))
+    }else{
+        # following lines inactivated because of problem in warn.recov and message.recov
+        # message.recov <- NULL
+        # warn.recov <- NULL
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") PLOT NOT SHOWN AS REQUESTED")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
+    # end drawing
+    
+    
+    
+    # output
+    # following lines inactivated because of problem in warn.recov and message.recov
+    # if( ! (is.null(warn) & is.null(warn.recov) & is.null(message.recov))){
+    # warn <- paste0(warn, "\n\n", if(length(warn.recov) > 0 | length(message.recov) > 0){paste0(paste0("MESSAGES FROM ggplot2 FUNCTIONS: ", ifelse( ! is.null(warn.recov), unique(message.recov), ""), ifelse( ! is.null(message.recov), unique(message.recov), ""), collapse = "\n\n"), "\n\n")})
+    # }else if( ! (is.null(warn) & is.null(warn.recov)) & is.null(message.recov)){
+    # warn <- paste0(warn, "\n\n", if(length(warn.recov) > 0){paste0(paste0("MESSAGES FROM ggplot2 FUNCTIONS: ", unique(warn.recov), collapse = "\n\n"), "\n\n")})
+    # }else if( ! (is.null(warn) & is.null(message.recov)) & is.null(warn.recov)){
+    # warn <- paste0(warn, "\n\n", if(length(message.recov) > 0){paste0(paste0("MESSAGES FROM ggplot2 FUNCTIONS: ", unique(message.recov), collapse = "\n\n"), "\n\n")})
+    # }
+    if(warn.print == TRUE & ! is.null(warn)){
+        on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
+    }
+    on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
+    if(return == TRUE){
+        tempo.output <- ggplot2::ggplot_build(fin.plot)
+        tempo.output$data <- tempo.output$data[-1] # remove the first data because corresponds to the initial empty boxplot
+        if(length(tempo.output$data) != length(coord.names)){
+            tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nlength(tempo.output$data) AND length(coord.names) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+        }else{
+            names(tempo.output$data) <- coord.names
+            tempo.output$data <- tempo.output$data[coord.names != "bad_remove"]
+        }
+        tempo <- tempo.output$layout$panel_params[[1]]
+        output <- list(
+            data = data1.ini, 
+            stat = stat.nolog, 
+            removed.row.nb = removed.row.nb, 
+            removed.rows = removed.rows, 
+            plot = c(tempo.output$data, y.second.tick.values = list(y.second.tick.values)), 
+            panel = facet.categ, 
+            axes = list(
+                x.range = tempo$x.range, 
+                x.labels = if(is.null(attributes(tempo$x$breaks))){tempo$x$breaks}else{tempo$x$scale$get_labels()}, # is.null(attributes(tempo$x$breaks)) test if it is number (TRUE) or character (FALSE)
+                x.positions = if(is.null(attributes(tempo$x$breaks))){tempo$x$breaks}else{unlist(attributes(tempo$x$breaks))}, 
+                y.range = tempo$y.range, 
+                y.labels = if(is.null(attributes(tempo$y$breaks))){tempo$y$breaks}else{tempo$y$scale$get_labels()}, 
+                y.positions = if(is.null(attributes(tempo$y$breaks))){tempo$y$breaks}else{unlist(attributes(tempo$y$breaks))}
+            ), 
+            warn = paste0("\n", warn, "\n\n"), 
+            ggplot = if(return.ggplot == TRUE){fin.plot}else{NULL}, # fin.plot plots the graph if return == TRUE
+            gtable = if(return.gtable == TRUE){grob.save}else{NULL} 
+        )
+        return(output) # this plots the graph if return.ggplot is TRUE and if no assignment
+    }
+    # end output
+    # end main code
 }
-# end loop part
 
 
 
 
-# legend display
-tempo.legend.final <- 'ggplot2::guides(
+
+# add density
+# rasterise all kind: https://cran.r-project.org/web/packages/ggrastr/vignettes/Raster_geoms.html
+# log not good: do not convert as in boxplot
+
+
+fun_gg_scatter <- function(
+    data1, 
+    x, 
+    y, 
+    categ = NULL, 
+    categ.class.order = NULL, 
+    color = NULL, 
+    geom = "geom_point", 
+    geom.step.dir = "hv", 
+    geom.stick.base = NULL, 
+    alpha = 0.5, 
+    dot.size = 2, 
+    dot.shape = 21, 
+    dot.border.size = 0.5, 
+    dot.border.color = NULL, 
+    line.size = 0.5, 
+    line.type = "solid", 
+    x.lim = NULL, 
+    x.lab = NULL, 
+    x.log = "no", 
+    x.tick.nb = NULL, 
+    x.second.tick.nb = NULL, 
+    x.include.zero = FALSE, 
+    x.left.extra.margin = 0.05, 
+    x.right.extra.margin = 0.05, 
+    x.text.angle = 0, 
+    y.lim = NULL, 
+    y.lab = NULL, 
+    y.log = "no", 
+    y.tick.nb = NULL, 
+    y.second.tick.nb = NULL, 
+    y.include.zero = FALSE, 
+    y.top.extra.margin = 0.05, 
+    y.bottom.extra.margin = 0.05, 
+    y.text.angle = 0, 
+    raster = FALSE, 
+    raster.ratio = 1, 
+    raster.threshold = NULL, 
+    text.size = 12, 
+    title = "", 
+    title.text.size = 12, 
+    legend.show = TRUE, 
+    legend.width = 0.5, 
+    legend.name = NULL, 
+    article = TRUE, 
+    grid = FALSE, 
+    add = NULL, 
+    return = FALSE, 
+    return.ggplot = FALSE,
+    return.gtable = TRUE,
+    plot = TRUE, 
+    warn.print = FALSE, 
+    lib.path = NULL
+){
+    # AIM
+    # Plot ggplot2 scatterplot with the possibility to overlay dots from up to 3 different data frames (-> three different legends) and lines from up to 3 different data frames (-> three different legends) -> up to 6 overlays totally
+    # For ggplot2 specifications, see: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html
+    # WARNINGS
+    # Rows containing NA in data1[, c(x, y, categ)] will be removed before processing, with a warning (see below)
+    # Size arguments (dot.size, dot.border.size, line.size, text.size and title.text.size) are in mm. See Hadley comment in https://stackoverflow.com/questions/17311917/ggplot2-the-unit-of-size. See also http://sape.inf.usi.ch/quick-reference/ggplot2/size). Unit object are not accepted, but conversion can be used (e.g., grid::convertUnit(grid::unit(0.2, "inches"), "mm", valueOnly = TRUE))
+    # ARGUMENTS
+    # data1: a dataframe compatible with ggplot2, or a list of data frames. Order matters for the order of the legend and for the layer staking (starting from below to top)
+    # x: single character string of the data1 column name for x-axis coordinates. If data1 is a list, then x must be a list of single character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc. Write NULL for each "geom_hline" in geom argument
+    # y: single character string of the data1 column name for y-axis coordinates. If data1 is a list, then y must be a list of single character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc. Write NULL for each "geom_vline" in geom argument
+    # categ: either NULL or a single character string or a list of single character strings, indicating the data1 column names to use for categories which creates legend display
+    # If categ == NULL, no categories -> no legend displayed
+    # If data1 is a data frame, categ must be a single character string of the data1 column name for categories
+    # If data1 is a list, then categ must be a list of single character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc. Some of the list compartments can be NULL (no legend display for these compartments), and other not
+    # categ.class.order: either (1) NULL or (2) a vector of character strings or (3) a list of these vectors, setting the order of the classes of categ in the legend display
+    # If categ.class.order is NULL, classes are represented according to the alphabetical order
+    # If data1 is a data frame, categ.class.order must be a vector of character strings specifying the different classes in the categ column name of data1
+    # If data1 is a list, then categ.class.order must be a list of vector of character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc. Some of the list compartments can be NULL (alphabetical order for these compartments), and other not
+    # color: either (1) NULL, or (2) a vector of character strings or integers, or (3) a list of vectors of character strings or integers
+    # If color is NULL, default colors of ggplot2
+    # If data1 is a data frame, color argument can be either:
+    # (1) a single color string. All the dots of the corresponding data1 will have this color, whatever the categ value (NULL or not)
+    # (2) if categ is non-null, a vector of string colors, one for each class of categ. Each color will be associated according to the categ.class.order argument if specified, or to the alphabetical order of categ classes otherwise
+    # (3) if categ is non-null, a vector or factor of string colors, like if it was one of the column of data1 data frame. WARNING: a single color per class of categ and a single class of categ per color must be respected
+    # Positive integers are also accepted instead of character strings, as long as above rules about length are respected. Integers will be processed by fun_gg_palette() using the max integer value among all the integers in color (see fun_gg_palette())
+    # If data1 is a list, then color argument must be either: 
+    # (1) a list of character strings or integers, of same size as data1, with compartment 1 related to compartment 1 of data1, etc.
+    # (2) a single character string or a single integer
+    # With a list (first possibility), the rules described for when data1 is a data frame apply to each compartment of the list. Some of the compartments can be NULL. In that case, a different grey color will be used for each NULL compartment. With a single value (second possibility), the same color will be used for all the dots and lines, whatever the data1 list
+    # geom: single character string of the kind of plot, or a list of single character strings
+    # Either:
+    # "geom_point" (scatterplot)
+    # "geom_line" (coordinates plotted then line connection, from the lowest to highest x coordinates first and from the lowest to highest y coordinates thenafter)
+    # "geom_path" (coordinates plotted then line connection respecting the row order in data1)
+    # "geom_step" coordinates plotted then line connection respecting the row order in data1 but drawn in steps). See the geom.step.dir argument
+    # "geom_hline" (horizontal line, no x value provided)
+    # "geom_vline" (vertical line, no y value provided)
+    # "geom_stick" (dots as vertical bars)
+    # If data1 is a list, then geom must be either:
+    # (1) a list of single character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc.
+    # (2) a single character string. In that case the same kind of plot will apply for the different compartments of the data1 list
+    # WARNING concerning "geom_hline" or "geom_vline":
+    # (1) x or y argument must be NULL, respectively
+    # (2) x.lim or y.lim argument must NOT be NULL, respectively, if only these kind of lines are drawn (if other geom present, then x.lim = NULL and y.lim = NULL will generate x.lim and y.lim defined by these other geom, which is not possible with "geom_hline" or "geom_vline" alone)
+    # (3) the function will draw n lines for n values in the x argument column name of the data1 data frame. If several colors required, the categ argument must be specified and the corresponding categ column name must exist in the data1 data frame with a different class name for each row
+    # geom.step.dir: single character string indicating the direction when using "geom_step" of the geom argument, or a list of single character strings
+    # Either:
+    # "vh" (vertical then horizontal)
+    # "hv" (horizontal then vertical)
+    # "mid" (step half-way between adjacent x-values)
+    # See https://ggplot2.tidyverse.org/reference/geom_path.html
+    # If data1 is a list, then geom.step.dir must be either:
+    # (1) a list of single character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc. The value in compartments related to other geom values than "geom_step" will be ignored
+    # (2) a single character string, which will be used for all the "geom_step" values of the geom argument, whatever the data1 list
+    # geom.stick.base: either (1) NULL or (2) a single numeric value or (3) a list of single numeric values, setting the base of the sticks when using "geom_stick" of the geom argument
+    # If geom.stick.base is NULL, the bottom limit of the y-axis is taken as the base
+    # If data1 is a list, then geom.stick.base must be either (1) a list of single numeric values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single numeric value. With a list (former possibility), the values in compartments related to other geom values than "geom_stick" will be ignored. With a single value (latter possibility), the same base will be used for all the sticks, whatever the data1 list
+    # Warning: the y-axis limits are not modified by the value of geom.stick.base, meaning that this value can be outside of the range of y.lim. Add the value of geom.stick.base also in the y.lim argument if required
+    # Warning: if geom.stick.base is NULL, the bottom limit of the y-axis is taken as the base. Thus, be careful with inverted y-axis
+    # alpha: single numeric value (from 0 to 1) of transparency. If data1 is a list, then alpha must be either (1) a list of single numeric values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single numeric value. In that case the same transparency will apply for the different compartments of the data1 list
+    # dot.size: single numeric value of dot shape radius? in mm. If data1 is a list, then dot.size must be either (1) a list of single numeric values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single numeric value. With a list (former possibility), the value in compartments related to lines will be ignored. With a single value (latter possibility), the same dot.size will be used for all the dots, whatever the data1 list
+    # dot.shape: value indicating the shape of the dots (see https://ggplot2.tidyverse.org/articles/ggplot2-specs.html) If data1 is a list, then dot.shape must be either (1) a list of single shape values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single shape value. With a list (former possibility), the value in compartments related to lines will be ignored. With a single value (latter possibility), the same dot.shape will be used for all the dots, whatever the data1 list
+    # dot.border.size: single numeric value of border dot width in mm. Write zero for no dot border. If data1 is a list, then dot.border.size must be either (1) a list of single numeric values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single numeric value. With a list (former possibility), the value in compartments related to lines will be ignored. With a single value (latter possibility), the same dot.border.size will be used for all the dots, whatever the data1 list
+    # dot.border.color: single character color string defining the color of the dot border (same border color for all the dots, whatever their categories). If dot.border.color == NULL, the border color will be the same as the dot color. A single integer is also accepted instead of a character string, that will be processed by fun_gg_palette()
+    # line.size: single numeric value of line width in mm. If data1 is a list, then line.size must be either (1) a list of single numeric values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single numeric value. With a list (former possibility), the value in compartments related to dots will be ignored. With a single value (latter possibility), the same line.size will be used for all the lines, whatever the data1 list
+    # line.type: value indicating the kind of lines (see https://ggplot2.tidyverse.org/articles/ggplot2-specs.html) If data1 is a list, then line.type must be either (1) a list of single line kind values, of same size as data1, with compartment 1 related to compartment 1 of data1, etc., or (2) a single line kind value. With a list (former possibility), the value in compartments related to dots will be ignored. With a single value (latter possibility), the same line.type will be used for all the lines, whatever the data1 list
+    # x.lim: 2 numeric values setting the x-axis range. Order of the 2 values matters (for inverted axis). If NULL, the range of the x column name of data1 will be used
+    # x.lab: a character string or expression for x-axis label. If NULL, will use the first value of x (x column name of the first data frame in data1). Warning message if the elements in x are different between data frames in data1
+    # x.log: either "no", "log2" (values in the x column name of the data1 data frame will be log2 transformed and x-axis will be log2 scaled) or "log10" (values in the x column name of the data1 data frame will be log10 transformed and x-axis will be log10 scaled)
+    # x.tick.nb: approximate number of desired values labeling the x-axis (i.e., main ticks, see the n argument of the the cute::fun_scale() function). If NULL and if x.log is "no", then the number of labeling values is set by ggplot2. If NULL and if x.log is "log2" or "log10", then the number of labeling values corresponds to all the exposant integers in the x.lim range (e.g., 10^1, 10^2 and 10^3, meaning 3 main ticks for x.lim = c(9, 1200)). WARNING: if non-NULL and if x.log is "log2" or "log10", labeling can be difficult to read (e.g., ..., 10^2, 10^2.5, 10^3, ...)
+    # x.second.tick.nb: number of desired secondary ticks between main ticks. Ignored if x.log is other than "no" (log scale plotted). Use argument return = TRUE and see $plot$x.second.tick.values to have the values associated to secondary ticks. IF NULL, no secondary ticks
+    # x.include.zero: logical. Does x.lim range include 0? Ignored if x.log is "log2" or "log10"
+    # x.left.extra.margin: single proportion (between 0 and 1) indicating if extra margins must be added to x.lim. If different from 0, add the range of the axis multiplied by x.left.extra.margin (e.g., abs(x.lim[2] - x.lim[1]) * x.left.extra.margin) to the left of x-axis
+    # x.right.extra.margin: idem as x.left.extra.margin but to the right of x-axis
+    # x.text.angle: integer value of the text angle for the x-axis labeling values, using the same rules as in ggplot2. Use positive value for clockwise rotation: 0 for horizontal, 90 for vertical, 180 for upside down etc. Use negative values for counterclockwise rotation: 0 for horizontal, -90 for vertical, -180 for upside down etc.
+    # y.lim: 2 numeric values setting the y-axis range. Order of the 2 values matters (for inverted axis). If NULL, the range of the y column name of data1 will be used
+    # y.lab: a character string or expression for y-axis label. If NULL, will use the first value of y (y column name of the first data frame in data1). Warning message if the elements in y are different between data frames in data1
+    # y.log: either "no", "log2" (values in the y column name of the data1 data frame will be log2 transformed and y-axis will be log2 scaled) or "log10" (values in the y column name of the data1 data frame will be log10 transformed and y-axis will be log10 scaled)
+    # y.tick.nb: approximate number of desired values labeling the y-axis (i.e., main ticks, see the n argument of the the cute::fun_scale() function). If NULL and if y.log is "no", then the number of labeling values is set by ggplot2. If NULL and if y.log is "log2" or "log10", then the number of labeling values corresponds to all the exposant integers in the y.lim range (e.g., 10^1, 10^2 and 10^3, meaning 3 main ticks for y.lim = c(9, 1200)). WARNING: if non-NULL and if y.log is "log2" or "log10", labeling can be difficult to read (e.g., ..., 10^2, 10^2.5, 10^3, ...)
+    # y.second.tick.nb: number of desired secondary ticks between main ticks. Ignored if y.log is other than "no" (log scale plotted). Use argument return = TRUE and see $plot$y.second.tick.values to have the values associated to secondary ticks. IF NULL, no secondary ticks
+    # y.include.zero: logical. Does y.lim range include 0? Ignored if y.log is "log2" or "log10"
+    # y.top.extra.margin: single proportion (between 0 and 1) indicating if extra margins must be added to y.lim. If different from 0, add the range of the axis multiplied by y.top.extra.margin (e.g., abs(y.lim[2] - y.lim[1]) * y.top.extra.margin) to the top of y-axis
+    # y.bottom.extra.margin: idem as y.top.extra.margin but to the bottom of y-axis
+    # y.text.angle: integer value of the text angle for the y-axis labeling values, using the same rules as in ggplot2. Use positive value for clockwise rotation: 0 for horizontal, 90 for vertical, 180 for upside down etc. Use negative values for counterclockwise rotation: 0 for horizontal, -90 for vertical, -180 for upside down etc.
+    # raster: logical. Dots in raster mode? If FALSE, dots from each "geom_point" from geom argument are plotted in vectorial mode (bigger pdf and long to display if lots of dots). If TRUE, dots from each "geom_point" from geom argument are plotted in matricial mode (smaller pdf and easy display if lots of dots, but it takes time to generate the layer). If TRUE, the raster.ratio argument is used to avoid an ellipsoid representation of the dots. If TRUE, solve the transparency problem with some GUI. Overriden by the non-NULL raster.threshold argument
+    # raster.ratio: single numeric value indicating the height / width ratio of the graphic device used (for instance provided by the $dim compartment in the output of the fun_open() function). The default value is 1 because by default R opens a square graphic device. But this argument has to be set when using other device dimensions. Ignored if raster == FALSE
+    # raster.threshold: positive integer value indicating the limit of the dot number above which "geom_point" layers from the geom argument switch from vectorial mode to matricial mode (see the raster argument). If any layer is matricial, then the raster.ratio argument is used to avoid an ellipsoid representation of the dots. If non-NULL, it overrides the raster argument
+    # text.size: numeric value of the font size of the (1) axis numbers and axis legends and (2) texts in the graphic legend (in mm)
+    # title: character string of the graph title
+    # title.text.size: numeric value of the title font size in mm
+    # legend.show: logical. Show legend? Not considered if categ argument is NULL, because this already generate no legend, excepted if legend.width argument is non-NULL. In that specific case (categ is NULL, legend.show is TRUE and legend.width is non-NULL), an empty legend space is created. This can be useful when desiring graphs of exactly the same width, whatever they have legends or not
+    # legend.width: single proportion (between 0 and 1) indicating the relative width of the legend sector (on the right of the plot) relative to the width of the plot. Value 1 means that the window device width is split in 2, half for the plot and half for the legend. Value 0 means no room for the legend, which will overlay the plot region. Write NULL to inactivate the legend sector. In such case, ggplot2 will manage the room required for the legend display, meaning that the width of the plotting region can vary between graphs, depending on the text in the legend
+    # legend.name: character string of the legend title. If legend.name is NULL and categ argument is not NULL, then legend.name <- categ. If data1 is a list, then legend.name must be a list of character strings, of same size as data1, with compartment 1 related to compartment 1 of data1, etc. Some of the list compartments can be NULL, and other not
+    # article: logical. If TRUE, use an article theme (article like). If FALSE, use a classic related ggplot theme. Use the add argument (e.g., add = "+ggplot2::theme_classic()" for the exact classic ggplot theme
+    # grid: logical. Draw lines in the background to better read the box values? Not considered if article == FALSE (grid systematically present)
+    # add: character string allowing to add more ggplot2 features (dots, lines, themes, facet, etc.). Ignored if NULL
+    # WARNING: (1) the string must start with "+", (2) the string must finish with ")" and (3) each function must be preceded by "ggplot2::". Example: "+ ggplot2::coord_flip() + ggplot2::theme_bw()"
+    # If the character string contains the "ggplot2::theme" string, then the article argument of fun_gg_scatter() (see above) is ignored with a warning. In addition, some arguments can be overwritten, like x.angle (check all the arguments)
+    # Handle the add argument with caution since added functions can create conflicts with the preexisting internal ggplot2 functions
+    # WARNING: the call of objects inside the quotes of add can lead to an error if the name of these objects are some of the fun_gg_scatter() arguments. Indeed, the function will use the internal argument instead of the global environment object. Example article <- "a" in the working environment and add = '+ ggplot2::ggtitle(article)'. The risk here is to have TRUE as title. To solve this, use add = '+ ggplot2::ggtitle(get("article", envir = .GlobalEnv))'
+    # return: logical. Return the graph parameters?
