cute_little_R_functions.R 884 KB
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################################################################
##                                                            ##
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##     CUTE FUNCTIONS                                         ##
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##                                                            ##
##     Gael A. Millot                                         ##
##                                                            ##
##                                                            ##
################################################################
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# color palette: see https://github.com/EmilHvitfeldt/r-color-palettes
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# https://usethis.r-lib.org/ and usethat also
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## LAST ROUND OF FORMATTING:
# 1) Arguments: one per line
# 2) Description:
# first capital letter everywhere
# AIM
# WARNINGS
# ARGUMENTS
# Update all argument description, saying, character vector, etc, as in fun_gg_boxplot
# RETURN
# Update as in fun_gg_boxplot
# REQUIRED PACKAGES
# REQUIRED FUNCTIONS FROM THE cute PACKAGE
# EXAMPLE
# one example of the example cheet
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# see http
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# DEBUGGING
# one updated
# 3) Categ (see fun_gg_boxplot for inside code)
# function name
# must have arg.user.setting
# end function name

# required function checking
# see boxplot
# end required function checking

# reserved words (to avoid bugs)
# end reserved words (to avoid bugs)

# arg with no default values
# see boxplot
# end arg with no default values

# argument primary checking
# end argument primary checking

# second round of checking and data preparation
# management of NA arguments
# must have arg.user.setting
# end management of NA arguments

# management of NULL arguments
# 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
# 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
# output
# if(warn.print == TRUE & ! is.null(warn)){
# end output
# end main code
# 4) example sheet as in fun_gg_boxplot
# 5) test the function with debugging_tools_for_r_dev
# 6) use fun_test()
# 7) write at the beginning of the function:
# todo list check OK
# Check r_debugging_tools-v1.4.R OK
# Check fun_test() (see cute_checks.docx) OK
# clear to go Apollo
# 8) check all(, na.rm = TRUE) and any(, na.rm = TRUE)

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# fun_mat_fill does not recognize half matrix anymore
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# package: 
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# Templates: https://prettydoc.statr.me/themes.html
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# http://r-pkgs.had.co.nz/
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# https://pkgdown.r-lib.org/
# https://rdrr.io/github/gastonstat/cointoss/
# doc:https://www.sphinx-doc.org/en/master/man/sphinx-autogen.html considering that https://www.ericholscher.com/blog/2014/feb/11/sphinx-isnt-just-for-python/
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# https://docs.readthedocs.io/en/stable/intro/getting-started-with-sphinx.html
# https://docs.gitlab.com/ee/user/project/pages/
# also register into biotools
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# change everywhere: if( ! is.null(arg.check)){

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# For heatmap: see https://bioinfo-fr.net/creer-des-heatmaps-a-partir-de-grosses-matrices-en-r
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# New function: fun_pdf_conc for Rosine code?
# https://stackoverflow.com/questions/17552917/merging-existing-pdf-files-using-r
# https://www.r-bloggers.com/2019/04/join-split-and-compress-pdf-files-with-pdftools/
# https://rdrr.io/cran/staplr/man/staple_pdf.html
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################################ OUTLINE ################################
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################ Object analysis    2
######## fun_check() #### check class, type, length, etc., of objects   2
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######## fun_secu() #### verif that local variables are not present in other envs   11
######## fun_info() #### recover object information 13
######## fun_head() #### head of the left or right of big 2D objects    15
######## fun_tail() #### tail of the left or right of big 2D objects    16
######## fun_comp_1d() #### comparison of two 1D datasets (vectors, factors, 1D tables) 17
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######## fun_comp_2d() #### comparison of two 2D datasets (row & col names, dimensions, etc.)   22
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######## fun_comp_list() #### comparison of two lists   29
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######## fun_test() #### test combinations of argument values of a function and return errors (and graphs)  32
################ Object modification    47
######## fun_name_change() #### check a vector of character strings and modify any string if present in another vector  47
######## fun_df_remod() #### remodeling a data frame to have column name as a qualitative values and vice-versa 48
######## fun_round() #### rounding number if decimal present    51
######## fun_mat_rotate() #### 90° clockwise matrix rotation    53
######## fun_mat_num2color() #### convert a numeric matrix into hexadecimal color matrix    54
######## fun_mat_op() #### assemble several matrices with operation 58
######## fun_mat_inv() #### return the inverse of a square matrix   60
######## fun_mat_fill() #### fill the empty half part of a symmetric square matrix  62
######## fun_permut() #### progressively breaks a vector order  65
######## fun_slide() #### return a computation made on a vector using a sliding window  76
################ Graphics management    85
######## fun_width() #### window width depending on classes to plot 85
######## fun_open() #### open a GUI or pdf graphic window   87
######## fun_prior_plot() #### set graph param before plotting (erase axes for instance)    91
######## fun_scale() #### select nice label numbers when setting number of ticks on an axis 95
######## fun_inter_ticks() #### define coordinates of secondary ticks   100
######## fun_post_plot() #### set graph param after plotting (axes redesign for instance)   105
######## fun_close() #### close specific graphic windows    117
################ Standard graphics  118
######## fun_empty_graph() #### text to display for empty graphs    118
################ gg graphics    120
######## fun_gg_palette() #### ggplot2 default color palette    120
######## fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle  122
######## fun_gg_get_legend() #### get the legend of ggplot objects  127
######## fun_gg_point_rast() #### ggplot2 raster scatterplot layer  129
######## fun_gg_boxplot() #### ggplot2 boxplot + background dots if required    133
######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally)   133
######## fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required  133
######## fun_gg_empty_graph() #### text to display for empty graphs 141
################ Graphic extraction 143
######## fun_trim() #### display values from a quantitative variable and trim according to defined cut-offs 143
######## fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation   152
################ Import 187
######## fun_pack() #### check if R packages are present and import into the working environment    187
######## fun_python_pack() #### check if python packages are present    189
################ Print / Exporting results (text & tables)  192
######## fun_report() #### print string or data object into output file 192
######## fun_get_message() #### return error/warning/other messages of an expression (that can be exported) 195
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################################ FUNCTIONS ################################
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################ Object analysis