+    # return.ggplot: logical. Return the ggplot object in the output list? Ignored if return argument is FALSE. WARNING: always assign the fun_gg_scatter() function (e.g., a <- fun_gg_scatter()) if return.ggplot argument is TRUE, otherwise, double plotting is performed. See $ggplot in the RETURN section below for more details
+    # return.gtable: logical. Return the ggplot object as gtable of grobs in the output list? Ignored if plot argument is FALSE. Indeed, the graph must be plotted to get the grobs dispositions. See $gtable in the RETURN section below for more details
+    # plot: logical. Plot the graphic? If FALSE and return argument is TRUE, graphical parameters and associated warnings are provided without plotting
+    # warn.print: logical. Print warnings at the end of the execution? ? If FALSE, warning messages are never printed, but can still be recovered in the returned list. Some of the warning messages (those delivered by the internal ggplot2 functions) are not apparent when using the argument plot = FALSE
+    # lib.path: character string indicating the absolute path of the required packages (see below). if NULL, the function will use the R library default folders
+    # RETURN
+    # a scatter plot if plot argument is TRUE
+    # a list of the graph info if return argument is TRUE:
+    # $data: the initial data with graphic information added. WARNING: if the x.log or y.log argument is not "no", x or y argument column of the data1 data frame are log2 or log10 converted in $data, respectively. Use 2^values or 10^$values to recover the initial values
+    # $removed.row.nb: a list of the removed rows numbers in data frames (because of NA). NULL if no row removed
+    # $removed.rows: a list of the removed rows in data frames (because of NA). NULL if no row removed
+    # $plot: the graphic box and dot coordinates
+    # $dots: dot coordinates
+    # y.second.tick.positions: coordinates of secondary ticks (only if y.second.tick.nb argument is non-null or if y.log argument is different from "no")
+    # y.second.tick.values: values of secondary ticks. NULL except if y.second.tick.nb argument is non-null or if y.log argument is different from "no")
+    # $panel: the variable names used for the panels (NULL if no panels). WARNING: NA can be present according to ggplot2 upgrade to v3.3.0
+    # $axes: the x-axis and y-axis info
+    # $warn: the warning messages. Use cat() for proper display. NULL if no warning. WARNING: warning messages delivered by the internal ggplot2 functions are not apparent when using the argument plot = FALSE
+    # $ggplot: ggplot object that can be used for reprint (use print($ggplot) or update (use $ggplot + ggplot2::...). NULL if return.ggplot argument is FALSE. Of note, a non-null $ggplot in the output list is sometimes annoying as the manipulation of this list prints the plot
+    # $gtable: gtable object that can be used for reprint (use gridExtra::grid.arrange(...$ggplot) or with additionnal grobs (see the grob decomposition in the examples). NULL if return.ggplot argument is FALSE. Contrary to $ggplot, a non-NULL $gtable in the output list is not annoying as the manipulation of this list does not print the plot
+    # REQUIRED PACKAGES
+    # ggplot2
+    # gridExtra
+    # lemon (in case of use in the add argument)
+    # scales
+    # if raster plots are drawn (see the raster and raster.threshold arguments):
+    # Cairo
+    # grid
+    # REQUIRED FUNCTIONS FROM THE cute PACKAGE
+    # fun_gg_empty_graph()
+    # fun_gg_palette()
+    # fun_gg_point_rast()
+    # fun_pack()
+    # fun_check()
+    # fun_round()
+    # fun_scale()
+    # fun_inter_ticks()
+    # EXAMPLES
+    # set.seed(1) ; obs1 <- data.frame(Km = c(2, 1, 6, 5, 4, 7), Time = c(2, 1, 6, 5, 4, 7)^2, Car = c("TUUT", "TUUT", "TUUT", "WIIM", "WIIM", "WIIM"), Color1 = rep(c("coral", "lightblue"), each = 3), stringsAsFactors = TRUE) ; fun_gg_scatter(data1 = obs1, x = "Km", y = "Time")
+    # DEBUGGING
+    # set.seed(1) ; obs1 <- data.frame(km = rnorm(1000, 10, 3), time = rnorm(1000, 10, 3), group1 = rep(c("A1", "A2"), 500), stringsAsFactors = TRUE) ; obs2 <-data.frame(km = rnorm(1000, 15, 3), time = rnorm(1000, 15, 3), group2 = rep(c("G1", "G2"), 500), stringsAsFactors = TRUE) ; set.seed(NULL) ; obs1$km[2:3] <- NA ; data1 = list(L1 = obs1, L2 = obs2) ; x = list(L1 = "km", L2 = "km") ; y = list(L1 = "time", L2 = "time") ; categ = list(L1 = "group1", L2 = "group2") ; categ = NULL ; categ.class.order = NULL ; color = NULL ; geom = "geom_point" ; geom.step.dir = "hv" ; geom.stick.base = NULL ; alpha = 0.5 ; dot.size = 2 ; dot.shape = 21 ; dot.border.size = 0.5 ; dot.border.color = NULL ; line.size = 0.5 ; line.type = "solid" ; x.lim = NULL ; x.lab = NULL ; x.log = "no" ; x.tick.nb = NULL ; x.second.tick.nb = NULL ; x.include.zero = FALSE ; x.left.extra.margin = 0.05 ; x.right.extra.margin = 0.05 ; x.text.angle = 0 ; y.lim = NULL ; y.lab = NULL ; y.log = "no" ; y.tick.nb = NULL ; y.second.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0.05 ; y.text.angle = 0 ; raster = FALSE ; raster.ratio = 1 ; raster.threshold = NULL ; text.size = 12 ; title = "" ; title.text.size = 12 ; legend.show = TRUE ; legend.width = 0.5 ; legend.name = NULL ; article = TRUE ; grid = FALSE ; add = NULL ; return = FALSE ; return.ggplot = FALSE ; return.gtable = TRUE ; plot = TRUE ; warn.print = FALSE ; lib.path = NULL
+    # function name
+    function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
+    arg.names <- names(formals(fun = sys.function(sys.parent(n = 2)))) # names of all the arguments
+    arg.user.setting <- as.list(match.call(expand.dots=FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
+    # end function name
+    # required function checking
+    req.function <- c(
+        "fun_check", 
+        "fun_gg_just", 
+        "fun_gg_empty_graph", 
+        "fun_gg_palette", 
+        "fun_gg_point_rast", 
+        "fun_round", 
+        "fun_pack", 
+        "fun_scale", 
+        "fun_inter_ticks"
+    )
+    tempo <- NULL
+    for(i1 in req.function){
+        if(length(find(i1, mode = "function"))== 0L){
+            tempo <- c(tempo, i1)
+        }
+    }
+    if( ! is.null(tempo)){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nREQUIRED cute FUNCTION", ifelse(length(tempo) > 1, "S ARE", " IS"), " MISSING IN THE R ENVIRONMENT:\n", paste0(tempo, collapse = "()\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end required function checking
+    # reserved words to avoid bugs (used in this function)
+    reserved.words <- c("fake_x", "fake_y", "fake_categ")
+    # end reserved words to avoid bugs (used in this function)
+    # arg with no default values
+    mandat.args <- c(
+        "data1", 
+        "x", 
+        "y"
+    )
+    tempo <- eval(parse(text = paste0("missing(", paste0(mandat.args, collapse = ") | missing("), ")")))
+    if(any(tempo)){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nFOLLOWING ARGUMENT", ifelse(length(mandat.args) > 1, "S HAVE", "HAS"), " NO DEFAULT VALUE AND REQUIRE ONE:\n", paste0(mandat.args, collapse = "\n"))
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end arg with no default values
+    # argument primary checking
+    arg.check <- NULL #
+    text.check <- NULL #
+    checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
+    ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$object.name))
+    tempo1 <- fun_check(data = data1, class = "data.frame", na.contain = TRUE, fun.name = function.name)
+    tempo2 <- fun_check(data = data1, class = "list", na.contain = TRUE, fun.name = function.name)
+    checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+    if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": data1 ARGUMENT MUST BE A DATA FRAME OR A LIST OF DATA FRAMES")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    if( ! is.null(x)){
+        tempo1 <- fun_check(data = x, class = "vector", mode = "character", na.contain = TRUE, length = 1, fun.name = function.name)
+        tempo2 <- fun_check(data = x, class = "list", na.contain = TRUE, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": x ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = x, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(y)){
+        tempo1 <- fun_check(data = y, class = "vector", mode = "character", na.contain = TRUE, length = 1, fun.name = function.name)
+        tempo2 <- fun_check(data = y, class = "list", na.contain = TRUE, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": y ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = y, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(categ)){
+        tempo1 <- fun_check(data = categ, class = "vector", mode = "character", length = 1, fun.name = function.name)
+        tempo2 <- fun_check(data = categ, class = "list", na.contain = TRUE, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": categ ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = categ, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(categ.class.order)){
+        if(is.null(categ)){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": categ.class.order ARGUMENT IS NOT NULL, BUT categ IS")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+        tempo1 <- fun_check(data = categ.class.order, class = "vector", mode = "character", fun.name = function.name)
+        tempo2 <- fun_check(data = categ.class.order, class = "list", na.contain = TRUE, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": categ.class.order ARGUMENT MUST BE A VECTOR OF CHARACTER STRINGS OR A LIST OF VECTOR OF CHARACTER STRINGS")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = categ.class.order, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(legend.name)){
+        tempo1 <- fun_check(data = legend.name, class = "vector", mode = "character", na.contain = TRUE, length = 1, fun.name = function.name)
+        tempo2 <- fun_check(data = legend.name, class = "list", na.contain = TRUE, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": legend.name ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = legend.name, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(color)){
+        tempo1 <- fun_check(data = color, class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name)
+        tempo2 <- fun_check(data = color, class = "factor", na.contain = TRUE, fun.name = function.name)
+        tempo3 <- fun_check(data = color, class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name)
+        tempo4 <- fun_check(data = color, class = "list", na.contain = TRUE, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo4$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE & tempo3$problem == TRUE & tempo4$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": color ARGUMENT MUST BE A VECTOR (OF CHARACTER STRINGS OR INTEGERS) OR A FACTOR OR A LIST OF THESE POSSIBILITIES")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = color, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo1 <- fun_check(data = geom, class = "vector", mode = "character", na.contain = FALSE, length = 1, fun.name = function.name)
+    tempo2 <- fun_check(data = geom, class = "list", na.contain = TRUE, fun.name = function.name)
+    checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+    if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": geom ARGUMENT MUST BE A SINGLE CHARACTER STRING OR A LIST OF CHARACTER STRINGS")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    tempo1 <- fun_check(data = geom.step.dir, options = c("vh", "hv", "mid"), na.contain = FALSE, length = 1, fun.name = function.name)
+    tempo2 <- fun_check(data = geom.step.dir, class = "list", na.contain = TRUE, fun.name = function.name)
+    checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+    if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": geom.step.dir ARGUMENT MUST BE A SINGLE CHARACTER STRING (\"vh\" OR \"hv\" OR \"mid\") OR A LIST OF THESE CHARACTER STRINGS")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    if( ! is.null(geom.stick.base)){
+        tempo1 <- fun_check(data = geom.stick.base, class = "vector", mode = "numeric", na.contain = FALSE, length = 1, fun.name = function.name)
+        tempo2 <- fun_check(data = color, class = "list", na.contain = TRUE, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": geom.stick.base ARGUMENT MUST BE A SINGLE NUMERIC VALUE OR A LIST OF SINGLE NUMERIC VALUES")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = geom.stick.base, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo1 <- fun_check(data = alpha, prop = TRUE, length = 1, fun.name = function.name)
+    tempo2 <- fun_check(data = alpha, class = "list", na.contain = TRUE, fun.name = function.name)
+    checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+    if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": alpha ARGUMENT MUST BE A SINGLE NUMERIC VALUE BETWEEN 0 AND 1 OR A LIST OF SUCH VALUES")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    tempo1 <- fun_check(data = dot.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name)
+    tempo2 <- fun_check(data = dot.size, class = "list", na.contain = TRUE, fun.name = function.name)
+    checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+    if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": dot.size ARGUMENT MUST BE A SINGLE NUMERIC VALUE OR A LIST OF SINGLE NUMERIC VALUES")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    tempo1 <- fun_check(data = dot.shape, class = "vector", length = 1, fun.name = function.name)
+    tempo2 <- fun_check(data = dot.shape, class = "list", na.contain = TRUE, fun.name = function.name)
+    checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+    if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": dot.shape ARGUMENT MUST BE A SINGLE SHAPE VALUE OR A LIST OF SINGLE SHAPE VALUES (SEE https://ggplot2.tidyverse.org/articles/ggplot2-specs.html)")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    tempo1 <- fun_check(data = dot.border.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name)
+    tempo2 <- fun_check(data = dot.border.size, class = "list", na.contain = TRUE, fun.name = function.name)
+    checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+    if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.size ARGUMENT MUST BE A SINGLE NUMERIC VALUE OR A LIST OF SINGLE NUMERIC VALUES")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    if( ! is.null(dot.border.color)){
+        tempo1 <- fun_check(data = dot.border.color, class = "vector", mode = "character", length = 1, fun.name = function.name)
+        tempo2 <- fun_check(data = dot.border.color, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, fun.name = function.name)
+        checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+        if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+            # integer colors -> gg_palette
+            tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.color MUST BE A SINGLE CHARACTER STRING OF COLOR OR A SINGLE INTEGER VALUE")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = dot.border.color, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo1 <- fun_check(data = line.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name)
+    tempo2 <- fun_check(data = line.size, class = "list", na.contain = TRUE, fun.name = function.name)
+    checked.arg.names <- c(checked.arg.names, tempo2$object.name)
+    if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": line.size ARGUMENT MUST BE A SINGLE NUMERIC VALUE OR A LIST OF SINGLE NUMERIC VALUES")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    tempo1 <- fun_check(data = line.type, class = "vector", typeof = "integer", double.as.integer.allowed = FALSE, length = 1, fun.name = function.name)
+    tempo2 <- fun_check(data = line.type, class = "vector", mode = "character", length = 1, fun.name = function.name)
+    tempo3 <- fun_check(data = line.type, class = "list", na.contain = TRUE, fun.name = function.name)
+    checked.arg.names <- c(checked.arg.names, tempo3$object.name)
+    if(tempo1$problem == TRUE & tempo2$problem == TRUE & tempo3$problem == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": line.type ARGUMENT MUST BE A SINGLE LINE KIND VALUE OR A LIST OF SINGLE LINE KIND VALUES (SEE https://ggplot2.tidyverse.org/articles/ggplot2-specs.html)")
+        text.check <- c(text.check, tempo.cat)
+        arg.check <- c(arg.check, TRUE)
+    }
+    if( ! is.null(x.lim)){
+        tempo <- fun_check(data = x.lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & any(x.lim %in% c(Inf, -Inf))){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": x.lim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = x.lim, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(x.lab)){
+        if(all(class(x.lab) %in% "expression")){ # to deal with math symbols
+            tempo <- fun_check(data = x.lab, class = "expression", length = 1, fun.name = function.name) ; eval(ee)
+        }else{
+            tempo <- fun_check(data = x.lab, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = x.lab, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = x.log, options = c("no", "log2", "log10"), length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(x.tick.nb)){
+        tempo <- fun_check(data = x.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & x.tick.nb < 0){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": x.tick.nb ARGUMENT MUST BE A NON-NULL POSITIVE INTEGER")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = x.tick.nb, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(x.second.tick.nb)){
+        tempo <- fun_check(data = x.second.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & x.second.tick.nb <= 0){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": x.second.tick.nb ARGUMENT MUST BE A NON-NULL POSITIVE INTEGER")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = x.second.tick.nb, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = x.include.zero, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = x.left.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = x.right.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = x.text.angle, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, neg.values = TRUE, fun.name = function.name) ; eval(ee)
+    if( ! is.null(y.lim)){
+        tempo <- fun_check(data = y.lim, class = "vector", mode = "numeric", length = 2, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & any(y.lim %in% c(Inf, -Inf))){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": y.lim ARGUMENT CANNOT CONTAIN -Inf OR Inf VALUES")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = y.lim, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(y.lab)){
+        if(all(class(y.lab) %in% "expression")){ # to deal with math symbols
+            tempo <- fun_check(data = y.lab, class = "expression", length = 1, fun.name = function.name) ; eval(ee)
+        }else{
+            tempo <- fun_check(data = y.lab, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = y.lab, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = y.log, options = c("no", "log2", "log10"), length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(y.tick.nb)){
+        tempo <- fun_check(data = y.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & y.tick.nb < 0){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": y.tick.nb ARGUMENT MUST BE A NON-NULL POSITIVE INTEGER")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = y.tick.nb, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if( ! is.null(y.second.tick.nb)){
+        tempo <- fun_check(data = y.second.tick.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE & y.second.tick.nb <= 0){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": y.second.tick.nb ARGUMENT MUST BE A NON-NULL POSITIVE INTEGER")
+            text.check <- c(text.check, tempo.cat)
+            arg.check <- c(arg.check, TRUE)
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = y.second.tick.nb, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = y.include.zero, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y.top.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y.bottom.extra.margin, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = y.text.angle, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, length = 1, neg.values = TRUE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = raster, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = raster.ratio, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    if( ! is.null(raster.threshold)){
+        tempo <- fun_check(data = raster.threshold, class = "vector", typeof = "integer", neg.values = FALSE, double.as.integer.allowed = TRUE, fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = raster.threshold, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = title, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = title.text.size, class = "vector", mode = "numeric", length = 1, neg.values = FALSE, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = legend.show, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(legend.width)){
+        tempo <- fun_check(data = legend.width, prop = TRUE, length = 1, fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = legend.width, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = article, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = grid, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(add)){
+        tempo <- fun_check(data = add, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = add, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    tempo <- fun_check(data = return, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = return.ggplot, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = return.gtable, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = plot, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
+    if( ! is.null(lib.path)){
+        tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
+        if(tempo$problem == FALSE){
+            if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
+                tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
+                text.check <- c(text.check, tempo.cat)
+                arg.check <- c(arg.check, TRUE)
+            }
+        }
+    }else{
+        # no fun_check test here, it is just for checked.arg.names
+        tempo <- fun_check(data = lib.path, class = "vector")
+        checked.arg.names <- c(checked.arg.names, tempo$object.name)
+    }
+    if(any(arg.check) == TRUE){
+        stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
+    }
+    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.7/r_debugging_tools-v1.7.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
+    # end argument primary checking
+    
+    
+    # second round of checking and data preparation
+    # management of NA arguments
+    tempo.arg <- names(arg.user.setting) # values provided by the user
+    tempo.log <- suppressWarnings(sapply(lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.na), FUN = any)) & lapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = length)== 1L # no argument provided by the user can be just NA
+    if(any(tempo.log) == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT JUST BE NA")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NA arguments
+    # management of NULL arguments
+    tempo.arg <-c(
+        "data1", 
+        # "x", # inactivated because of hline or vline
+        # "y", # inactivated because of hline or vline
+        "geom", 
+        "geom.step.dir", 
+        # "geom.stick.base", # inactivated because can be null
+        "alpha", 
+        "dot.size", 
+        "dot.shape", 
+        "dot.border.size", 
+        "line.size", 
+        "line.type", 
+        "x.log", 
+        "x.include.zero", 
+        "x.left.extra.margin", 
+        "x.right.extra.margin", 
+        "x.text.angle", 
+        "y.log", 
+        "y.include.zero", 
+        "y.top.extra.margin", 
+        "y.bottom.extra.margin", 
+        "y.text.angle", 
+        "raster", 
+        "raster.ratio", 
+        "text.size", 
+        "title", 
+        "title.text.size", 
+        "legend.show", 
+        # "legend.width", # inactivated because can be null
+        "article", 
+        "grid", 
+        "return", 
+        "return.ggplot", 
+        "return.gtable", 
+        "plot", 
+        "warn.print"
+    )
+    tempo.log <- sapply(lapply(tempo.arg, FUN = get, env = sys.nframe(), inherit = FALSE), FUN = is.null)
+    if(any(tempo.log) == TRUE){
+        tempo.cat <- paste0("ERROR IN ", function.name, ":\n", ifelse(sum(tempo.log, na.rm = TRUE) > 1, "THESE ARGUMENTS\n", "THIS ARGUMENT\n"), paste0(tempo.arg[tempo.log], collapse = "\n"),"\nCANNOT BE NULL")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }
+    # end management of NULL arguments
+    # code that protects set.seed() in the global environment
+    # end code that protects set.seed() in the global environment
+    # warning initiation
+    ini.warning.length <- options()$warning.length
+    options(warning.length = 8170)
+    warn <- NULL
+    warn.count <- 0
+    # end warning initiation
+    # other checkings
+    # check list lengths (and names of data1 compartments if present)
+    list.color <- NULL
+    list.geom <- NULL
+    list.geom.step.dir <- NULL
+    list.geom.stick.base <- NULL
+    list.alpha <- NULL
+    list.dot.size <- NULL
+    list.dot.shape <- NULL
+    list.dot.border.size <- NULL
+    list.dot.border.color <- NULL
+    list.line.size <- NULL
+    list.line.type <- NULL
+    if(all(class(data1) == "list")){
+        if(length(data1) > 6){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": data1 ARGUMENT MUST BE A LIST OF 6 DATA FRAMES MAXIMUM (6 OVERLAYS MAX)")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+        if(is.null(names(data1))){
+            names(data1) <- paste0("L", 1:length(data1))
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") NULL NAME COMPARTMENT OF data1 LIST -> NAMES RESPECTIVELY ATTRIBUTED TO EACH COMPARTMENT:\n", paste(names(data1), collapse = " "))
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+        if( ! is.null(x)){
+            if( ! (all(class(x) == "list") & length(data1) == length(x))){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": x ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+        }else{
+            x <- vector("list", length(data1))
+        }
+        if( ! is.null(y)){
+            if( ! (all(class(y) == "list") & length(data1) == length(y))){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": y ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+        }else{
+            y <- vector("list", length(data1))
+        }
+        if( ! is.null(categ)){
+            if( ! (all(class(categ) == "list") & length(data1) == length(categ))){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": categ ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+        }
+        if( ! is.null(categ.class.order)){
+            if( ! (all(class(categ.class.order) == "list") & length(data1) == length(categ.class.order))){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": categ.class.order ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+        }
+        if( ! is.null(color)){
+            if( ! ((all(class(color) == "list") & length(data1) == length(color)) | ((all(mode(color) == "character") | all(mode(color) == "numeric")) & length(color)== 1L))){ # list of same length as data1 or single value
+                tempo.cat <- paste0("ERROR IN ", function.name, ": color ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE CHARACTER STRING OR INTEGER")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else if((all(mode(color) == "character") | all(mode(color) == "numeric")) & length(color)== 1L){ # convert the single value into a list of single value
+                list.color <- vector(mode = "list", length = length(data1))
+                list.color[] <- color
+            }
+        }
+        if( ! ((all(class(geom) == "list") & length(data1) == length(geom)) | (all(mode(geom) == "character") & length(geom)== 1L))){ # list of same length as data1 or single value
+            tempo.cat <- paste0("ERROR IN ", function.name, ": geom ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE CHARACTER VALUE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if(all(mode(geom) == "character") & length(geom)== 1L){ # convert the single value into a list of single value
+            list.geom <- vector(mode = "list", length = length(data1))
+            list.geom[] <- geom
+        }
+        if( ! ((all(class(geom.step.dir) == "list") & length(data1) == length(geom.step.dir)) | (all(mode(geom.step.dir) == "character") & length(geom.step.dir)== 1L))){ # list of same length as data1 or single value
+            tempo.cat <- paste0("ERROR IN ", function.name, ": geom.step.dir ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE CHARACTER VALUE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if(all(mode(geom.step.dir) == "character") & length(geom.step.dir)== 1L){ # convert the single value into a list of single value
+            list.geom.step.dir <- vector(mode = "list", length = length(data1))
+            list.geom.step.dir[] <- geom.step.dir
+        }
+        if( ! is.null(geom.stick.base)){
+            if( ! ((all(class(geom.stick.base) == "list") & length(data1) == length(geom.stick.base)) | (all(mode(geom.stick.base) == "numeric") & length(geom.stick.base)== 1L))){ # list of same length as data1 or single value
+                tempo.cat <- paste0("ERROR IN ", function.name, ": geom.stick.base ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE NUMERIC VALUE")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else if(all(mode(geom.stick.base) == "numeric") & length(geom.stick.base)== 1L){ # convert the single value into a list of single value
+                list.geom.stick.base <- vector(mode = "list", length = length(data1))
+                list.geom.stick.base[] <- geom.stick.base
+            }
+        }
+        if( ! ((all(class(alpha) == "list") & length(data1) == length(alpha)) | (all(mode(alpha) == "numeric") & length(alpha)== 1L))){ # list of same length as data1 or single value
+            tempo.cat <- paste0("ERROR IN ", function.name, ": alpha ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE NUMERIC VALUE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if(all(mode(alpha) == "numeric") & length(alpha)== 1L){ # convert the single value into a list of single value
+            list.alpha <- vector(mode = "list", length = length(data1))
+            list.alpha[] <- alpha
+        }
+        if( ! ((all(class(dot.size) == "list") & length(data1) == length(dot.size)) | (all(mode(dot.size) == "numeric") & length(dot.size)== 1L))){ # list of same length as data1 or single value
+            tempo.cat <- paste0("ERROR IN ", function.name, ": dot.size ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE NUMERIC VALUE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if(all(mode(dot.size) == "numeric") & length(dot.size)== 1L){ # convert the single value into a list of single value
+            list.dot.size <- vector(mode = "list", length = length(data1))
+            list.dot.size[] <- dot.size
+        }
+        if( ! ((all(class(dot.shape) == "list") & length(data1) == length(dot.shape)) | (all(mode(dot.shape) != "list") & length(dot.shape)== 1L))){ # list of same length as data1 or single value
+            tempo.cat <- paste0("ERROR IN ", function.name, ": dot.shape ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE SHAPE VALUE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if(all(mode(dot.shape) != "list") & length(dot.shape)== 1L){ # convert the single value into a list of single value
+            list.dot.shape <- vector(mode = "list", length = length(data1))
+            list.dot.shape[] <- dot.shape
+        }
+        if( ! ((all(class(dot.border.size) == "list") & length(data1) == length(dot.border.size)) | (all(mode(dot.border.size) == "numeric") & length(dot.border.size)== 1L))){ # list of same length as data1 or single value
+            tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.size ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE NUMERIC VALUE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if(all(mode(dot.border.size) == "numeric") & length(dot.border.size)== 1L){ # convert the single value into a list of single value
+            list.dot.border.size <- vector(mode = "list", length = length(data1))
+            list.dot.border.size[] <- dot.border.size
+        }
+        if( ! is.null(dot.border.color)){
+            if( ! ((all(class(dot.border.color) == "list") & length(data1) == length(dot.border.color)) | ((all(mode(dot.border.color) == "character") | all(mode(dot.border.color) == "numeric")) & length(dot.border.color)== 1L))){ # list of same length as data1 or single value
+                tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.color ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE CHARACTER STRING OR INTEGER")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else if((all(mode(dot.border.color) == "character") | all(mode(dot.border.color) == "numeric")) & length(dot.border.color)== 1L){ # convert the single value into a list of single value
+                list.dot.border.color <- vector(mode = "list", length = length(data1))
+                list.dot.border.color[] <- dot.border.color
+            }
+        }
+        if( ! ((all(class(line.size) == "list") & length(data1) == length(line.size)) | (all(mode(line.size) == "numeric") & length(line.size)== 1L))){ # list of same length as data1 or single value
+            tempo.cat <- paste0("ERROR IN ", function.name, ": line.size ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE NUMERIC VALUE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if(all(mode(line.size) == "numeric") & length(line.size)== 1L){ # convert the single value into a list of single value
+            list.line.size <- vector(mode = "list", length = length(data1))
+            list.line.size[] <- line.size
+        }
+        if( ! ((all(class(line.type) == "list") & length(data1) == length(line.type)) | (all(mode(line.type) != "list") & length(line.type)== 1L))){ # list of same length as data1 or single value
+            tempo.cat <- paste0("ERROR IN ", function.name, ": line.type ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST, OR A SINGLE LINE KIND VALUE")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if(all(mode(line.type) != "list") & length(line.type)== 1L){ # convert the single value into a list of single value
+            list.line.type <- vector(mode = "list", length = length(data1))
+            list.line.type[] <- line.type
+        }
+        if( ! is.null(legend.name)){
+            if( ! (all(class(legend.name) == "list") & length(data1) == length(legend.name))){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": legend.name ARGUMENT MUST BE A LIST OF SAME LENGTH AS data1 IF data1 IS A LIST")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+        }
+    }
+    # end check list lengths (and names of data1 compartments if present)
+    # conversion into lists
+    if(all(is.data.frame(data1))){
+        data1 <- list(L1 = data1)
+        if(all(class(x) == "list")){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": x ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            x <- list(L1 = x)
+        }
+        if(all(class(y) == "list")){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": y ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            y <- list(L1 = y)
+        }
+        if( ! is.null(categ)){
+            if(all(class(categ) == "list")){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": categ ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else{
+                categ <- list(L1 = categ)
+            }
+        }
+        if( ! is.null(categ.class.order)){
+            if(all(class(categ.class.order) == "list")){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": categ.class.order ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else{
+                categ.class.order <- list(L1 = categ.class.order)
+            }
+        }
+        if( ! is.null(color)){
+            if(all(class(color) == "list")){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": color ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else{
+                color <- list(L1 = color)
+            }
+        }
+        if(all(class(geom) == "list")){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": geom ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            geom <- list(L1 = geom)
+        }
+        if(all(class(geom.step.dir) == "list")){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": geom.step.dir ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            geom.step.dir <- list(L1 = geom.step.dir)
+        }
+        if( ! is.null(geom.stick.base)){
+            if(all(class(geom.stick.base) == "list")){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": geom.stick.base ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else{
+                geom.stick.base <- list(L1 = geom.stick.base)
+            }
+        }
+        if(all(class(alpha) == "list")){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": alpha ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            alpha <- list(L1 = alpha)
+        }
+        if(all(class(dot.size) == "list")){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": dot.size ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            dot.size <- list(L1 = dot.size)
+        }
+        if(all(class(dot.shape) == "list")){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": dot.shape ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            dot.shape <- list(L1 = dot.shape)
+        }
+        if(all(class(dot.border.size) == "list")){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.size ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            dot.border.size <- list(L1 = dot.border.size)
+        }
+        if( ! is.null(dot.border.color)){
+            if(all(class(dot.border.color) == "list")){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": dot.border.color ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else{
+                dot.border.color <- list(L1 = dot.border.color)
+            }
+        }
+        if(all(class(line.size) == "list")){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": line.size ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            line.size <- list(L1 = line.size)
+        }
+        if(all(class(line.type) == "list")){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": line.type ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            line.type <- list(L1 = line.type)
+        }
+        if( ! is.null(legend.name)){
+            if(all(class(legend.name) == "list")){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": legend.name ARGUMENT CANNOT BE A LIST IF data1 IS A DATA FRAME")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else{
+                legend.name <- list(L1 = legend.name)
+            }
+        }
+    }else if( ! all(sapply(data1, FUN = "class") == "data.frame")){ # if not a data frame, data1 can only be a list, as tested above
+        tempo.cat <- paste0("ERROR IN ", function.name, ": data1 ARGUMENT MUST BE A DATA FRAME OR A LIST OF DATA FRAMES")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+    }
+    # single value converted into list now reattributed to the argument name
+    if( ! is.null(color)){
+        if( ! is.null(list.color)){
+            color <- list.color
+        }
+    }
+    if( ! is.null(list.geom)){
+        geom <- list.geom
+    }
+    if( ! is.null(list.geom.step.dir)){
+        geom.step.dir <- list.geom.step.dir
+    }
+    if( ! is.null(geom.stick.base)){
+        if( ! is.null(list.geom.stick.base)){
+            geom.stick.base <- list.geom.stick.base
+        }
+    }
+    if( ! is.null(list.alpha)){
+        alpha <- list.alpha
+    }
+    if( ! is.null(list.dot.size)){
+        dot.size <- list.dot.size
+    }
+    if( ! is.null(list.dot.shape)){
+        dot.shape <- list.dot.shape
+    }
+    if( ! is.null(list.dot.border.size)){
+        dot.border.size <- list.dot.border.size
+    }
+    if( ! is.null(dot.border.color)){
+        if( ! is.null(list.dot.border.color)){
+            dot.border.color <- list.dot.border.color
+        }
+    }
+    if( ! is.null(list.line.size)){
+        line.size <- list.line.size
+    }
+    if( ! is.null(list.line.type)){
+        line.type <- list.line.type
+    }
+    # end single value converted into list now reattributed to the argument name
+    # data, x, y, geom, alpha, dot.size, shape, dot.border.size, line.size, line.type, legend.name are list now
+    # if non-null, categ, categ.class.order, legend.name, color, dot.border.color are list now
+    # end conversion into lists
+    # verif of add
+    if( ! is.null(add)){
+        if( ! grepl(pattern = "^\\s*\\+", add)){ # check that the add string start by +
+            tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST START WITH \"+\": ", paste(unique(add), collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            
+        }else if( ! grepl(pattern = "(ggplot2|lemon)\\s*::", add)){ #
+            tempo.cat <- paste0("ERROR IN ", function.name, ": FOR EASIER FUNCTION DETECTION, add ARGUMENT MUST CONTAIN \"ggplot2::\" OR \"lemon::\" IN FRONT OF EACH GGPLOT2 FUNCTION: ", paste(unique(add), collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if( ! grepl(pattern = ")\\s*$", add)){ # check that the add string finished by )
+            tempo.cat <- paste0("ERROR IN ", function.name, ": add ARGUMENT MUST FINISH BY \")\": ", paste(unique(add), collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+    }
+    # end verif of add
+    # management of add containing facet
+    facet.categ <- NULL
+    if( ! is.null(add)){
+        facet.check <- TRUE
+        tempo <- unlist(strsplit(x = add, split = "\\s*\\+\\s*(ggplot2|lemon)\\s*::\\s*")) #
+        tempo <- sub(x = tempo, pattern = "^facet_wrap", replacement = "ggplot2::facet_wrap")
+        tempo <- sub(x = tempo, pattern = "^facet_grid", replacement = "ggplot2::facet_grid")
+        tempo <- sub(x = tempo, pattern = "^facet_rep", replacement = "lemon::facet_rep")
+        if(length(data1) > 1 & (any(grepl(x = tempo, pattern = "ggplot2::facet_wrap|lemon::facet_rep_wrap")) | grepl(x = add, pattern = "ggplot2::facet_grid|lemon::facet_rep_grid"))){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nfacet PANELS CANNOT BE USED IF MORE THAN ONE DATA FRAME IN THE data1 ARGUMENT\nPLEASE REWRITE THE add STRING AND RERUN")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            if(any(grepl(x = tempo, pattern = "ggplot2::facet_wrap|lemon::facet_rep_wrap"))){
+                tempo1 <- suppressWarnings(eval(parse(text = tempo[grepl(x = tempo, pattern = "ggplot2::facet_wrap|lemon::facet_rep_wrap")])))
+                facet.categ <- list(names(tempo1$params$facets)) # list of length 1
+                tempo.text <- "facet_wrap OR facet_rep_wrap"
+                facet.check <- FALSE
+            }else if(grepl(x = add, pattern = "ggplot2::facet_grid|lemon::facet_rep_grid")){
+                tempo1 <- suppressWarnings(eval(parse(text = tempo[grepl(x = tempo, pattern = "ggplot2::facet_grid|lemon::facet_rep_grid")])))
+                facet.categ <- list(c(names(tempo1$params$rows), names(tempo1$params$cols))) # list of length 1
+                tempo.text <- "facet_grid OR facet_rep_grid"
+                facet.check <- FALSE
+            }
+            if(facet.check == FALSE & ! all(facet.categ %in% names(data1[[1]]))){ # WARNING: all(facet.categ %in% names(data1)) is TRUE when facet.categ is NULL
+                tempo.cat <- paste0("ERROR IN ", function.name, "\nDETECTION OF \"", tempo.text, "\" STRING IN THE add ARGUMENT BUT PROBLEM OF VARIABLE DETECTION (COLUMN NAMES OF data1)\nTHE DETECTED VARIABLES ARE:\n", paste(facet.categ, collapse = " "), "\nTHE data1 COLUMN NAMES ARE:\n", paste(names(data1[[1]]), collapse = " "), "\nPLEASE REWRITE THE add STRING AND RERUN")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+        }
+    }
+    # if facet.categ is not NULL, it is a list of length 1 now