######## fun_check() #### check class, type, length, etc., of objects


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# todo list check OK
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# Check r_debugging_tools-v1.4.R OK
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# Check fun_test() (see cute_checks.docx) OK
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# clear to go Apollo
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fun_check <- function(
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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
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){
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# 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")
# 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 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 == 0 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 indicating all the possible option values for the data argument
# 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: only considered if set to FALSE, to check for non-negative values when class is set to "vector", "numeric", "matrix", "array", "data.frame", "table", or typeof is set to "double", "integer", or mode is set to "numeric". Ignored in other cases, notably with prop argument (which checks for values between 0 and 1 anyhow)
# print: logical. Print the error message if $problem is TRUE? Warning: set by default to FALSE, which facilitates the control of the error 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
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# 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
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# 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)){
if( ! (all(class(fun.name) == "character") & 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 ==
}
}
# end fun.name checked first because required next
# arg with no default values
if(missing(data)){
tempo.cat <- paste0("ERROR IN fun_check()", ifelse(is.null(fun.name), "", paste0(" IN ", fun.name)), ": ARGUMENT data HAS NO DEFAULT VALUE AND REQUIRES ONE")
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-v1.4/r_debugging_tools-v1.4.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 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))){
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 ARGUMENTS ARE: ", paste(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)))], 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 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){
tempo.cat <- paste0("ERROR IN fun.check():\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
# 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( ! (length(data.name) == 1 & all(class(data.name) == "character"))){
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(class(neg.values) == "logical") & length(neg.values) == 1 & any(is.na(neg.values)) != TRUE)){
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 ==
}
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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") & any(is.na(class)) != TRUE & length(class) == 1)){ # length == 1 here because of class(matrix()) since R4.0.0
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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\"")
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"))){
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 ==
}
}
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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")) & length(typeof) == 1 & any(is.na(typeof)) != TRUE)){ # "language" is the type of object of class "call"
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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\"")
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 ==
}
}
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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")) & length(mode) == 1 & any(is.na(mode)) != TRUE)){
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\", , \"language\"")
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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) & length(length) == 1 & ! grepl(length, pattern = "\\.") & any(is.na(length)) != TRUE)){
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) | (length(prop) == 1 & any(is.na(prop)) != TRUE))){
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"))){
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(class(double.as.integer.allowed) == "logical") & length(double.as.integer.allowed) == 1 & any(is.na(double.as.integer.allowed)) != TRUE)){
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) & length(all.options.in.data) == 1 & any(is.na(all.options.in.data)) != TRUE)){
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(class(na.contain) == "logical") & length(na.contain) == 1 & any(is.na(na.contain)) != TRUE)){
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(class(print) == "logical") & length(print) == 1 & any(is.na(print)) != TRUE)){
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
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text <- paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT")
if(( ! is.null(options)) & all(typeof(data) == "character")){
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text <- ""
if( ! all(data %in% options, na.rm = TRUE)){
problem <- TRUE
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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 = " "))
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}
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
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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 = " "))
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}
}
if( ! is.null(length)){
if(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 ", length(data))
}
}
if(text == ""){
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text <- paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT")
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}
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}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")
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}
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(class(data) %in% c("factor", "ordered"))){ # to deal with ordered factors
class <- c("factor", "ordered")
}
}
if(is.null(options)){
for(i2 in 1:length(arg.names)){
if( ! is.null(get(arg.names[i2], env = sys.nframe(), inherit = FALSE))){
# script to execute
tempo.script <- '
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problem <- TRUE ;
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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 ") ;
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}else{
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text <- paste0(text, " AND ") ; 
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}
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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)})
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'
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# end script to execute
if(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")))){