+    # end management of add containing facet
+    # legend name filling
+    if(is.null(legend.name) & ! is.null(categ)){
+        legend.name <- categ
+    }else if(is.null(legend.name) & is.null(categ)){
+        legend.name <- vector("list", length(data1)) # null list
+    }
+    # legend.name not NULL anymore (list)
+    # end legend name filling
+    # ini categ for legend display
+    fin.lg.disp <- vector("list", 6) # will be used at the end to display or not legends
+    fin.lg.disp[] <- FALSE
+    legend.disp <- vector("list", length(data1))
+    if(is.null(categ) | legend.show == FALSE){
+        legend.disp[] <- FALSE
+    }else{
+        for(i2 in 1:length(data1)){
+            if(is.null(categ[[i2]])){
+                legend.disp[[i2]] <- FALSE
+            }else{
+                legend.disp[[i2]] <- TRUE
+            }
+        }
+    }
+    # end ini categ for legend display
+    # integer colors into gg_palette
+    tempo.check.color <- NULL
+    for(i1 in 1:length(data1)){
+        if(any(is.na(color[[i1]]))){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), ": color ARGUMENT CANNOT CONTAIN NA")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+        tempo.check.color <- c(tempo.check.color, fun_check(data = color[[i1]], data.name = ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), class = "integer", double.as.integer.allowed = TRUE, na.contain = TRUE, fun.name = function.name)$problem)
+    }
+    tempo.check.color <- ! tempo.check.color # invert TRUE and FALSE because if integer, then problem = FALSE
+    if(any(tempo.check.color == TRUE)){ # convert integers into colors
+        tempo.integer <- unlist(color[tempo.check.color])
+        tempo.color <- fun_gg_palette(max(tempo.integer, na.rm = TRUE))
+        for(i1 in 1:length(data1)){
+            if(tempo.check.color[i1] == TRUE){
+                color[[i1]] <-tempo.color[color[[i1]]]
+            }
+        }
+    }
+    # end integer colors into gg_palette
+    # loop (checking inside list compartment)
+    compart.null.color <- 0 # will be used to attribute a color when color is non-null but a compartment of color is NULL
+    data1.ini <- data1 # to report NA removal
+    removed.row.nb <- vector("list", length = length(data1)) # to report NA removal. Contains NULL
+    removed.rows <- vector("list", length = length(data1)) # to report NA removal. Contains NULL
+    for(i1 in 1:length(data1)){
+        tempo <- fun_check(data = data1[[i1]], data.name = ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), class = "data.frame", na.contain = TRUE, fun.name = function.name)
+        if(tempo$problem == TRUE){
+            stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+        # reserved word checking
+        if(any(names(data1[[i1]]) %in% reserved.words)){ # I do not use fun_name_change() because cannot control y before creating "fake_y". But ok because reserved are not that common
+            tempo.cat <- paste0("ERROR IN ", function.name, ": COLUMN NAMES OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " ARGUMENT CANNOT BE ONE OF THESE WORDS\n", paste(reserved.words, collapse = " "), "\nTHESE ARE RESERVED FOR THE ", function.name, " FUNCTION")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+        if( ! (is.null(add))){
+            if(any(sapply(X = reserved.words, FUN = grepl, x = add))){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\nDETECTION OF COLUMN NAMES OF data1 IN THE add ARGUMENT STRING, THAT CORRESPOND TO RESERVED STRINGS FOR ", function.name, "\nFOLLOWING COLUMN NAMES HAVE TO BE CHANGED:\n", paste(arg.names[sapply(X = reserved.words, FUN = grepl, x = add)], collapse = "\n"), "\nFOR INFORMATION, THE RESERVED WORDS ARE:\n", paste(reserved.words, collapse = "\n"))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else if(any(sapply(X = arg.names, FUN = grepl, x = add))){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") NAMES OF ", function.name, " ARGUMENTS DETECTED IN THE add STRING:\n", paste(arg.names[sapply(X = arg.names, FUN = grepl, x = add)], collapse = "\n"), "\nRISK OF WRONG OBJECT USAGE INSIDE ", function.name)
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+        }
+        # end reserved word checking
+        # check of geom now because required for y argument
+        tempo <- fun_check(data = geom[[i1]], data.name = ifelse(length(geom)== 1L, "geom", paste0("geom NUMBER ", i1)), options = c("geom_point", "geom_line", "geom_path", "geom_step", "geom_hline", "geom_vline", "geom_stick"), length = 1, fun.name = function.name)
+        if(tempo$problem == TRUE){
+            stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+        if(geom[[i1]] == "geom_step" & is.null(geom.step.dir[[i1]])){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(geom.step.dir)== 1L, "geom.step.dir", paste0("ELEMENT ", i1, " OF geom.step.dir ARGUMENT")), ": geom.step.dir ARGUMENT CANNOT BE NULL IF ", ifelse(length(geom)== 1L, "geom", paste0("ELEMENT ", i1, " OF geom")), " ARGUMENT IS \"geom_step\"\nHERE geom.step.dir ARGUMENT IS: ", paste(geom.step.dir[[i1]], collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if(geom[[i1]] == "geom_step" & ! is.null(geom.step.dir[[i1]])){
+            tempo <- fun_check(data = geom.step.dir[[i1]], data.name = ifelse(length(geom.step.dir)== 1L, "geom.step.dir", paste0("geom.step.dir NUMBER ", i1)), options = c("vh", "hv", "mid"), length = 1, fun.name = function.name)
+            if(tempo$problem == TRUE){
+                stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+        }
+        if( ! (is.null(geom.stick.base))){
+            if(geom[[i1]] == "geom_stick" & ! is.null(geom.stick.base[[i1]])){
+                tempo <- fun_check(data = geom.stick.base[[i1]], data.name = ifelse(length(geom.stick.base)== 1L, "geom.stick.base", paste0("geom.stick.base NUMBER ", i1)), mode = "numeric", length = 1, na.contain = FALSE, fun.name = function.name)
+                if(tempo$problem == TRUE){
+                    stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+                }
+            }
+        }
+        # end check of geom now because required for y argument
+        if(is.null(x[[i1]])){
+            if(all(geom[[i1]] != "geom_hline")){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(x)== 1L, "x", paste0("ELEMENT ", i1, " OF x ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ": x ARGUMENT CANNOT BE NULL EXCEPT IF ", ifelse(length(geom)== 1L, "x", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_hline\"\nHERE geom ARGUMENT IS: ", paste(geom[[i1]], collapse = " "))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else{
+                x[[i1]] <- "fake_x"
+                data1[[i1]] <- cbind(data1[[i1]], fake_x = NA, stringsAsFactors = TRUE)
+                data1[[i1]][, "fake_x"] <- as.numeric(data1[[i1]][, "fake_x"])
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") NULL ", ifelse(length(x)== 1L, "x", paste0("ELEMENT ", i1, " OF x")), " ARGUMENT ASSOCIATED TO ", ifelse(length(geom)== 1L, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT ", geom[[i1]], " -> FAKE COLUMN ADDED TO DATA FRAME ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", NAMED \"fake_x\" FOR FINAL DRAWING")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+        }else{
+            if(all(geom[[i1]] == "geom_hline")){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(x)== 1L, "x", paste0("ELEMENT ", i1, " OF x ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ": x ARGUMENT MUST BE NULL IF ", ifelse(length(geom)== 1L, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_hline\"")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+            tempo <- fun_check(data = x[[i1]], data.name = ifelse(length(x)== 1L, "x", paste0("ELEMENT ", i1, " OF x ARGUMENT")), class = "vector", mode = "character", length = 1, fun.name = function.name)
+            if(tempo$problem == TRUE){
+                stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+        }
+        if(is.null(y[[i1]])){
+            if(all(geom[[i1]] != "geom_vline")){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(y)== 1L, "y", paste0("ELEMENT ", i1, " OF y ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ": y ARGUMENT CANNOT BE NULL EXCEPT IF ", ifelse(length(geom)== 1L, "y", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_vline\"\nHERE geom ARGUMENT IS: ", paste(geom[[i1]], collapse = " "))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else{
+                y[[i1]] <- "fake_y"
+                data1[[i1]] <- cbind(data1[[i1]], fake_y = NA, stringsAsFactors = TRUE)
+                data1[[i1]][, "fake_y"] <- as.numeric(data1[[i1]][, "fake_y"])
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") NULL ", ifelse(length(y)== 1L, "y", paste0("ELEMENT ", i1, " OF y")), " ARGUMENT ASSOCIATED TO ", ifelse(length(geom)== 1L, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT ", geom[[i1]], " -> FAKE COLUMN ADDED TO DATA FRAME ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", NAMED \"fake_y\" FOR FINAL DRAWING")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+        }else{
+            if(all(geom[[i1]] == "geom_vline")){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(y)== 1L, "y", paste0("ELEMENT ", i1, " OF y ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ": y ARGUMENT MUST BE NULL IF ", ifelse(length(geom)== 1L, "geom", paste0("geom NUMBER ", i1)), " ARGUMENT IS \"geom_vline\"")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+            tempo <- fun_check(data = y[[i1]], data.name = ifelse(length(y)== 1L, "y", paste0("ELEMENT ", i1, " OF y ARGUMENT")), class = "vector", mode = "character", length = 1, fun.name = function.name)
+            if(tempo$problem == TRUE){
+                stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+        }
+        # x[[i1]] and y[[i1]] not NULL anymore
+        if( ! (x[[i1]] %in% names(data1[[i1]]))){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(x)== 1L, "x", paste0("ELEMENT ", i1, " OF x")), " ARGUMENT MUST BE A COLUMN NAME OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT\nHERE IT IS: ", paste(x[[i1]], collapse = " "))))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+        if( ! (y[[i1]] %in% names(data1[[i1]]))){
+            tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(y)== 1L, "y", paste0("ELEMENT ", i1, " OF y")), " ARGUMENT MUST BE A COLUMN NAME OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT\nHERE IT IS: ", paste(y[[i1]], collapse = " "))))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+        tempo <- fun_check(data = data1[[i1]][, x[[i1]]], data.name = ifelse(length(x)== 1L, "x ARGUMENT (AS COLUMN NAME OF data1 DATA FRAME)", paste0("ELEMENT ", i1, " OF x ARGUMENT", " (AS COLUMN NAME OF data1 DATA FRAME NUMBER ", i1, ")")), class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name)
+        if(tempo$problem == TRUE){
+            stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+        tempo <- fun_check(data = data1[[i1]][, y[[i1]]], data.name = ifelse(length(y)== 1L, "y ARGUMENT (AS COLUMN NAME OF data1 DATA FRAME)", paste0("ELEMENT ", i1, " OF y ARGUMENT", " (AS COLUMN NAME OF data1 DATA FRAME NUMBER ", i1, ")")), class = "vector", mode = "numeric", na.contain = TRUE, fun.name = function.name)
+        if(tempo$problem == TRUE){
+            stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+        if(x[[i1]] == "fake_x" & y[[i1]] == "fake_y"){ # because the code cannot accept to be both "fake_x" and "fake_y" at the same time
+            tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 2\nTHE CODE CANNOT ACCEPT x AND y TO BE \"fake_x\" AND \"fake_y\" IN THE SAME DATA FRAME ", i1, " ")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+        
+        if(( ! is.null(categ)) & ( ! is.null(categ[[i1]]))){ # is.null(categ[[i1]]) works even if categ is NULL # is.null(categ[[i1]]) works even if categ is NULL # if categ[[i1]] = NULL, fake_categ will be created later on
+            tempo <- fun_check(data = categ[[i1]], data.name = ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")),, class = "vector", mode = "character", length = 1, fun.name = function.name)
+            if(tempo$problem == TRUE){
+                stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+            if( ! (categ[[i1]] %in% names(data1[[i1]]))){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ")), " ARGUMENT MUST BE A COLUMN NAME OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT\nHERE IT IS: ", paste(categ[[i1]], collapse = " "))))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+            tempo1 <- fun_check(data = data1[[i1]][, categ[[i1]]], data.name = ifelse(length(categ)== 1L, "categ OF data1 ARGUMENT", paste0("ELEMENT ", i1, " OF categ ARGUMENT IN DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name)
+            tempo2 <- fun_check(data = data1[[i1]][, categ[[i1]]], data.name = ifelse(length(categ)== 1L, "categ OF data1 ARGUMENT", paste0("ELEMENT ", i1, " OF categ ARGUMENT IN DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), class = "factor", na.contain = TRUE, fun.name = function.name)
+            if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(categ)== 1L, "categ OF data1 ARGUMENT", paste0("ELEMENT ", i1, " OF categ ARGUMENT IN DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " MUST BE A FACTOR OR CHARACTER VECTOR")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else if(tempo1$problem == FALSE){
+                data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") IN ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", THE CHARACTER COLUMN HAS BEEN CONVERTED TO FACTOR")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                
+            }
+            if(geom[[i1]] == "geom_vline" | geom[[i1]] == "geom_hline"){
+                if(length(unique(data1[[i1]][, categ[[i1]]])) != nrow(data1[[i1]])){
+                    tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(geom)== 1L, "geom OF data1 ARGUMENT", paste0("geom NUMBER ", i1, " OF DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " ARGUMENT IS ", geom[[i1]], ", MEANING THAT ", ifelse(length(categ)== 1L, "categ OF data1 ARGUMENT", paste0("ELEMENT ", i1, " OF categ ARGUMENT IN DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " MUST HAVE A DIFFERENT CLASS PER LINE OF data1 (ONE x VALUE PER CLASS)")
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+                }
+            }
+        }else if(( ! is.null(categ)) & is.null(categ[[i1]])){ # is.null(categ[[i1]]) works even if categ is NULL # if categ[[i1]] = NULL, fake_categ will be created. WARNING: is.null(categ[[i1]]) means no legend display (see above), because categ has not been precised. This also means a single color for data1[[i1]]
+            if(length(color[[i1]]) > 1){ # 0 means is.null(color[[i1]]) or is.null(color) and 1 is ok -> single color for data1[[i1]]
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") NULL ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ")), " ARGUMENT BUT CORRESPONDING COLORS IN ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " HAS LENGTH OVER 1\n", paste(color[[i1]], collapse = " "), "\nWHICH IS NOT COMPATIBLE WITH NULL CATEG -> COLOR RESET TO A SINGLE COLOR")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                color[i1] <- list(NULL) # will provide a single color below # Warning color[[i1]] <- NULL removes the compartment
+            }
+            categ[[i1]] <- "fake_categ"
+            data1[[i1]] <- cbind(data1[[i1]], fake_categ = "", stringsAsFactors = TRUE)
+            # inactivated because give a different color to different "Line_" categ while a single color for all the data1[[i1]] required. Thus, put back after the color management
+            # if(geom[[i1]] == "geom_hline" | geom[[i1]] == "geom_vline"){
+            # data1[[i1]][, "fake_categ"] <- paste0("Line_", 1:nrow(data1[[i1]]))
+            # }else{
+            data1[[i1]][, "fake_categ"] <- data1[[i1]][, "fake_categ"] # as.numeric("") create a vector of NA but class numeric
+            # }
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") NULL ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ")), " ARGUMENT -> FOR DATA FRAME ", ifelse(length(data1)== 1L, "data1 ARGUMENT:", paste0("NUMBER ", i1, " OF data1 ARGUMENT:")), "\n- FAKE \"fake_categ\" COLUMN ADDED FILLED WITH \"\"(OR WITH \"Line_...\" FOR LINES)\n- SINGLE COLOR USED FOR PLOTTING\n- NO LEGEND DISPLAYED")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+        # OK: if categ is not NULL, all the non-null categ columns of data1 are factors from here
+        
+        # management of log scale and Inf removal
+        if(x[[i1]] != "fake_x"){
+            if(any(( ! is.finite(data1[[i1]][, x[[i1]]])) & ( ! is.na(data1[[i1]][, x[[i1]]])))){ # is.finite also detects NA: ( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])) detects only Inf
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") PRESENCE OF -Inf OR Inf VALUES IN ", ifelse(length(categ)== 1L, "x", paste0("ELEMENT ", i1, " OF x ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+        }
+        if(y[[i1]] != "fake_y"){
+            if(any(( ! is.finite(data1[[i1]][, y[[i1]]])) & ( ! is.na(data1[[i1]][, y[[i1]]])))){ # is.finite also detects NA: ( ! is.finite(data1[, y])) & ( ! is.na(data1[, y])) detects only Inf
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") PRESENCE OF -Inf OR Inf VALUES IN ", ifelse(length(categ)== 1L, "y", paste0("ELEMENT ", i1, " OF y ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+        }
+        # log conversion
+        if(x.log != "no"){
+            tempo1 <- ! is.finite(data1[[i1]][, x[[i1]]]) # where are initial NA and Inf
+            data1[[i1]][, x[[i1]]] <- suppressWarnings(get(x.log)(data1[[i1]][, x[[i1]]]))# no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
+            if(any( ! (tempo1 | is.finite(data1[[i1]][, x[[i1]]])))){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") LOG CONVERSION INTRODUCED -Inf OR Inf OR NaN VALUES IN ", ifelse(length(categ)== 1L, "x", paste0("ELEMENT ", i1, " OF x ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+        }
+        if(y.log != "no"){
+            tempo1 <- ! is.finite(data1[[i1]][, y[[i1]]]) # where are initial NA and Inf
+            data1[[i1]][, y[[i1]]] <- suppressWarnings(get(y.log)(data1[[i1]][, y[[i1]]]))# no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
+            if(any( ! (tempo1 | is.finite(data1[[i1]][, y[[i1]]])))){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") LOG CONVERSION INTRODUCED -Inf OR Inf OR NaN VALUES IN ", ifelse(length(categ)== 1L, "y", paste0("ELEMENT ", i1, " OF y ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+        }
+        # Inf removal
+        # removed.row.nb[[i1]] <- NULL # already NULL and Warning this removes the compartment
+        removed.rows[[i1]] <- data.frame(stringsAsFactors = FALSE)
+        if(any(( ! is.finite(data1[[i1]][, x[[i1]]])) & ( ! is.na(data1[[i1]][, x[[i1]]])))){ # is.finite also detects NA: ( ! is.finite(data1[[i1]][, x[[i1]]])) & ( ! is.na(data1[[i1]][, x[[i1]]])) detects only Inf
+            removed.row.nb[[i1]] <- c(removed.row.nb[[i1]], which(( ! is.finite(data1[[i1]][, x[[i1]]])) & ( ! is.na(data1[[i1]][, x[[i1]]]))))
+        }
+        if(any(( ! is.finite(data1[[i1]][, y[[i1]]])) & ( ! is.na(data1[[i1]][, y[[i1]]])))){ # is.finite also detects NA: ( ! is.finite(data1[[i1]][, y[[i1]]])) & ( ! is.na(data1[[i1]][, y[[i1]]])) detects only Inf
+            removed.row.nb[[i1]] <- c(removed.row.nb[[i1]], which(( ! is.finite(data1[[i1]][, y[[i1]]])) & ( ! is.na(data1[[i1]][, y[[i1]]]))))
+        }
+        if( ! is.null(removed.row.nb[[i1]])){
+            removed.row.nb[[i1]] <- unique(removed.row.nb[[i1]]) # to remove the duplicated positions (NA in both x and y)
+            removed.rows[[i1]] <- rbind(removed.rows[[i1]], data1.ini[[i1]][removed.row.nb[[i1]], ]) # here data1.ini used to have the y = O rows that will be removed because of Inf creation after log transformation
+            data1[[i1]] <- data1[[i1]][-removed.row.nb[[i1]], ]
+            data1.ini[[i1]] <- data1.ini[[i1]][-removed.row.nb[[i1]], ] #
+        }
+        # From here, data1 and data.ini have no more Inf
+        # end Inf removal
+        # x.lim and y.lim dealt later on, after the end f the loop
+        # end management of log scale and Inf removal
+        # na detection and removal
+        column.check <- unique(unlist(c( # unlist because creates a list
+            if(x[[i1]] == "fake_x"){NULL}else{x[[i1]]}, 
+            if(y[[i1]] == "fake_y"){NULL}else{y[[i1]]}, 
+            if( ! is.null(categ)){if(is.null(categ[[i1]])){NULL}else{categ[[i1]]}}, 
+            if( ! is.null(facet.categ)){if(is.null(facet.categ[[i1]])){NULL}else{facet.categ[[i1]]}}
+        ))) # dot.categ because can be a 3rd column of data1
+        if(any(is.na(data1[[i1]][, column.check]))){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") NA DETECTED IN COLUMNS ", paste(column.check, collapse = " "), " OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " AND CORRESPONDING ROWS REMOVED (SEE $removed.row.nb AND $removed.rows)")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            for(i3 in 1:length(column.check)){
+                if(any(is.na(data1[[i1]][, column.check[i3]]))){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("NA REMOVAL DUE TO COLUMN ", column.check[i3], " OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")))
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }
+            tempo <- unique(unlist(lapply(lapply(c(data1[[i1]][column.check]), FUN = is.na), FUN = which)))
+            removed.row.nb[[i1]] <- c(removed.row.nb[[i1]], tempo)
+            removed.rows[[i1]] <- rbind(removed.rows[[i1]], data1.ini[[i1]][tempo, ]) #  # tempo used because removed.row.nb is not empty. Here data1.ini used to have the non NA rows that will be removed because of NAN creation after log transformation (neg values for instance)
+            column.check <- column.check[ ! (column.check == x[[i1]] | column.check == y[[i1]])] # remove x and y to keep quali columns
+            if(length(tempo) != 0){
+                data1[[i1]] <- data1[[i1]][-tempo, ] # WARNING tempo here and not removed.row.nb because the latter contain more numbers thant the former
+                data1.ini[[i1]] <- data1.ini[[i1]][-tempo, ] # WARNING tempo here and not removed.row.nb because the latter contain more numbers than the former
+                for(i4 in 1:length(column.check)){
+                    if(any( ! unique(removed.rows[[i1]][, column.check[i4]]) %in% unique(data1[[i1]][, column.check[i4]]))){
+                        warn.count <- warn.count + 1
+                        tempo.warn <- paste0("(", warn.count,") IN COLUMN ", column.check[i4], " OF ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", THE FOLLOWING CLASSES HAVE DISAPPEARED AFTER NA REMOVAL\n(IF COLUMN USED IN THE PLOT, THIS CLASS WILL NOT BE DISPLAYED):\n", paste(unique(removed.rows[[i1]][, column.check[i4]])[ ! unique(removed.rows[[i1]][, column.check[i4]]) %in% unique(data1[[i1]][, column.check[i4]])], collapse = " "))
+                        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                        tempo.levels <- levels(data1[[i1]][, column.check[i4]])[levels(data1[[i1]][, column.check[i4]]) %in% unique(as.character(data1[[i1]][, column.check[i4]]))]
+                        data1[[i1]][, column.check[i4]] <- factor(as.character(data1[[i1]][, column.check[i4]]), levels = tempo.levels)
+                        if(column.check[i4] %in% categ[[i1]] & ! is.null(categ.class.order)){
+                            categ.class.order[[i1]] <- levels(data1[[i1]][, column.check[i4]])[levels(data1[[i1]][, column.check[i4]]) %in% unique(data1[[i1]][, column.check[i4]])] # remove the absent class in the categ.class.order vector
+                            data1[[i1]][, column.check[i4]] <- factor(as.character(data1[[i1]][, column.check[i4]]), levels = unique(categ.class.order[[i1]]))
+                        }
+                    }
+                }
+            }
+        }
+        # end na detection and removal
+        # From here, data1 and data.ini have no more NA or NaN in x, y, categ (if categ != NULL) and facet.categ (if categ != NULL)
+        if( ! is.null(categ.class.order)){
+            # the following check will be done several times but I prefer to keep it here, after the creation of categ
+            if(is.null(categ[[i1]]) & ! is.null(categ.class.order[[i1]])){
+                tempo.cat <- paste0("ERROR IN ", function.name, "\nCOMPARTMENT ", i1, " OF categ ARGUMENT CANNOT BE NULL IF COMPARTMENT ", i1, " OF categ.class.order ARGUMENT IS NOT NULL: ", paste(categ.class.order, collapse = " "))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else{
+                if(is.null(categ.class.order[[i1]])){
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") THE categ.class.order COMPARTMENT ", i1, " IS NULL. ALPHABETICAL ORDER WILL BE APPLIED")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    data1[[i1]][, categ[[i1]]] <- factor(as.character(data1[[i1]][, categ[[i1]]])) # if already a factor, change nothing, if characters, levels according to alphabetical order
+                    categ.class.order[[i1]] <- levels(data1[[i1]][, categ[[i1]]]) # character vector that will be used later
+                }else{
+                    tempo <- fun_check(data = categ.class.order[[i1]], data.name = paste0("COMPARTMENT ", i1 , " OF categ.class.order ARGUMENT"), class = "vector", mode = "character", length = length(levels(data1[[i1]][, categ[[i1]]])), fun.name = function.name) # length(data1[, categ[i1]) -> if data1[, categ[i1] was initially character vector, then conversion as factor after the NA removal, thus class number ok. If data1[, categ[i1] was initially factor, no modification after the NA removal, thus class number ok
+                    if(tempo$problem == TRUE){
+                        stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+                    }
+                }
+                if(any(duplicated(categ.class.order[[i1]]))){
+                    tempo.cat <- paste0("ERROR IN ", function.name, "\nCOMPARTMENT ", i1, " OF categ.class.order ARGUMENT CANNOT HAVE DUPLICATED CLASSES: ", paste(categ.class.order[[i1]], collapse = " "))
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+                }else if( ! (all(categ.class.order[[i1]] %in% unique(data1[[i1]][, categ[[i1]]])) & all(unique(data1[[i1]][, categ[[i1]]]) %in% categ.class.order[[i1]]))){
+                    tempo.cat <- paste0("ERROR IN ", function.name, "\nCOMPARTMENT ", i1, " OF categ.class.order ARGUMENT MUST BE CLASSES OF COMPARTMENT ", i1, " OF categ ARGUMENT\nHERE IT IS:\n", paste(categ.class.order[[i1]], collapse = " "), "\nFOR COMPARTMENT ", i1, " OF categ.class.order AND IT IS:\n", paste(unique(data1[[i1]][, categ[[i1]]]), collapse = " "), "\nFOR COLUMN ", categ[[i1]], " OF data1 NUMBER ", i1)
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+                }else{
+                    data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]], levels = categ.class.order[[i1]]) # reorder the factor
+                }
+                names(categ.class.order)[i1] <- categ[[i1]]
+            }
+        }
+        # OK: if categ.class.order is not NULL, all the NULL categ.class.order columns of data1 are character from here
+        
+        if( ! is.null(legend.name[[i1]])){
+            tempo <- fun_check(data = legend.name[[i1]], data.name = ifelse(length(legend.name)== 1L, "legend.name", paste0("legend.name NUMBER ", i1)),, class = "vector", mode = "character", length = 1, fun.name = function.name)
+            if(tempo$problem == TRUE){
+                stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+        }
+        if( ! is.null(color)){ # if color is NULL, will be filled later on
+            # check the nature of color
+            if(is.null(color[[i1]])){
+                compart.null.color <- compart.null.color + 1
+                color[[i1]] <- grey(compart.null.color / 8) # cannot be more than 7 overlays. Thus 7 different greys. 8/8 is excluded because white dots
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") NULL COLOR IN ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " ASSOCIATED TO ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", SINGLE COLOR ", paste(color[[i1]], collapse = " "), " HAS BEEN ATTRIBUTED")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+            tempo1 <- fun_check(data = color[[i1]], data.name = ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), class = "vector", mode = "character", na.contain = TRUE, fun.name = function.name) # na.contain = TRUE in case of colum of data1
+            tempo2 <- fun_check(data = color[[i1]], data.name = ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), class = "factor", na.contain = TRUE, fun.name = function.name) # idem
+            if(tempo1$problem == TRUE & tempo2$problem == TRUE){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST BE A FACTOR OR CHARACTER VECTOR OR INTEGER VECTOR") # integer possible because dealt above
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else if( ! (all(color[[i1]] %in% colors() | grepl(pattern = "^#", color[[i1]])))){ # check that all strings of low.color start by #
+                tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors(): ", paste(unique(color[[i1]]), collapse = " "))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+            if(any(is.na(color[[i1]]))){
+                warn.count <- warn.count + 1
+                tempo.warn <- paste0("(", warn.count,") IN ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), ", THE COLORS:\n", paste(unique(color[[i1]]), collapse = " "), "\nCONTAINS NA")
+                warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            }
+            # end check the nature of color
+            # check the length of color
+            if(is.null(categ) & length(color[[i1]]) != 1){
+                tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST BE A SINGLE COLOR IF categ IS NULL")
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }else if( ! is.null(categ)){
+                # No problem of NA management by ggplot2 because already removed
+                if(categ[[i1]] == "fake_categ" & length(color[[i1]]) != 1){
+                    tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST BE A SINGLE COLOR IF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IS NULL")
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+                }else if(length(color[[i1]]) == length(unique(data1[[i1]][, categ[[i1]]]))){ # here length(color) is equal to the different number of categ
+                    data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") IN ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", THE FOLLOWING COLORS:\n", paste(color[[i1]], collapse = " "), "\nHAVE BEEN ATTRIBUTED TO THESE CLASSES:\n", paste(levels(factor(data1[[i1]][, categ[[i1]]])), collapse = " "))
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }else if(length(color[[i1]]) == length(data1[[i1]][, categ[[i1]]])){# here length(color) is equal to nrow(data1[[i1]]) -> Modif to have length(color) equal to the different number of categ (length(color) == length(levels(data1[[i1]][, categ[[i1]]])))
+                    data1[[i1]] <- cbind(data1[[i1]], color = color[[i1]], stringsAsFactors = TRUE)
+                    tempo.check <- unique(data1[[i1]][ , c(categ[[i1]], "color")])
+                    if( ! (nrow(data1[[i1]]) == length(color[[i1]]) & nrow(tempo.check) == length(unique(data1[[i1]][ , categ[[i1]]])))){
+                        tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color")), " ARGUMENT HAS THE LENGTH OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), "\nBUT IS INCORRECTLY ASSOCIATED TO EACH CLASS OF THIS categ:\n", paste(unique(mapply(FUN = "paste", data1[[i1]][ ,categ[[i1]]], data1[[i1]][ ,"color"])), collapse = "\n"))
+                        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+                    }else{
+                        data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
+                        color[[i1]] <- unique(color[[i1]][order(data1[[i1]][, categ[[i1]]])]) # Modif to have length(color) equal to the different number of categ (length(color) == length(levels(data1[[i1]][, categ[[i1]]])))
+                        warn.count <- warn.count + 1
+                        tempo.warn <- paste0("(", warn.count, ") FROM FUNCTION ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " HAS THE LENGTH OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " COLUMN VALUES\nCOLORS HAVE BEEN RESPECTIVELY ASSOCIATED TO EACH CLASS OF categ AS:\n", paste(levels(factor(data1[[i1]][, categ[[i1]]])), collapse = " "), "\n", paste(color[[i1]], collapse = " "))
+                        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    }
+                }else if(length(color[[i1]])== 1L){
+                    data1[[i1]][, categ[[i1]]] <- factor(data1[[i1]][, categ[[i1]]]) # if already a factor, change nothing, if characters, levels according to alphabetical order
+                    color[[i1]] <- rep(color[[i1]], length(levels(data1[[i1]][, categ[[i1]]])))
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") IN ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), ", COLOR HAS LENGTH 1 MEANING THAT ALL THE DIFFERENT CLASSES OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), "\n", paste(levels(factor(data1[[i1]][, categ[[i1]]])), collapse = " "), "\nWILL HAVE THE SAME COLOR\n", paste(color[[i1]], collapse = " "))
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }else{
+                    tempo.cat <- paste0("ERROR IN ", function.name, ": ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST BE\n(1) LENGTH 1\nOR (2) THE LENGTH OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), " COLUMN VALUES\nOR (3) THE LENGTH OF THE CLASSES IN THIS COLUMN\nHERE IT IS COLOR LENGTH ", length(color[[i1]]), " VERSUS CATEG LENGTH ", length(data1[[i1]][, categ[[i1]]]), " AND CATEG CLASS LENGTH ", length(unique(data1[[i1]][, categ[[i1]]])), "\nPRESENCE OF NA IN THE COLUMN x, y OR categ OF data1 COULD BE THE PROBLEME")
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+                }
+            }
+        }
+        if((geom[[i1]] == "geom_hline" | geom[[i1]] == "geom_vline") & ! is.null(categ[[i1]])){ # add here after the color management, to deal with the different lines to plot inside any data[[i1]]
+            if(categ[[i1]] == "fake_categ"){
+                data1[[i1]][, "fake_categ"] <- factor(paste0("Line_", formatC(1:nrow(data1[[i2]]), width = nchar(nrow(data1[[i2]])), flag = "0")))
+            }
+        }
+        tempo <- fun_check(data = alpha[[i1]], data.name = ifelse(length(alpha)== 1L, "alpha", paste0("alpha NUMBER ", i1)), prop = TRUE, length = 1, fun.name = function.name)
+        if(tempo$problem == TRUE){
+            stop(paste0("\n\n================\n\n", tempo$text, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+    }
+    # end loop (checking inside list compartment)
+    if(length(data1) > 1){
+        if(length(unique(unlist(x)[ ! x == "fake_x"])) > 1){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") THE x ARGUMENT DOES NOT CONTAIN IDENTICAL COLUMN NAMES:\n", paste(unlist(x), collapse = " "), "\nX-AXIS OVERLAYING DIFFERENT VARIABLES?")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    if(length(data1) > 1){
+        if(length(unique(unlist(y)[ ! y == "fake_y"])) > 1){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") THE y ARGUMENT DOES NOT CONTAIN IDENTICAL COLUMN NAMES:\n", paste(unlist(y), collapse = " "), "\nY-AXIS OVERLAYING DIFFERENT VARIABLES?")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    if(sum(geom %in% "geom_point") > 3){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": geom ARGUMENT CANNOT HAVE MORE THAN THREE \"geom_point\" ELEMENTS")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+    }else if(length(geom) - sum(geom %in% "geom_point") > 3){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": geom ARGUMENT CANNOT HAVE MORE THAN THREE LINE ELEMENTS")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+    }
+    # x.lim management before transfo by x.log
+    if(x.log != "no" & ! is.null(x.lim)){
+        if(any(x.lim <= 0)){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nx.lim ARGUMENT CANNOT HAVE ZERO OR NEGATIVE VALUES WITH THE x.log ARGUMENT SET TO ", x.log, ":\n", paste(x.lim, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if(any( ! is.finite(if(x.log == "log10"){log10(x.lim)}else{log2(x.lim)}))){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nx.lim ARGUMENT RETURNS INF/NA WITH THE x.log ARGUMENT SET TO ", x.log, "\nAS SCALE COMPUTATION IS ", ifelse(x.log == "log10", "log10", "log2"), ":\n", paste(if(x.log == "log10"){log10(x.lim)}else{log2(x.lim)}, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+    }
+    if(x.log != "no" & x.include.zero == TRUE){
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") x.log ARGUMENT SET TO ", x.log, " AND x.include.zero ARGUMENT SET TO TRUE -> x.include.zero ARGUMENT RESET TO FALSE BECAUSE 0 VALUE CANNOT BE REPRESENTED IN LOG SCALE")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        x.include.zero <- FALSE
+    }
+    # end x.lim management before transfo by x.log
+    # y.lim management before transfo by y.log
+    if(y.log != "no" & ! is.null(y.lim)){
+        if(any(y.lim <= 0)){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT CANNOT HAVE ZERO OR NEGATIVE VALUES WITH THE y.log ARGUMENT SET TO ", y.log, ":\n", paste(y.lim, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if(any( ! is.finite(if(y.log == "log10"){log10(y.lim)}else{log2(y.lim)}))){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT RETURNS INF/NA WITH THE y.log ARGUMENT SET TO ", y.log, "\nAS SCALE COMPUTATION IS ", ifelse(y.log == "log10", "log10", "log2"), ":\n", paste(if(y.log == "log10"){log10(y.lim)}else{log2(y.lim)}, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+    }
+    if(y.log != "no" & y.include.zero == TRUE){
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") y.log ARGUMENT SET TO ", y.log, " AND y.include.zero ARGUMENT SET TO TRUE -> y.include.zero ARGUMENT RESET TO FALSE BECAUSE 0 VALUE CANNOT BE REPRESENTED IN LOG SCALE")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        y.include.zero <- FALSE
+    }
+    # end y.lim management before transfo by y.log
+    # end other checkings
+    # reserved word checking
+    #already done above
+    # end reserved word checking
+    # end second round of checking and data preparation
+    
+    
+    # package checking
+    fun_pack(req.package = c(
+        "gridExtra", 
+        "ggplot2", 
+        "lemon", 
+        "scales"
+    ), lib.path = lib.path)
+    # packages Cairo and grid tested by fun_gg_point_rast()
+    # end package checking
+    
+    
+    
+    
+    # main code
+    # axes management
+    if(is.null(x.lim)){
+        if(any(unlist(mapply(FUN = "[[", data1, x, SIMPLIFY = FALSE)) %in% c(Inf, -Inf))){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") THE x COLUMN IN data1 CONTAINS -Inf OR Inf VALUES THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+        x.lim <- suppressWarnings(range(unlist(mapply(FUN = "[[", data1, x, SIMPLIFY = FALSE)), na.rm = TRUE, finite = TRUE)) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only. y.lim added here. If NULL, ok if y argument has values
+    }else if(x.log != "no"){
+        x.lim <- get(x.log)(x.lim) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
+    }
+    if(x.log != "no"){
+        if(any( ! is.finite(x.lim))){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\nx.lim ARGUMENT CANNOT HAVE ZERO OR NEGATIVE VALUES WITH THE x.log ARGUMENT SET TO ", x.log, ":\n", paste(x.lim, collapse = " "), "\nPLEASE, CHECK DATA VALUES (PRESENCE OF ZERO OR INF VALUES)")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+    }
+    if(suppressWarnings(all(x.lim %in% c(Inf, -Inf)))){ # happen when x is only NULL
+        if(all(unlist(geom) %in% c("geom_vline", "geom_stick"))){
+            tempo.cat <- paste0("ERROR IN ", function.name, " NOT POSSIBLE TO DRAW geom_vline OR geom_stick KIND OF LINES ALONE IF x.lim ARGUMENT IS SET TO NULL, SINCE NO X-AXIS DEFINED (", ifelse(length(x)== 1L, "x", paste0("ELEMENT ", i1, " OF x")), " ARGUMENT MUST BE NULL FOR THESE KIND OF LINES)")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            tempo.cat <- paste0("ERROR IN ", function.name, " x.lim ARGUMENT MADE OF NA, -Inf OR Inf ONLY: ", paste(x.lim, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+    }
+    x.lim.order <- order(x.lim) # to deal with inverse axis
+    # print(x.lim.order)
+    x.lim <- sort(x.lim)
+    x.lim[1] <- x.lim[1] - abs(x.lim[2] - x.lim[1]) * ifelse(diff(x.lim.order) > 0, x.right.extra.margin, x.left.extra.margin) # diff(x.lim.order) > 0 means not inversed axis
+    x.lim[2] <- x.lim[2] + abs(x.lim[2] - x.lim[1]) * ifelse(diff(x.lim.order) > 0, x.left.extra.margin, x.right.extra.margin) # diff(x.lim.order) > 0 means not inversed axis
+    if(x.include.zero == TRUE){ # no need to check x.log != "no" because done before
+        x.lim <- range(c(x.lim, 0), na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+    }
+    x.lim <- x.lim[x.lim.order]
+    if(any(is.na(x.lim))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 3")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+    }
+    if(is.null(y.lim)){
+        if(any(unlist(mapply(FUN = "[[", data1, y, SIMPLIFY = FALSE)) %in% c(Inf, -Inf))){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") THE y COLUMN IN data1 CONTAINS -Inf OR Inf VALUES THAT WILL NOT BE CONSIDERED IN THE PLOT RANGE")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+        y.lim <- suppressWarnings(range(unlist(mapply(FUN = "[[", data1, y, SIMPLIFY = FALSE)), na.rm = TRUE, finite = TRUE)) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only. y.lim added here. If NULL, ok if y argument has values
+    }else if(y.log != "no"){
+        y.lim <- get(y.log)(y.lim) # no env = sys.nframe(), inherit = FALSE in get() because look for function in the classical scope
+    }
+    if(y.log != "no"){
+        if(any( ! is.finite(y.lim))){
+            tempo.cat <- paste0("ERROR IN ", function.name, "\ny.lim ARGUMENT CANNOT HAVE ZERO OR NEGATIVE VALUES WITH THE y.log ARGUMENT SET TO ", y.log, ":\n", paste(y.lim, collapse = " "), "\nPLEASE, CHECK DATA VALUES (PRESENCE OF ZERO OR INF VALUES)")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+    }
+    if(suppressWarnings(all(y.lim %in% c(Inf, -Inf)))){ # happen when y is only NULL
+        if(all(unlist(geom) == "geom_vline")){
+            tempo.cat <- paste0("ERROR IN ", function.name, " NOT POSSIBLE TO DRAW geom_vline KIND OF LINES ALONE IF y.lim ARGUMENT IS SET TO NULL, SINCE NO Y-AXIS DEFINED (", ifelse(length(y)== 1L, "y", paste0("ELEMENT ", i1, " OF y")), " ARGUMENT MUST BE NULL FOR THESE KIND OF LINES)")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else{
+            tempo.cat <- paste0("ERROR IN ", function.name, " y.lim ARGUMENT MADE OF NA, -Inf OR Inf ONLY: ", paste(y.lim, collapse = " "))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+    }
+    y.lim.order <- order(y.lim) # to deal with inverse axis
+    y.lim <- sort(y.lim)
+    y.lim[1] <- y.lim[1] - abs(y.lim[2] - y.lim[1]) * ifelse(diff(y.lim.order) > 0, y.bottom.extra.margin, y.top.extra.margin) # diff(y.lim.order) > 0 means not inversed axis
+    y.lim[2] <- y.lim[2] + abs(y.lim[2] - y.lim[1]) * ifelse(diff(y.lim.order) > 0, y.top.extra.margin, y.bottom.extra.margin) # diff(y.lim.order) > 0 means not inversed axis
+    if(y.include.zero == TRUE){ # no need to check y.log != "no" because done before
+        y.lim <- range(c(y.lim, 0), na.rm = TRUE, finite = TRUE) # finite = TRUE removes all the -Inf and Inf except if only this. In that case, whatever the -Inf and/or Inf present, output -Inf;Inf range. Idem with NA only
+    }
+    y.lim <- y.lim[y.lim.order]
+    if(any(is.na(y.lim))){
+        tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 4")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+    }
+    # end axes management
+    
+    
+    
+    