if( ! all(data %% 1 == 0, 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
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
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(class(data) %in% "numeric") | all(class(data) %in% "integer") | all(class(data) %in% "character") | all(class(data) %in% "logical"))){ # test class == "vector". No need of na.rm = TRUE for all because %in% does not output 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) == "ggplot2") & ! all(class(data) %in% c("gg", "ggplot"))){ # test ggplot object
eval(parse(text = tempo.script)) # execute tempo.script
}
}
}
}
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if(prop == TRUE & all(typeof(data) == "double")){
if(is.null(data) | any(data < 0 | data > 1, na.rm = TRUE)){ # works if data is NULL
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problem <- TRUE
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if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
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text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
}else{
text <- paste0(text, " AND ")
}
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text <- paste0(text, "THE ", data.name, " OBJECT MUST BE DECIMAL VALUES BETWEEN 0 AND 1")
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}
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}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")
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}
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if(all(class(data) %in% "expression")){  # no need of na.rm = TRUE for all because %in% does not output NA
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data <- as.character(data) # to evaluate the presence of NA
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}
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if(na.contain == FALSE & (mode(data) %in% c("logical", "numeric", "complex", "character", "list", "expression", "name", "symbol"))){ # before it was ! (class(data) %in% c("function", "environment"))
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if(any(is.na(data)) == TRUE){ # not on the same line because when data is class envir or function , do not like that
problem <- TRUE
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if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
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text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
}else{
text <- paste0(text, " AND ")
}
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text <- paste0(text, "THE ", data.name, " OBJECT CONTAINS NA WHILE NOT AUTHORIZED")
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}
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}
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if(neg.values == FALSE & all(typeof(data) %in% c("integer", "double"))){
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if(any(data < 0, na.rm = TRUE)){
problem <- TRUE
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if(identical(text, paste0(ifelse(is.null(fun.name), "", paste0("IN ", fun.name, ": ")), "NO PROBLEM DETECTED FOR THE ", data.name, " OBJECT"))){
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text <- paste0(ifelse(is.null(fun.name), "ERROR", paste0("ERROR IN ", fun.name)), ": ")
}else{
text <- paste0(text, " AND ")
}
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text <- paste0(text, "THE ", data.name, " OBJECT MUST BE 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 ")
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}
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text <- paste0(text, "THE ", data.name, " OBJECT MUST BE NON NEGATIVE BUT IS NOT EVEN MODE NUMERIC")
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}
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if(print == TRUE & problem == TRUE){
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cat(paste0("\n\n================\n\n", text, "\n\n================\n\n"))
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}
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# output
output <- list(problem = problem, text = text, object.name = data.name)
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return(output)
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# end output
# end main code
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}
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######## fun_secu() #### verif that local variables are not present in other envs
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fun_secu <- function(pos = 1, name = NULL){
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# AIM
# Verify that local variables are not present in other environments, in order to avoid scope preference usage. The fun_secu() function checks by default the parent environment. This means that when used inside a function, it checks the local environment of this function. When used in the Global environment, it would check this environment
# 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. Thus, if fun_secu() is used in the working environment, with pos ==1, variables of the working env will be checked if they also exist in the above envs (Scope of R). If fun_secu() is used in a function, with pos ==1, variables presents in the local env of the function will be checked if they also exist in the above envs (Scope of R, which includes the working environment (Global env))
# 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 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")) == 0){
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 ==
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}
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# 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)
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}
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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-v1.4/r_debugging_tools-v1.4.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) == 1 # 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")
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stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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}
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# 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\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 ==
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}
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# 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()) == 1, -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()) == 1, -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))]
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}
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# end dealing with source()
# might have a problem if(length(tempo.name) == 0){
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()) == 1, -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)])
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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)
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}