+    # create a fake categ if NULL to deal with legend display
+    if(is.null(categ)){
+        categ <- vector("list", length(data1))
+        categ[] <- "fake_categ"
+        for(i2 in 1:length(data1)){
+            data1[[i2]] <- cbind(data1[[i2]], fake_categ = "", stringsAsFactors = TRUE)
+            if(geom[[i2]] == "geom_hline" | geom[[i2]] == "geom_vline"){
+                data1[[i2]][, "fake_categ"] <- factor(paste0("Line_", 1:nrow(data1[[i2]])))
+            }
+        }
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") NULL categ ARGUMENT -> FAKE \"fake_categ\" COLUMN ADDED TO EACH DATA FRAME OF data1, AND FILLED WITH \"\"")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
+    # categ is not NULL anymore
+    if(is.null(categ.class.order)){
+        categ.class.order <- vector("list", length = length(data1))
+        tempo.categ.class.order <- NULL
+        for(i2 in 1:length(categ.class.order)){
+            categ.class.order[[i2]] <- levels(data1[[i2]][, categ[[i2]]])
+            names(categ.class.order)[i2] <- categ[[i2]]
+            tempo.categ.class.order <- c(tempo.categ.class.order, ifelse(i2 != 1, "\n", ""), categ.class.order[[i2]])
+        }
+        if(any(unlist(legend.disp))){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") THE categ.class.order SETTING IS NULL. ALPHABETICAL ORDER WILL BE APPLIED FOR CLASS ORDERING:\n", paste(tempo.categ.class.order, collapse = " "))
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    # end create a fake categ if NULL to deal with legend display
+    # categ.class.order is not NULL anymore
+    
+    
+    # vector of color with length as in levels(categ) of data1
+    if(is.null(color)){
+        color <- vector("list", length(data1))
+        length.categ.list <- lapply(lapply(mapply(FUN = "[[", data1, categ, SIMPLIFY = FALSE), FUN = unique), FUN = function(x){length(x[ ! is.na(x)])})
+        length.categ.list[sapply(categ, FUN = "==", "fake_categ")] <- 1 # when is.null(color), a single color for all the dots or lines of data[[i1]] that contain "fake_categ" category
+        total.categ.length <- sum(unlist(length.categ.list), na.rm = TRUE)
+        tempo.color <- fun_gg_palette(total.categ.length)
+        tempo.count <- 0
+        for(i2 in 1:length(data1)){
+            color[[i2]] <- tempo.color[(1:length.categ.list[[i2]]) + tempo.count]
+            tempo.count <- tempo.count + length.categ.list[[i2]]
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") NULL color ARGUMENT -> COLORS RESPECTIVELY ATTRIBUTED TO EACH CLASS OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i2, " OF categ ARGUMENT")), " (", categ[[i2]], ") IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i2, " OF data1 ARGUMENT")), ":\n", paste(color[[i2]], collapse = " "), "\n", paste(if(all(levels(data1[[i2]][, categ[[i2]]]) == "")){'\"\"'}else{levels(data1[[i2]][, categ[[i2]]])}, collapse = " "))
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    # end vector of color with length as in levels(categ) of data1
+    # color is not NULL anymore
+    
+    
+    
+    
+    
+    # last check
+    for(i1 in 1:length(data1)){
+        if(categ[[i1]] != "fake_categ" & length(color[[i1]]) != length(unique(data1[[i1]][, categ[[i1]]]))){
+            tempo.cat <- paste0("ERROR IN ", function.name, " LAST CHECK: ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST HAVE THE LENGTH OF LEVELS OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), "\nHERE IT IS COLOR LENGTH ", length(color[[i1]]), " VERSUS CATEG LEVELS LENGTH ", length(unique(data1[[i1]][, categ[[i1]]])), "\nREMINDER: A SINGLE COLOR PER CLASS OF CATEG AND A SINGLE CLASS OF CATEG PER COLOR MUST BE RESPECTED")
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }else if(categ[[i1]] == "fake_categ" & length(color[[i1]]) != 1){
+            tempo.cat <- paste0("ERROR IN ", function.name, " LAST CHECK: ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST HAVE LENGTH 1 WHEN ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IS NULL\nHERE IT IS COLOR LENGTH ", length(color[[i1]]))
+            stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+        }
+    }
+    # end last check
+    
+    
+    
+    
+    
+    # conversion of geom_hline and geom_vline
+    for(i1 in 1:length(data1)){
+        if(geom[[i1]] == "geom_hline" | geom[[i1]] == "geom_vline"){
+            final.data.frame <- data.frame()
+            for(i3 in 1:nrow(data1[[i1]])){
+                tempo.data.frame <- rbind(data1[[i1]][i3, ], data1[[i1]][i3, ], stringsAsFactors = TRUE)
+                if(geom[[i1]] == "geom_hline"){
+                    tempo.data.frame[, x[[i1]]] <- x.lim
+                }else if(geom[[i1]] == "geom_vline"){
+                    tempo.data.frame[, y[[i1]]] <- y.lim
+                }else{
+                    tempo.cat <- paste0("ERROR IN ", function.name, ": CODE INCONSISTENCY 5")
+                    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+                }
+                # 3 lines below inactivated because I put that above
+                # if(is.null(categ[[i1]])){
+                # data1[, "fake_categ"] <- paste0("Line_", i3)
+                # }
+                final.data.frame <- rbind(final.data.frame, tempo.data.frame, stringsAsFactors = TRUE)
+            }
+            data1[[i1]] <- final.data.frame
+            geom[[i1]] <- "geom_line"
+            if(length(color[[i1]])== 1L){
+                color[[i1]] <- rep(color[[i1]], length(unique(data1[[i1]][ , categ[[i1]]])))
+            }else if(length(color[[i1]]) != length(unique(data1[[i1]][ , categ[[i1]]]))){
+                tempo.cat <- paste0("ERROR IN ", function.name, " geom_hline AND geom_vline CONVERSION TO FIT THE XLIM AND YLIM LIMITS OF THE DATA: ", ifelse(length(color)== 1L, "color", paste0("ELEMENT NUMBER ", i1, " OF color ARGUMENT")), " MUST HAVE THE LENGTH OF LEVELS OF ", ifelse(length(categ)== 1L, "categ", paste0("ELEMENT ", i1, " OF categ ARGUMENT")), " IN ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i1, " OF data1 ARGUMENT")), "\nHERE IT IS COLOR LENGTH ", length(color[[i1]]), " VERSUS CATEG LEVELS LENGTH ", length(unique(data1[[i1]][, categ[[i1]]])))
+                stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+            }
+        }
+    }
+    # end conversion of geom_hline and geom_vline
+    
+    
+    
+    
+    # kind of geom_point (vectorial or raster)
+    scatter.kind <- vector("list", length = length(data1)) # list of same length as data1, that will be used to use either ggplot2::geom_point() (vectorial dot layer) or fun_gg_point_rast() (raster dot layer)
+    fix.ratio <- FALSE
+    if(is.null(raster.threshold)){
+        if(raster == TRUE){
+            scatter.kind[] <- "fun_gg_point_rast" # not important to fill everything: will be only used when geom == "geom_point"
+            fix.ratio <- TRUE
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") RASTER PLOT GENERATED -> ASPECT RATIO OF THE PLOT REGION SET BY THE raster.ratio ARGUMENT (", fun_round(raster.ratio, 2), ") TO AVOID A BUG OF ELLIPSOID DOT DRAWING")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }else{
+            scatter.kind[] <- "ggplot2::geom_point"
+        }
+    }else{
+        for(i2 in 1:length(data1)){
+            if(geom[[i2]] == "geom_point"){
+                if(nrow(data1[[i2]]) <= raster.threshold){
+                    scatter.kind[[i2]] <- "ggplot2::geom_point"
+                }else{
+                    scatter.kind[[i2]] <- "fun_gg_point_rast"
+                    fix.ratio <- TRUE
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") ", ifelse(length(data1)== 1L, "data1 ARGUMENT", paste0("DATA FRAME NUMBER ", i2, " OF data1 ARGUMENT")), " LAYER AS RASTER (NOT VECTORIAL)")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                }
+            }
+        }
+        if(any(unlist(scatter.kind) == "fun_gg_point_rast")){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") RASTER PLOT GENERATED -> ASPECT RATIO OF THE PLOT REGION SET BY THE raster.ratio ARGUMENT (", fun_round(raster.ratio, 2), ") TO AVOID A BUG OF ELLIPSOID DOT DRAWING")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }
+    # end kind of geom_point (vectorial or raster)
+    
+    
+    
+    
+    # no need loop part
+    coord.names <- NULL
+    tempo.gg.name <- "gg.indiv.plot."
+    tempo.gg.count <- 0
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::ggplot()", if(is.null(add)){""}else{add})))) # add added here to have the facets
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::xlab(if(is.null(x.lab)){x[[1]]}else{x.lab}))
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ylab(if(is.null(y.lab)){y[[1]]}else{y.lab}))
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::ggtitle(title))
+    # text angle management
+    x.tempo.just <- fun_gg_just(angle = x.text.angle, pos = "bottom", kind = "axis")
+    y.tempo.just <- fun_gg_just(angle = y.text.angle, pos = "left", kind = "axis")
+    # end text angle management
+    add.check <- TRUE
+    if( ! is.null(add)){ # if add is NULL, then = 0
+        if(grepl(pattern = "ggplot2::theme", add) == TRUE){
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") \"ggplot2::theme\" STRING DETECTED IN THE add ARGUMENT\n-> INTERNAL GGPLOT2 THEME FUNCTIONS theme() AND theme_classic() HAVE BEEN INACTIVATED, TO BE USED BY THE USER\n-> article ARGUMENT WILL BE IGNORED\nIT IS RECOMMENDED TO USE \"+ theme(aspect.ratio = raster.ratio)\" IF RASTER MODE IS ACTIVATED")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+            add.check <- FALSE
+        }
+    }
+    if(add.check == TRUE & article == TRUE){
+        # WARNING: not possible to add several times theme(). NO message but the last one overwrites the others
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::theme_classic(base_size = text.size))
+        if(grid == TRUE){
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
+                text = ggplot2::element_text(size = text.size), 
+                plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
+                legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
+                line = ggplot2::element_line(size = 0.5), 
+                axis.line.y.left = ggplot2::element_line(colour = "black"), # draw lines for the y axis
+                axis.line.x.bottom = ggplot2::element_line(colour = "black"), # draw lines for the x axis
+                panel.grid.major.x = ggplot2::element_line(colour = "grey85", size = 0.75), 
+                panel.grid.minor.x = ggplot2::element_line(colour = "grey90", size = 0.25), 
+                panel.grid.major.y = ggplot2::element_line(colour = "grey85", size = 0.75), 
+                panel.grid.minor.y = ggplot2::element_line(colour = "grey90", size = 0.25), 
+                axis.text.x = ggplot2::element_text(angle = x.tempo.just$angle, hjust = x.tempo.just$hjust, vjust = x.tempo.just$vjust),
+                axis.text.y = ggplot2::element_text(angle = y.tempo.just$angle, hjust = y.tempo.just$hjust, vjust = y.tempo.just$vjust), 
+                aspect.ratio = if(fix.ratio == TRUE){raster.ratio}else{NULL} # for raster
+            ))
+        }else{
+            assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
+                text = ggplot2::element_text(size = text.size), 
+                plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
+                line = ggplot2::element_line(size = 0.5), 
+                legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
+                axis.line.y.left = ggplot2::element_line(colour = "black"), 
+                axis.line.x.bottom = ggplot2::element_line(colour = "black"), 
+                axis.text.x = ggplot2::element_text(angle = x.tempo.just$angle, hjust = x.tempo.just$hjust, vjust = x.tempo.just$vjust),
+                axis.text.y = ggplot2::element_text(angle = y.tempo.just$angle, hjust = y.tempo.just$hjust, vjust = y.tempo.just$vjust), 
+                aspect.ratio = if(fix.ratio == TRUE){raster.ratio}else{NULL} # for raster
+            ))
+        }
+    }else if(add.check == TRUE & article == FALSE){
+        assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), m.gg <- ggplot2::theme(
+            text = ggplot2::element_text(size = text.size), 
+            plot.title = ggplot2::element_text(size = title.text.size), # stronger than text
+            line = ggplot2::element_line(size = 0.5), 
+            legend.key = ggplot2::element_rect(color = "white", size = 1.5), # size of the frame of the legend
+            panel.background = ggplot2::element_rect(fill = "grey95"), 
+            axis.line.y.left = ggplot2::element_line(colour = "black"), 
+            axis.line.x.bottom = ggplot2::element_line(colour = "black"), 
+            panel.grid.major.x = ggplot2::element_line(colour = "grey85", size = 0.75), 
+            panel.grid.minor.x = ggplot2::element_line(colour = "grey90", size = 0.25), 
+            panel.grid.major.y = ggplot2::element_line(colour = "grey85", size = 0.75), 
+            panel.grid.minor.y = ggplot2::element_line(colour = "grey90", size = 0.25), 
+            strip.background = ggplot2::element_rect(fill = "white", colour = "black"), 
+            axis.text.x = ggplot2::element_text(angle = x.tempo.just$angle, hjust = x.tempo.just$hjust, vjust = x.tempo.just$vjust),
+            axis.text.y = ggplot2::element_text(angle = y.tempo.just$angle, hjust = y.tempo.just$hjust, vjust = y.tempo.just$vjust), 
+            aspect.ratio = if(fix.ratio == TRUE){raster.ratio}else{NULL} # for raster
+            # do not work -> legend.position = "none" # to remove the legend completely: https://www.datanovia.com/en/blog/how-to-remove-legend-from-a-ggplot/
+        ))
+    }
+    # end no need loop part
+    
+    
+    # loop part
+    point.count <- 0
+    line.count <- 0
+    lg.order <- vector(mode = "list", length = 6) # order of the legend
+    lg.order <- lapply(lg.order, as.numeric) # order of the legend
+    lg.color <- vector(mode = "list", length = 6) # color of the legend
+    lg.dot.shape <- vector(mode = "list", length = 6) # etc.
+    lg.dot.size <- vector(mode = "list", length = 6) # etc.
+    lg.dot.size <- lapply(lg.dot.size, as.numeric) # etc.
+    lg.dot.border.size <- vector(mode = "list", length = 6) # etc.
+    lg.dot.border.size <- lapply(lg.dot.border.size, as.numeric) # etc.
+    lg.dot.border.color <- vector(mode = "list", length = 6) # etc.
+    lg.line.size <- vector(mode = "list", length = 6) # etc.
+    lg.line.size <- lapply(lg.line.size, as.numeric) # etc.
+    lg.line.type <- vector(mode = "list", length = 6) # etc.
+    lg.alpha <- vector(mode = "list", length = 6) # etc.
+    lg.alpha <- lapply(lg.alpha, as.numeric) # etc.
+    for(i1 in 1:length(data1)){
+        if(geom[[i1]] == "geom_point"){
+            point.count <- point.count + 1
+            if(point.count== 1L){
+                fin.lg.disp[[1]] <- legend.disp[[point.count + line.count]]
+                lg.order[[1]] <- point.count + line.count
+                lg.color[[1]] <- color[[i1]] # if color == NULL -> NULL
+                lg.dot.shape[[1]] <- dot.shape[[i1]]
+                lg.dot.size[[1]] <- dot.size[[i1]]
+                lg.dot.border.size[[1]] <- dot.border.size[[i1]]
+                lg.dot.border.color[[1]] <- dot.border.color[[i1]] # if dot.border.color == NULL -> NULL
+                if(plot == TRUE & fin.lg.disp[[1]] == TRUE & dot.shape[[1]] %in% 0:14 & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list())== 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE DOTS (DOT LAYER NUMBER ", point.count, ") IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    lg.alpha[[1]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
+                }else{
+                    lg.alpha[[1]] <- alpha[[i1]]
+                }
+                class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
+                for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
+                    tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
+                    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = scatter.kind[[i1]]))(data = tempo.data.frame, mapping = ggplot2::aes_string(x = x[[i1]], y = y[[i1]], fill = categ[[i1]]), shape = dot.shape[[i1]], size = dot.size[[i1]], stroke = dot.border.size[[i1]], color = if(dot.shape[[i1]] %in% 21:24 & ! is.null(dot.border.color)){dot.border.color[[i1]]}else{color[[i1]][i5]}, alpha = alpha[[i1]], show.legend = if(i5== 1L){TRUE}else{FALSE})) # WARNING: a single color allowed for color argument outside aesthetic, but here a single color for border --> loop could be inactivated but kept for commodity # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.). Used here to avoid multiple layers of legend which corrupt transparency
+                    coord.names <- c(coord.names, paste0(geom[[i1]], ".", class.categ[i5]))
+                }
+                assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_fill_manual(name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = as.character(color[[i1]]), breaks = class.categ)) # values are the values of fill, breaks reorder the classes according to class.categ in the legend, order argument of guide_legend determines the order of the different aesthetics in the legend (not order of classes). See guide_legend settings of scale_..._manual below
+            }
+            if(point.count== 2L){
+                fin.lg.disp[[2]] <- legend.disp[[point.count + line.count]]
+                lg.order[[2]] <- point.count + line.count
+                lg.color[[2]] <- color[[i1]] # if color == NULL -> NULL
+                lg.dot.shape[[2]] <- dot.shape[[i1]]
+                lg.dot.size[[2]] <- dot.size[[i1]]
+                lg.dot.border.size[[2]] <- dot.border.size[[i1]]
+                lg.dot.border.color[[2]] <- dot.border.color[[i1]] # if dot.border.color == NULL -> NULL
+                if(plot == TRUE & fin.lg.disp[[2]] == TRUE & dot.shape[[2]] %in% 0:14 & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list())== 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE DOTS (DOT LAYER NUMBER ", point.count, ") IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    lg.alpha[[2]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
+                }else{
+                    lg.alpha[[2]] <- alpha[[i1]]
+                }
+                class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
+                for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
+                    tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
+                    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = scatter.kind[[i1]]))(data = tempo.data.frame, mapping = ggplot2::aes_string(x = x[[i1]], y = y[[i1]], shape = categ[[i1]]), size = dot.size[[i1]], stroke = dot.border.size[[i1]], fill = color[[i1]][i5], color = if(dot.shape[[i1]] %in% 21:24 & ! is.null(dot.border.color)){dot.border.color[[i1]]}else{color[[i1]][i5]}, alpha = alpha[[i1]], show.legend = FALSE)) # WARNING: a single color allowed for fill argument outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.). Used here to avoid multiple layers of legend which corrupt transparency
+                    coord.names <- c(coord.names, paste0(geom[[i1]], ".", class.categ[i5]))
+                }
+                assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_shape_manual(name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(dot.shape[[i1]], length(color[[i1]])), breaks = class.categ)) # values are the values of shape, breaks reorder the classes according to class.categ in the legend. See guide_legend settings of scale_..._manual below
+                
+            }
+            if(point.count== 3L){
+                fin.lg.disp[[3]] <- legend.disp[[point.count + line.count]]
+                lg.order[[3]] <- point.count + line.count
+                lg.color[[3]] <- color[[i1]] # if color == NULL -> NULL
+                lg.dot.shape[[3]] <- dot.shape[[i1]]
+                lg.dot.size[[3]] <- dot.size[[i1]]
+                lg.dot.border.size[[3]] <- dot.border.size[[i1]]
+                lg.dot.border.color[[3]] <- dot.border.color[[i1]] # if dot.border.color == NULL -> NULL
+                if(plot == TRUE & fin.lg.disp[[3]] == TRUE & dot.shape[[3]] %in% 0:14 & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list())== 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE DOTS (DOT LAYER NUMBER ", point.count, ") IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    lg.alpha[[3]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
+                }else{
+                    lg.alpha[[3]] <- alpha[[i1]]
+                }
+                class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
+                for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
+                    tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
+                    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = scatter.kind[[i1]]))(data = tempo.data.frame, mapping = ggplot2::aes_string(x = x[[i1]], y = y[[i1]], stroke = categ[[i1]]), shape = dot.shape[[i1]], size = dot.size[[i1]], fill = color[[i1]][i5], stroke = dot.border.size[[i1]], color = if(dot.shape[[i1]] %in% 21:24 & ! is.null(dot.border.color)){dot.border.color[[i1]]}else{color[[i1]][i5]}, alpha = alpha[[i1]], show.legend = FALSE)) # WARNING: a single color allowed for color argument outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.). Used here to avoid multiple layers of legend which corrupt transparency
+                    coord.names <- c(coord.names, paste0(geom[[i1]], ".", class.categ[i5]))
+                }
+                assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "stroke", name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(dot.border.size[[i1]], length(color[[i1]])), breaks = class.categ)) # values are the values of stroke, breaks reorder the classes according to class.categ in the legend. See guide_legend settings of scale_..._manual below
+                
+            }
+        }else{
+            line.count <- line.count + 1
+            if(line.count== 1L){
+                fin.lg.disp[[4]] <- legend.disp[[point.count + line.count]]
+                lg.order[[4]] <- point.count + line.count
+                lg.color[[4]] <- color[[i1]] # if color == NULL -> NULL
+                lg.line.size[[4]] <- line.size[[i1]]
+                lg.line.type[[4]] <- line.type[[i1]]
+                if(plot == TRUE & fin.lg.disp[[4]] == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list())== 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE LINES (LINE LAYER NUMBER ", line.count, ") IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    lg.alpha[[4]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
+                }else{
+                    lg.alpha[[4]] <- alpha[[i1]]
+                }
+                class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
+                for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
+                    tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
+                    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::", # no CR here te0("ggpl
+                                                                                                                 ifelse(geom[[i1]] == 'geom_stick', 'geom_segment', geom[[i1]]), # geom_segment because geom_stick converted to geom_segment for plotting
+                                                                                                                 "(data = tempo.data.frame, mapping = ggplot2::aes(x = ", 
+                                                                                                                 x[[i1]], 
+                                                                                                                 ifelse(geom[[i1]] == 'geom_stick', ", yend = ", ", y = "), 
+                                                                                                                 y[[i1]], 
+                                                                                                                 if(geom[[i1]] == 'geom_stick'){paste0(', xend = ', x[[i1]], ', y = ', ifelse(is.null(geom.stick.base), y.lim[1], geom.stick.base[[i1]]))}, 
+                                                                                                                 ", linetype = ", 
+                                                                                                                 categ[[i1]], 
+                                                                                                                 "), color = \"", 
+                                                                                                                 color[[i1]][i5], 
+                                                                                                                 "\", size = ", 
+                                                                                                                 line.size[[i1]], 
+                                                                                                                 ifelse(geom[[i1]] == 'geom_path', ', lineend = \"round\"', ''), 
+                                                                                                                 ifelse(geom[[i1]] == 'geom_step', paste0(', direction = \"', geom.step.dir[[i1]], '\"'), ''), 
+                                                                                                                 ", alpha = ", 
+                                                                                                                 alpha[[i1]], 
+                                                                                                                 ", show.legend = ", 
+                                                                                                                 ifelse(i5== 1L, TRUE, FALSE), 
+                                                                                                                 ")"
+                    )))) # WARNING: a single color allowed for color argument outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.). Used here to avoid multiple layers of legend which corrupt transparency
+                    coord.names <- c(coord.names, paste0(geom[[i1]], ".", class.categ[i5]))
+                }
+                assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "linetype", name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(line.type[[i1]], length(color[[i1]])), breaks = class.categ)) # values are the values of linetype. 1 means solid. Regarding the alpha bug, I have tried different things without success: alpha in guide alone, in geom alone, in both, with different values, breaks reorder the classes according to class.categ in the legend
+            }
+            if(line.count== 2L){
+                fin.lg.disp[[5]] <- legend.disp[[point.count + line.count]]
+                lg.order[[5]] <- point.count + line.count
+                lg.color[[5]] <- color[[i1]] # if color == NULL -> NULL
+                lg.line.size[[5]] <- line.size[[i1]]
+                lg.line.type[[5]] <- line.type[[i1]]
+                if(plot == TRUE & fin.lg.disp[[5]] == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list())== 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE LINES (LINE LAYER NUMBER ", line.count, ") IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    lg.alpha[[5]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
+                }else{
+                    lg.alpha[[5]] <- alpha[[i1]]
+                }
+                class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
+                for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
+                    tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
+                    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::", # no CR here te0("ggpl
+                                                                                                                 ifelse(geom[[i1]] == 'geom_stick', 'geom_segment', geom[[i1]]), # geom_segment because geom_stick converted to geom_segment for plotting
+                                                                                                                 "(data = tempo.data.frame, mapping = ggplot2::aes(x = ", 
+                                                                                                                 x[[i1]], 
+                                                                                                                 ifelse(geom[[i1]] == 'geom_stick', ", yend = ", ", y = "), 
+                                                                                                                 y[[i1]], 
+                                                                                                                 if(geom[[i1]] == 'geom_stick'){paste0(', xend = ', x[[i1]], ', y = ', ifelse(is.null(geom.stick.base), y.lim[1], geom.stick.base[[i1]]))}, 
+                                                                                                                 ", alpha = ", 
+                                                                                                                 categ[[i1]], 
+                                                                                                                 "), color = \"", 
+                                                                                                                 color[[i1]][i5], 
+                                                                                                                 "\", size = ", 
+                                                                                                                 line.size[[i1]], 
+                                                                                                                 ", linetype = ", 
+                                                                                                                 ifelse(is.numeric(line.type[[i1]]), "", "\""), 
+                                                                                                                 line.type[[i1]], 
+                                                                                                                 ifelse(is.numeric(line.type[[i1]]), "", "\""), 
+                                                                                                                 ifelse(geom[[i1]] == 'geom_path', ', lineend = \"round\"', ''), 
+                                                                                                                 ifelse(geom[[i1]] == 'geom_step', paste0(', direction = \"', geom.step.dir[[i1]], '\"'), ''), 
+                                                                                                                 ", show.legend = FALSE)"
+                    )))) # WARNING: a single color allowed for color argument outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.). Used here to avoid multiple layers of legend which corrupt transparency
+                    coord.names <- c(coord.names, paste0(geom[[i1]], ".", class.categ[i5]))
+                }
+                assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "alpha", name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(alpha[[i1]], length(color[[i1]])), breaks = class.categ)) # values are the values of linetype. 1 means solid. Regarding the alpha bug, I have tried different things without success: alpha in guide alone, in geom alone, in both, with different values, breaks reorder the classes according to class.categ in the legend
+            }
+            if(line.count== 3L){
+                fin.lg.disp[[6]] <- legend.disp[[point.count + line.count]]
+                lg.order[[6]] <- point.count + line.count
+                lg.color[[6]] <- color[[i1]] # if color == NULL -> NULL
+                lg.line.size[[6]] <- line.size[[i1]]
+                lg.line.type[[6]] <- line.type[[i1]]
+                if(plot == TRUE & fin.lg.disp[[6]] == TRUE & ((length(dev.list()) > 0 & names(dev.cur()) == "windows") | (length(dev.list())== 0L & Sys.info()["sysname"] == "Windows"))){ # if any Graph device already open and this device is "windows", or if no Graph device opened yet and we are on windows system -> prevention of alpha legend bug on windows using value 1
+                    warn.count <- warn.count + 1
+                    tempo.warn <- paste0("(", warn.count,") GRAPHIC DEVICE USED ON A WINDOWS SYSTEM ->\nTRANSPARENCY OF THE LINES (LINE LAYER NUMBER ", line.count, ") IS INACTIVATED IN THE LEGEND TO PREVENT A WINDOWS DEPENDENT BUG (SEE https://github.com/tidyverse/ggplot2/issues/2452)\nTO OVERCOME THIS ON WINDOWS, USE ANOTHER DEVICE (pdf() FOR INSTANCE)")
+                    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+                    lg.alpha[[6]] <- 1 # to avoid a bug on windows: if alpha argument is different from 1 for lines (transparency), then lines are not correctly displayed in the legend when using the R GUI (bug https://github.com/tidyverse/ggplot2/issues/2452). No bug when using a pdf
+                }else{
+                    lg.alpha[[6]] <- alpha[[i1]]
+                }
+                class.categ <- levels(factor(data1[[i1]][, categ[[i1]]]))
+                for(i5 in 1:length(color[[i1]])){ # or length(class.categ). It is the same because already checked that lengths are the same
+                    tempo.data.frame <- data1[[i1]][data1[[i1]][, categ[[i1]]] == class.categ[i5], ]
+                    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = paste0("ggplot2::", # no CR here te0("ggpl
+                                                                                                                 ifelse(geom[[i1]] == 'geom_stick', 'geom_segment', geom[[i1]]), # geom_segment because geom_stick converted to geom_segment for plotting
+                                                                                                                 "(data = tempo.data.frame, mapping = ggplot2::aes(x = ", 
+                                                                                                                 x[[i1]], 
+                                                                                                                 ifelse(geom[[i1]] == 'geom_stick', ", yend = ", ", y = "), 
+                                                                                                                 y[[i1]], 
+                                                                                                                 if(geom[[i1]] == 'geom_stick'){paste0(', xend = ', x[[i1]], ', y = ', ifelse(is.null(geom.stick.base), y.lim[1], geom.stick.base[[i1]]))}, 
+                                                                                                                 ", size = ", 
+                                                                                                                 categ[[i1]], 
+                                                                                                                 "), color = \"", 
+                                                                                                                 color[[i1]][i5], 
+                                                                                                                 "\", linetype = ", 
+                                                                                                                 ifelse(is.numeric(line.type[[i1]]), "", "\""), 
+                                                                                                                 line.type[[i1]], 
+                                                                                                                 ifelse(is.numeric(line.type[[i1]]), "", "\""), 
+                                                                                                                 ifelse(geom[[i1]] == 'geom_path', ', lineend = \"round\"', ''), 
+                                                                                                                 ifelse(geom[[i1]] == 'geom_step', paste0(', direction = \"', geom.step.dir[[i1]], '\"'), ''), 
+                                                                                                                 ", alpha = ", 
+                                                                                                                 alpha[[i1]], 
+                                                                                                                 ", show.legend = FALSE)"
+                    )))) # WARNING: a single color allowed for color argument outside aesthetic, hence the loop # legend.show option do not remove the legend, only the aesthetic of the legend (dot, line, etc.). Used here to avoid multiple layers of legend which corrupt transparency
+                    coord.names <- c(coord.names, paste0(geom[[i1]], ".", class.categ[i5]))
+                }
+                assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_discrete_manual(aesthetics = "size", name = if(is.null(legend.name)){NULL}else{legend.name[[i1]]}, values = rep(line.size[[i1]], length(color[[i1]])), breaks = class.categ)) # values are the values of linetype. 1 means solid. Regarding the alpha bug, I have tried different things without success: alpha in guide alone, in geom alone, in both, breaks reorder the classes according to class.categ in the legend
+            }
+        }
+    }
+    # end loop part
+    
+    
+    
+    
+    # legend display
+    tempo.legend.final <- 'ggplot2::guides(
 fill = if(fin.lg.disp[[1]] == TRUE){
 ggplot2::guide_legend(
 order = lg.order[[1]], 
@@ -13517,25 +13505,25 @@ FALSE
 }
 )' # clip = "off" to have secondary ticks outside plot region does not work
 if( ! is.null(legend.width)){
-if(any(unlist(legend.disp))){ # means some TRUE
-tempo.graph.info <- suppressMessages(ggplot2::ggplot_build(eval(parse(text = paste0(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), ' + ', tempo.legend.final))))) # will be recovered later again, when ylim will be considered
-legend.final <- fun_gg_get_legend(ggplot_built = tempo.graph.info, fun.name = function.name) # get legend
-fin.lg.disp[] <- FALSE # remove all the legends. Must be done even if fin.lg.disp is not appearing in the code thenafter. Otherwise twice the legend
-if(is.null(legend.final) & plot == TRUE){ # even if any(unlist(legend.disp)) is TRUE
-legend.final <- fun_gg_empty_graph() # empty graph instead of legend
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") LEGEND REQUESTED (NON-NULL categ ARGUMENT OR legend.show ARGUMENT SET TO TRUE)\nBUT IT SEEMS THAT THE PLOT HAS NO LEGEND -> EMPTY LEGEND SPACE CREATED BECAUSE OF THE NON-NULL legend.width ARGUMENT\n")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
-}else if(plot == TRUE){ # means all FALSE
-legend.final <- ggplot2::ggplot()+ggplot2::theme_void() # empty graph instead of legend
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") LEGEND REQUESTED (NON-NULL categ ARGUMENT OR legend.show ARGUMENT SET TO TRUE)\nBUT IT SEEMS THAT THE PLOT HAS NO LEGEND -> EMPTY LEGEND SPACE CREATED BECAUSE OF THE NON-NULL legend.width ARGUMENT\n")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
-}
+    if(any(unlist(legend.disp))){ # means some TRUE
+        tempo.graph.info <- suppressMessages(ggplot2::ggplot_build(eval(parse(text = paste0(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), ' + ', tempo.legend.final))))) # will be recovered later again, when ylim will be considered
+        legend.final <- fun_gg_get_legend(ggplot_built = tempo.graph.info, fun.name = function.name) # get legend
+        fin.lg.disp[] <- FALSE # remove all the legends. Must be done even if fin.lg.disp is not appearing in the code thenafter. Otherwise twice the legend
+        if(is.null(legend.final) & plot == TRUE){ # even if any(unlist(legend.disp)) is TRUE
+            legend.final <- fun_gg_empty_graph() # empty graph instead of legend
+            warn.count <- warn.count + 1
+            tempo.warn <- paste0("(", warn.count,") LEGEND REQUESTED (NON-NULL categ ARGUMENT OR legend.show ARGUMENT SET TO TRUE)\nBUT IT SEEMS THAT THE PLOT HAS NO LEGEND -> EMPTY LEGEND SPACE CREATED BECAUSE OF THE NON-NULL legend.width ARGUMENT\n")
+            warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+        }
+    }else if(plot == TRUE){ # means all FALSE
+        legend.final <- ggplot2::ggplot()+ggplot2::theme_void() # empty graph instead of legend
+        warn.count <- warn.count + 1
+        tempo.warn <- paste0("(", warn.count,") LEGEND REQUESTED (NON-NULL categ ARGUMENT OR legend.show ARGUMENT SET TO TRUE)\nBUT IT SEEMS THAT THE PLOT HAS NO LEGEND -> EMPTY LEGEND SPACE CREATED BECAUSE OF THE NON-NULL legend.width ARGUMENT\n")
+        warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    }
 }
 if( ! any(unlist(legend.disp))){
-fin.lg.disp[] <- FALSE # remove all the legends. Must be done even if fin.lg.disp is not appearing in the code thenafter. Otherwise twice the legend
+    fin.lg.disp[] <- FALSE # remove all the legends. Must be done even if fin.lg.disp is not appearing in the code thenafter. Otherwise twice the legend
 }
 assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(text = tempo.legend.final)))
 # end legend display
@@ -13548,135 +13536,135 @@ assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), eval(parse(t
 tempo.coord <- suppressMessages(ggplot2::ggplot_build(eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + ", ' + ggplot2::scale_x_continuous(expand = c(0, 0), limits = sort(x.lim), oob = scales::rescale_none) + ggplot2::scale_y_continuous(expand = c(0, 0), limits = sort(y.lim), oob = scales::rescale_none)'))))$layout$panel_params[[1]]) # here I do not need the x-axis and y-axis orientation, I just need the number of main ticks
 # x.second.tick.positions # coordinates of secondary ticks (only if x.second.tick.nb argument is non-null or if x.log argument is different from "no")
 if(x.log != "no"){ # integer main ticks for log2 and log10
-tempo.scale <- (as.integer(min(x.lim, na.rm = TRUE)) - 1):(as.integer(max(x.lim, na.rm = TRUE)) + 1)
-}else{
-tempo <- if(is.null(attributes(tempo.coord$x$breaks))){tempo.coord$x$breaks}else{unlist(attributes(tempo.coord$x$breaks))}
-if(all(is.na(tempo))){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nONLY NA IN tempo.coord$x$breaks")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-if(length(unique(x.lim)) <= 1){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nIT SEEMS THAT X-AXIS VALUES HAVE A NULL RANGE: ", paste(x.lim, collapse = " "), "\nPLEASE, USE THE x.lim ARGUMENT WITH 2 DIFFERENT VALUES TO SOLVE THIS")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-tempo.scale <- fun_scale(lim = x.lim, n = ifelse(is.null(x.tick.nb), length(tempo[ ! is.na(tempo)]), x.tick.nb)) # in ggplot 3.3.0, tempo.coord$x.major_source replaced by tempo.coord$x$breaks. If fact: n = ifelse(is.null(x.tick.nb), length(tempo[ ! is.na(tempo)]), x.tick.nb)) replaced by n = ifelse(is.null(x.tick.nb), 4, x.tick.nb))
-}
+    tempo.scale <- (as.integer(min(x.lim, na.rm = TRUE)) - 1):(as.integer(max(x.lim, na.rm = TRUE)) + 1)
+}else{
+    tempo <- if(is.null(attributes(tempo.coord$x$breaks))){tempo.coord$x$breaks}else{unlist(attributes(tempo.coord$x$breaks))}
+    if(all(is.na(tempo))){
+        tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nONLY NA IN tempo.coord$x$breaks")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+    }
+    if(length(unique(x.lim)) <= 1){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nIT SEEMS THAT X-AXIS VALUES HAVE A NULL RANGE: ", paste(x.lim, collapse = " "), "\nPLEASE, USE THE x.lim ARGUMENT WITH 2 DIFFERENT VALUES TO SOLVE THIS")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+    }else{
+        tempo.scale <- fun_scale(lim = x.lim, n = ifelse(is.null(x.tick.nb), length(tempo[ ! is.na(tempo)]), x.tick.nb)) # in ggplot 3.3.0, tempo.coord$x.major_source replaced by tempo.coord$x$breaks. If fact: n = ifelse(is.null(x.tick.nb), length(tempo[ ! is.na(tempo)]), x.tick.nb)) replaced by n = ifelse(is.null(x.tick.nb), 4, x.tick.nb))
+    }
 }
 x.second.tick.values <- NULL
 x.second.tick.pos <- NULL
 if(x.log != "no"){
-tempo <- fun_inter_ticks(lim = x.lim, log = x.log)
-x.second.tick.values <- tempo$values
-x.second.tick.pos <- tempo$coordinates
-# if(vertical == TRUE){ # do not remove in case the bug is fixed
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
-geom = "segment", x = x.second.tick.pos, 
-xend = x.second.tick.pos, 
-y = if(diff(y.lim) > 0){tempo.coord$y.range[1]}else{tempo.coord$y.range[2]}, 
-yend = if(diff(y.lim) > 0){tempo.coord$y.range[1] + abs(diff(tempo.coord$y.range)) / 80}else{tempo.coord$y.range[2] - abs(diff(tempo.coord$y.range)) / 80}
-))
-# }else{ # not working because of the ggplot2 bug
-# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", y = x.second.tick.pos, yend = x.second.tick.pos, x = tempo.coord$x.range[1], xend = tempo.coord$x.range[1] + diff(tempo.coord$x.range) / 80))
-# }
-coord.names <- c(coord.names, "x.second.tick.positions")
+    tempo <- fun_inter_ticks(lim = x.lim, log = x.log)
+    x.second.tick.values <- tempo$values
+    x.second.tick.pos <- tempo$coordinates
+    # if(vertical == TRUE){ # do not remove in case the bug is fixed
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
+        geom = "segment", x = x.second.tick.pos, 
+        xend = x.second.tick.pos, 
+        y = if(diff(y.lim) > 0){tempo.coord$y.range[1]}else{tempo.coord$y.range[2]}, 
+        yend = if(diff(y.lim) > 0){tempo.coord$y.range[1] + abs(diff(tempo.coord$y.range)) / 80}else{tempo.coord$y.range[2] - abs(diff(tempo.coord$y.range)) / 80}
+    ))
+    # }else{ # not working because of the ggplot2 bug
+    # assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", y = x.second.tick.pos, yend = x.second.tick.pos, x = tempo.coord$x.range[1], xend = tempo.coord$x.range[1] + diff(tempo.coord$x.range) / 80))
+    # }
+    coord.names <- c(coord.names, "x.second.tick.positions")
 }else if(( ! is.null(x.second.tick.nb)) & x.log == "no"){
-# if(x.second.tick.nb > 0){ #inactivated because already checked before
-if(length(tempo.scale) < 2){
-tempo.cat1 <- c("x.tick.nb", "x.second.tick.nb")
-tempo.cat2 <- sapply(list(x.tick.nb, x.second.tick.nb), FUN = paste0, collapse = " ")
-tempo.sep <- sapply(mapply(" ", max(nchar(tempo.cat1)) - nchar(tempo.cat1) + 3, FUN = rep, SIMPLIFY = FALSE), FUN = paste0, collapse = "")
-tempo.cat <- paste0("ERROR IN ", function.name, "\nTHE NUMBER OF GENERATED TICKS FOR THE X-AXIS IS NOT CORRECT: ", length(tempo.scale), "\nUSING THESE ARGUMENT SETTINGS (NO DISPLAY MEANS NULL VALUE):\n", paste0(tempo.cat1, tempo.sep, tempo.cat2, collapse = "\n"), "\nPLEASE, TEST OTHER VALUES")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-tempo <- fun_inter_ticks(lim = x.lim, log = x.log, breaks = tempo.scale, n = x.second.tick.nb)
-}
-x.second.tick.values <- tempo$values
-x.second.tick.pos <- tempo$coordinates
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
-geom = "segment", 
-x = x.second.tick.pos, 
-xend = x.second.tick.pos, 
-y = if(diff(y.lim) > 0){tempo.coord$y.range[1]}else{tempo.coord$y.range[2]}, 
-yend = if(diff(y.lim) > 0){tempo.coord$y.range[1] + abs(diff(tempo.coord$y.range)) / 80}else{tempo.coord$y.range[2] - abs(diff(tempo.coord$y.range)) / 80}
-))
-coord.names <- c(coord.names, "x.second.tick.positions")
+    # if(x.second.tick.nb > 0){ #inactivated because already checked before
+    if(length(tempo.scale) < 2){
+        tempo.cat1 <- c("x.tick.nb", "x.second.tick.nb")
+        tempo.cat2 <- sapply(list(x.tick.nb, x.second.tick.nb), FUN = paste0, collapse = " ")
+        tempo.sep <- sapply(mapply(" ", max(nchar(tempo.cat1)) - nchar(tempo.cat1) + 3, FUN = rep, SIMPLIFY = FALSE), FUN = paste0, collapse = "")
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nTHE NUMBER OF GENERATED TICKS FOR THE X-AXIS IS NOT CORRECT: ", length(tempo.scale), "\nUSING THESE ARGUMENT SETTINGS (NO DISPLAY MEANS NULL VALUE):\n", paste0(tempo.cat1, tempo.sep, tempo.cat2, collapse = "\n"), "\nPLEASE, TEST OTHER VALUES")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else{
+        tempo <- fun_inter_ticks(lim = x.lim, log = x.log, breaks = tempo.scale, n = x.second.tick.nb)
+    }
+    x.second.tick.values <- tempo$values
+    x.second.tick.pos <- tempo$coordinates
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
+        geom = "segment", 
+        x = x.second.tick.pos, 
+        xend = x.second.tick.pos, 
+        y = if(diff(y.lim) > 0){tempo.coord$y.range[1]}else{tempo.coord$y.range[2]}, 
+        yend = if(diff(y.lim) > 0){tempo.coord$y.range[1] + abs(diff(tempo.coord$y.range)) / 80}else{tempo.coord$y.range[2] - abs(diff(tempo.coord$y.range)) / 80}
+    ))
+    coord.names <- c(coord.names, "x.second.tick.positions")
 }
 # for the ggplot2 bug with x.log, this does not work: eval(parse(text = ifelse(vertical == FALSE & x.log == "log10", "ggplot2::scale_x_continuous", "ggplot2::scale_x_continuous")))
 assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_x_continuous(
-breaks = tempo.scale, 
-minor_breaks = x.second.tick.pos, 
-labels = if(x.log == "log10"){scales::trans_format("identity", scales::math_format(10^.x))}else if(x.log == "log2"){scales::trans_format("identity", scales::math_format(2^.x))}else if(x.log == "no"){ggplot2::waiver()}else{tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 10") ; stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)}, 
-expand = c(0, 0), # remove space after after axis limits
-limits = sort(x.lim), # NA indicate that limits must correspond to data limits but xlim() already used
-oob = scales::rescale_none, 
-trans = ifelse(diff(x.lim) < 0, "reverse", "identity") # equivalent to ggplot2::scale_x_reverse() but create the problem of x-axis label disappearance with x.lim decreasing. Thus, do not use. Use xlim() below and after this
+    breaks = tempo.scale, 
+    minor_breaks = x.second.tick.pos, 
+    labels = if(x.log == "log10"){scales::trans_format("identity", scales::math_format(10^.x))}else if(x.log == "log2"){scales::trans_format("identity", scales::math_format(2^.x))}else if(x.log == "no"){ggplot2::waiver()}else{tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 10") ; stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)}, 
+    expand = c(0, 0), # remove space after after axis limits
+    limits = sort(x.lim), # NA indicate that limits must correspond to data limits but xlim() already used
+    oob = scales::rescale_none, 
+    trans = ifelse(diff(x.lim) < 0, "reverse", "identity") # equivalent to ggplot2::scale_x_reverse() but create the problem of x-axis label disappearance with x.lim decreasing. Thus, do not use. Use xlim() below and after this
 ))
 # end x.second.tick.positions
 # y.second.tick.positions # coordinates of secondary ticks (only if y.second.tick.nb argument is non-null or if y.log argument is different from "no")
 if(y.log != "no"){ # integer main ticks for log2 and log10
-tempo.scale <- (as.integer(min(y.lim, na.rm = TRUE)) - 1):(as.integer(max(y.lim, na.rm = TRUE)) + 1)
-}else{
-tempo <- if(is.null(attributes(tempo.coord$y$breaks))){tempo.coord$y$breaks}else{unlist(attributes(tempo.coord$y$breaks))}
-if(all(is.na(tempo))){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nONLY NA IN tempo.coord$y$breaks")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}
-if(length(unique(y.lim)) <= 1){
-tempo.cat <- paste0("ERROR IN ", function.name, "\nIT SEEMS THAT Y-AXIS VALUES HAVE A NULL RANGE: ", paste(y.lim, collapse = " "), "\nPLEASE, USE THE y.lim ARGUMENT WITH 2 DIFFERENT VALUES TO SOLVE THIS")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-tempo.scale <- fun_scale(lim = y.lim, n = ifelse(is.null(y.tick.nb), length(tempo[ ! is.na(tempo)]), y.tick.nb)) # in ggplot 3.3.0, tempo.coord$y.major_source replaced by tempo.coord$y$breaks. If fact: n = ifelse(is.null(y.tick.nb), length(tempo[ ! is.na(tempo)]), y.tick.nb)) replaced by n = ifelse(is.null(y.tick.nb), 4, y.tick.nb))
-}
+    tempo.scale <- (as.integer(min(y.lim, na.rm = TRUE)) - 1):(as.integer(max(y.lim, na.rm = TRUE)) + 1)
+}else{
+    tempo <- if(is.null(attributes(tempo.coord$y$breaks))){tempo.coord$y$breaks}else{unlist(attributes(tempo.coord$y$breaks))}
+    if(all(is.na(tempo))){
+        tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nONLY NA IN tempo.coord$y$breaks")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+    }
+    if(length(unique(y.lim)) <= 1){
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nIT SEEMS THAT Y-AXIS VALUES HAVE A NULL RANGE: ", paste(y.lim, collapse = " "), "\nPLEASE, USE THE y.lim ARGUMENT WITH 2 DIFFERENT VALUES TO SOLVE THIS")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+    }else{
+        tempo.scale <- fun_scale(lim = y.lim, n = ifelse(is.null(y.tick.nb), length(tempo[ ! is.na(tempo)]), y.tick.nb)) # in ggplot 3.3.0, tempo.coord$y.major_source replaced by tempo.coord$y$breaks. If fact: n = ifelse(is.null(y.tick.nb), length(tempo[ ! is.na(tempo)]), y.tick.nb)) replaced by n = ifelse(is.null(y.tick.nb), 4, y.tick.nb))
+    }
 }
 y.second.tick.values <- NULL
 y.second.tick.pos <- NULL
 if(y.log != "no"){
-tempo <- fun_inter_ticks(lim = y.lim, log = y.log)
-y.second.tick.values <- tempo$values
-y.second.tick.pos <- tempo$coordinates
-# if(vertical == TRUE){ # do not remove in case the bug is fixed
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
-geom = "segment", 
-y = y.second.tick.pos, 
-yend = y.second.tick.pos, 
-x = if(diff(x.lim) > 0){tempo.coord$x.range[1]}else{tempo.coord$x.range[2]}, 
-xend = if(diff(x.lim) > 0){tempo.coord$x.range[1] + abs(diff(tempo.coord$x.range)) / 80}else{tempo.coord$x.range[2] - abs(diff(tempo.coord$x.range)) / 80}
-))
-# }else{ # not working because of the ggplot2 bug
-# assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", x = y.second.tick.pos, xend = y.second.tick.pos, y = tempo.coord$y.range[1], yend = tempo.coord$y.range[1] + diff(tempo.coord$y.range) / 80))
-# }
-coord.names <- c(coord.names, "y.second.tick.positions")
+    tempo <- fun_inter_ticks(lim = y.lim, log = y.log)
+    y.second.tick.values <- tempo$values
+    y.second.tick.pos <- tempo$coordinates
+    # if(vertical == TRUE){ # do not remove in case the bug is fixed
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
+        geom = "segment", 
+        y = y.second.tick.pos, 
+        yend = y.second.tick.pos, 
+        x = if(diff(x.lim) > 0){tempo.coord$x.range[1]}else{tempo.coord$x.range[2]}, 
+        xend = if(diff(x.lim) > 0){tempo.coord$x.range[1] + abs(diff(tempo.coord$x.range)) / 80}else{tempo.coord$x.range[2] - abs(diff(tempo.coord$x.range)) / 80}
+    ))
+    # }else{ # not working because of the ggplot2 bug
+    # assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(geom = "segment", x = y.second.tick.pos, xend = y.second.tick.pos, y = tempo.coord$y.range[1], yend = tempo.coord$y.range[1] + diff(tempo.coord$y.range) / 80))
+    # }
+    coord.names <- c(coord.names, "y.second.tick.positions")
 }else if(( ! is.null(y.second.tick.nb)) & y.log == "no"){
-# if(y.second.tick.nb > 0){ #inactivated because already checked before
-if(length(tempo.scale) < 2){
-tempo.cat1 <- c("y.tick.nb", "y.second.tick.nb")
-tempo.cat2 <- sapply(list(y.tick.nb, y.second.tick.nb), FUN = paste0, collapse = " ")
-tempo.sep <- sapply(mapply(" ", max(nchar(tempo.cat1)) - nchar(tempo.cat1) + 3, FUN = rep, SIMPLIFY = FALSE), FUN = paste0, collapse = "")
-tempo.cat <- paste0("ERROR IN ", function.name, "\nTHE NUMBER OF GENERATED TICKS FOR THE Y-AXIS IS NOT CORRECT: ", length(tempo.scale), "\nUSING THESE ARGUMENT SETTINGS (NO DISPLAY MEANS NULL VALUE):\n", paste0(tempo.cat1, tempo.sep, tempo.cat2, collapse = "\n"), "\nPLEASE, TEST OTHER VALUES")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
-}else{
-tempo <- fun_inter_ticks(lim = y.lim, log = y.log, breaks = tempo.scale, n = y.second.tick.nb)
-}
-y.second.tick.values <- tempo$values
-y.second.tick.pos <- tempo$coordinates
-assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
-geom = "segment", 
-y = y.second.tick.pos, 
-yend = y.second.tick.pos, 
-x = if(diff(x.lim) > 0){tempo.coord$x.range[1]}else{tempo.coord$x.range[2]}, 
-xend = if(diff(x.lim) > 0){tempo.coord$x.range[1] + abs(diff(tempo.coord$x.range)) / 80}else{tempo.coord$x.range[2] - abs(diff(tempo.coord$x.range)) / 80}
-))
-coord.names <- c(coord.names, "y.second.tick.positions")
+    # if(y.second.tick.nb > 0){ #inactivated because already checked before
+    if(length(tempo.scale) < 2){
+        tempo.cat1 <- c("y.tick.nb", "y.second.tick.nb")
+        tempo.cat2 <- sapply(list(y.tick.nb, y.second.tick.nb), FUN = paste0, collapse = " ")
+        tempo.sep <- sapply(mapply(" ", max(nchar(tempo.cat1)) - nchar(tempo.cat1) + 3, FUN = rep, SIMPLIFY = FALSE), FUN = paste0, collapse = "")
+        tempo.cat <- paste0("ERROR IN ", function.name, "\nTHE NUMBER OF GENERATED TICKS FOR THE Y-AXIS IS NOT CORRECT: ", length(tempo.scale), "\nUSING THESE ARGUMENT SETTINGS (NO DISPLAY MEANS NULL VALUE):\n", paste0(tempo.cat1, tempo.sep, tempo.cat2, collapse = "\n"), "\nPLEASE, TEST OTHER VALUES")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
+    }else{
+        tempo <- fun_inter_ticks(lim = y.lim, log = y.log, breaks = tempo.scale, n = y.second.tick.nb)
+    }
+    y.second.tick.values <- tempo$values
+    y.second.tick.pos <- tempo$coordinates
+    assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::annotate(
+        geom = "segment", 
+        y = y.second.tick.pos, 
+        yend = y.second.tick.pos, 
+        x = if(diff(x.lim) > 0){tempo.coord$x.range[1]}else{tempo.coord$x.range[2]}, 
+        xend = if(diff(x.lim) > 0){tempo.coord$x.range[1] + abs(diff(tempo.coord$x.range)) / 80}else{tempo.coord$x.range[2] - abs(diff(tempo.coord$x.range)) / 80}
+    ))
+    coord.names <- c(coord.names, "y.second.tick.positions")
 }
 # for the ggplot2 bug with y.log, this does not work: eval(parse(text = ifelse(vertical == FALSE & y.log == "log10", "ggplot2::scale_x_continuous", "ggplot2::scale_y_continuous")))
 assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::scale_y_continuous(
-breaks = tempo.scale, 
-minor_breaks = y.second.tick.pos, 
-labels = if(y.log == "log10"){scales::trans_format("identity", scales::math_format(10^.x))}else if(y.log == "log2"){scales::trans_format("identity", scales::math_format(2^.x))}else if(y.log == "no"){ggplot2::waiver()}else{tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 10") ; stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)}, 
-expand = c(0, 0), # remove space after axis limits
-limits = sort(y.lim), # NA indicate that limits must correspond to data limits but ylim() already used
-oob = scales::rescale_none, 
-trans = ifelse(diff(y.lim) < 0, "reverse", "identity") # equivalent to ggplot2::scale_y_reverse() but create the problem of y-axis label disappearance with y.lim decreasing. Thus, do not use. Use ylim() below and after this
+    breaks = tempo.scale, 
+    minor_breaks = y.second.tick.pos, 
+    labels = if(y.log == "log10"){scales::trans_format("identity", scales::math_format(10^.x))}else if(y.log == "log2"){scales::trans_format("identity", scales::math_format(2^.x))}else if(y.log == "no"){ggplot2::waiver()}else{tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 10") ; stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)}, 
+    expand = c(0, 0), # remove space after axis limits
+    limits = sort(y.lim), # NA indicate that limits must correspond to data limits but ylim() already used
+    oob = scales::rescale_none, 
+    trans = ifelse(diff(y.lim) < 0, "reverse", "identity") # equivalent to ggplot2::scale_y_reverse() but create the problem of y-axis label disappearance with y.lim decreasing. Thus, do not use. Use ylim() below and after this
 ))
 # end y.second.tick.positions
 assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::coord_cartesian(xlim = x.lim, ylim = y.lim)) # clip = "off" to have secondary ticks outside plot region. The problem is that points out of bounds are also drawn outside the plot region. Thus, I cannot use it # at that stage, x.lim and y.lim not NULL anymore
@@ -13689,15 +13677,15 @@ assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::coo
 fin.plot <- eval(parse(text = paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + ")))
 grob.save <- NULL
 if(plot == TRUE){
-if( ! is.null(legend.width)){ # any(unlist(legend.disp)) == TRUE removed to have empty legend space # not & any(unlist(fin.lg.disp)) == TRUE here because converted to FALSE
-grob.save <- suppressMessages(suppressWarnings(gridExtra::grid.arrange(fin.plot, legend.final, ncol=2, widths=c(1, legend.width))))
-}else{
-grob.save <- suppressMessages(suppressWarnings(print(fin.plot)))
-}
+    if( ! is.null(legend.width)){ # any(unlist(legend.disp)) == TRUE removed to have empty legend space # not & any(unlist(fin.lg.disp)) == TRUE here because converted to FALSE
+        grob.save <- suppressMessages(suppressWarnings(gridExtra::grid.arrange(fin.plot, legend.final, ncol=2, widths=c(1, legend.width))))
+    }else{
+        grob.save <- suppressMessages(suppressWarnings(print(fin.plot)))
+    }
 }else{
-warn.count <- warn.count + 1
-tempo.warn <- paste0("(", warn.count,") PLOT NOT SHOWN AS REQUESTED")
-warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
+    warn.count <- warn.count + 1
+    tempo.warn <- paste0("(", warn.count,") PLOT NOT SHOWN AS REQUESTED")
+    warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
 }
 # end drawing
 
@@ -13705,49 +13693,49 @@ warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn
 
 # output
 if(warn.print == TRUE & ! is.null(warn)){
-on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
+    on.exit(warning(paste0("FROM ", function.name, ":\n\n", warn), call. = FALSE))
 }
 on.exit(exp = options(warning.length = ini.warning.length), add = TRUE)
 if(return == TRUE){
-output <- suppressMessages(ggplot2::ggplot_build(fin.plot))
-# output$data <- output$data[-1] # yes for boxplot but not for scatter # remove the first data because corresponds to the initial empty boxplot
-if(length(output$data) != length(coord.names)){
-tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, ": length(output$data) AND length(coord.names) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
-stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
-}else{
-names(output$data) <- coord.names
-}
-if(is.null(unlist(removed.row.nb))){
-removed.row.nb <- NULL
-removed.rows <- NULL
-}else{
-for(i3 in 1:length(data1)){
-if( ! is.null(removed.row.nb[[i3]])){
-removed.row.nb[[i3]] <- sort(removed.row.nb[[i3]])
-removed.rows[[i3]] <- data1.ini[[i3]][removed.row.nb[[i3]], ]
-}
-}
-}
-tempo <- output$layout$panel_params[[1]]
-output <- list(
-data = data1, 
-removed.row.nb = removed.row.nb, 
-removed.rows = removed.rows, 
-plot = c(output$data, x.second.tick.values = list(x.second.tick.values), y.second.tick.values = list(y.second.tick.values)), 
-panel = facet.categ, 
-axes = list(
-x.range = tempo$x.range, 
-x.labels = if(is.null(attributes(tempo$x$breaks))){tempo$x$breaks}else{tempo$x$scale$get_labels()}, # is.null(attributes(tempo$x$breaks)) test if it is number (TRUE) or character (FALSE)
-x.positions = if(is.null(attributes(tempo$x$breaks))){tempo$x$breaks}else{unlist(attributes(tempo$x$breaks))}, 
-y.range = tempo$y.range, 
-y.labels = if(is.null(attributes(tempo$y$breaks))){tempo$y$breaks}else{tempo$y$scale$get_labels()}, 
-y.positions = if(is.null(attributes(tempo$y$breaks))){tempo$y$breaks}else{unlist(attributes(tempo$y$breaks))}
-), 
-warn = paste0("\n", warn, "\n\n"), 
-ggplot = if(return.ggplot == TRUE){fin.plot}else{NULL}, # fin.plot plots the graph if return == TRUE
-gtable = if(return.gtable == TRUE){grob.save}else{NULL} #
-)
-return(output) # this plots the graph if return.ggplot is TRUE and if no assignment
+    output <- suppressMessages(ggplot2::ggplot_build(fin.plot))
+    # output$data <- output$data[-1] # yes for boxplot but not for scatter # remove the first data because corresponds to the initial empty boxplot
+    if(length(output$data) != length(coord.names)){
+        tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, ": length(output$data) AND length(coord.names) MUST BE IDENTICAL. CODE HAS TO BE MODIFIED")
+        stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE)
+    }else{
+        names(output$data) <- coord.names
+    }
+    if(is.null(unlist(removed.row.nb))){
+        removed.row.nb <- NULL
+        removed.rows <- NULL
+    }else{
+        for(i3 in 1:length(data1)){
+            if( ! is.null(removed.row.nb[[i3]])){
+                removed.row.nb[[i3]] <- sort(removed.row.nb[[i3]])
+                removed.rows[[i3]] <- data1.ini[[i3]][removed.row.nb[[i3]], ]
+            }
+        }
+    }
+    tempo <- output$layout$panel_params[[1]]
+    output <- list(
+        data = data1, 
+        removed.row.nb = removed.row.nb, 
+        removed.rows = removed.rows, 
+        plot = c(output$data, x.second.tick.values = list(x.second.tick.values), y.second.tick.values = list(y.second.tick.values)), 
+        panel = facet.categ, 
+        axes = list(
+            x.range = tempo$x.range, 
+            x.labels = if(is.null(attributes(tempo$x$breaks))){tempo$x$breaks}else{tempo$x$scale$get_labels()}, # is.null(attributes(tempo$x$breaks)) test if it is number (TRUE) or character (FALSE)
+            x.positions = if(is.null(attributes(tempo$x$breaks))){tempo$x$breaks}else{unlist(attributes(tempo$x$breaks))}, 
+            y.range = tempo$y.range, 
+            y.labels = if(is.null(attributes(tempo$y$breaks))){tempo$y$breaks}else{tempo$y$scale$get_labels()}, 
+            y.positions = if(is.null(attributes(tempo$y$breaks))){tempo$y$breaks}else{unlist(attributes(tempo$y$breaks))}
+        ), 
+        warn = paste0("\n", warn, "\n\n"), 
+        ggplot = if(return.ggplot == TRUE){fin.plot}else{NULL}, # fin.plot plots the graph if return == TRUE
+        gtable = if(return.gtable == TRUE){grob.save}else{NULL} #
+    )
+    return(output) # this plots the graph if return.ggplot is TRUE and if no assignment
 }
 # end output
 # end main code
diff --git a/fun_gg_boxplot.docx b/fun_gg_boxplot.docx
index e2ece13f9d6a10dd18eb33fee73de2ac25a6237a..249ad42bac9df66e5ff94db11b077cbbbc2f667a 100755
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diff --git a/fun_gg_scatter.docx b/fun_gg_scatter.docx
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