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######## fun_info() #### broad description of an object
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# todo list check OK
# Check r_debugging_tools-v1.4.R OK
fun_info <- function(
data, 
n = NULL, 
warn.print = TRUE
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# 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: the 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 CUTE_LITTLE_R_FUNCTION
# fun_check()
# fun_get_message()
# EXAMPLES
# fun_info(data = 1:3)
# see http
# DEBUGGING
# mat1 <- matrix(1:3) ; data = mean ; 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"
)
tempo <- NULL
for(i1 in req.function){
if(length(find(i1, mode = "function")) == 0){
tempo <- c(tempo, i1)
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if( ! is.null(tempo)){
tempo.cat <- paste0("ERROR IN ", function.name, ". REQUIRED\n", paste0(tempo, collapse = "()\n"), "()\nFUNCTION", ifelse(length(tempo) > 1, "S ARE", " 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 ==
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# end required function checking
# reserved words
# end reserved words
# arg with no default values
mandat.args <- c(
"data"
)
tempo <- eval(parse(text = paste0("missing(", paste0(mandat.args, collapse = ") | missing("), ")")))
if(any(tempo)){
tempo.cat <- paste0("ERROR IN ", function.name, ": ARGUMENT", ifelse(length(mandat.args) > 1, paste0("S\n", paste0(mandat.args, collapse = "\n")), paste0("\n", mandat.args)), "\nHAVE NO DEFAULT VALUE AND REQUIRE ONE")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
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# 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)
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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) # == in stop() to be able to add several messages between == #
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# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.4/r_debugging_tools-v1.4.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) == 1 # 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(
"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){
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
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 ==
}
# 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")){
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"))){
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 <- list("HEAD" = head(data))
output <- c(output, tempo)
tempo <- list("TAIL" = tail(data))
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]]) == 2){
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")){
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")){
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") 
tempo.class <- sapply(data, FUN = "class")
if(any(unlist(tempo.class) %in% "ordered")){
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")){
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") 
tempo.class <- sapply(data, FUN = "class")
if(any(unlist(tempo.class) %in% "ordered")){
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)){
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)
}
return(output)
# end output
# end main code
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}
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######## fun_head() #### head of the left or right of big 2D objects
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fun_head <- function(
data1, 
n = 6, 
side = "l"
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){
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# 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)
# obs1 = matrix(1:30, ncol = 5, dimnames = list(letters[1:6], LETTERS[1:5])) ; obs1 ; fun_head(obs1, 3, "right")
# DEBUGGING
# data1 = matrix(1:30, ncol = 5) # for function 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")) == 0){
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-v1.4/r_debugging_tools-v1.4.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])
}
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}
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######## fun_tail() #### tail of the left or right of big 2D objects
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fun_tail <- function(
data1, 
n = 10, 
side = "l"
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){
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# 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)
# 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) # for function 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")) == 0){
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-v1.4/r_debugging_tools-v1.4.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])
}
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}


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######## fun_comp_1d() #### comparison of two 1D datasets (vectors, factors, 1D tables)
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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: position, in data1, of the levels identical in data2 (NULL if data1 and data2 are not factors)
# $same.levels.pos2: position, in data2, of the levels identical in data1 (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.name: 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.name.pos1: position, in data1, of the element names identical in data2. NULL if no identical names
# $same.name.pos2: position, in data2, of the elements names identical in data1. NULL if no identical names
# $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.element.pos1: position, in data1, of the elements identical in data2. NULL if no identical elements
# $same.element.pos2: position, in data2, of the elements identical in data1. NULL if no identical elements
# $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-v1.4/r_debugging_tools-v1.4.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 <- NULL
same.levels.pos1 <- NULL
same.levels.pos2 <- NULL
common.levels <- NULL
same.name <- NULL # not FALSE to deal with absence of name
name <- NULL
any.id.name <- FALSE
same.name.pos1 <- NULL
same.name.pos2 <- NULL
common.names <- NULL
any.id.element <- FALSE
same.element.pos1 <- NULL
same.element.pos2 <- 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))
common.levels <- levels(data1)
}
if( ! is.null(names(data1))){
same.name <- TRUE
name <- names(data1)
any.id.name <- TRUE
same.name.pos1 <- 1:length(data1)
same.name.pos2 <- 1:length(data2)
common.names <- names(data1)
}
any.id.element <- TRUE
same.element.pos1 <- 1:length(data1)
same.element.pos2 <- 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))
}
if(any(levels(data2) %in% levels(data1))){
any.id.levels <- TRUE
same.levels.pos2 <- which(levels(data2) %in% 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.name <- TRUE
name <- names(data1)
}else{
same.name <- FALSE
}
if(any(names(data1) %in% names(data2))){
any.id.name <- TRUE
same.name.pos1 <- which(names(data1) %in% names(data2))
}
if(any(names(data2) %in% names(data1))){
any.id.name <- TRUE
same.name.pos2 <- which(names(data2) %in% names(data1))
}
if(any.id.name == TRUE){
common.names <- unique(c(names(data1)[same.name.pos1], names(data2)[same.name.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.element.pos1 <- which(data1 %in% data2)
}
if(any(data2 %in% data1)){
any.id.element <- TRUE
same.element.pos2 <- which(data2 %in% data1)
}
if(any.id.element == TRUE){
common.elements <- unique(c(data1[same.element.pos1], data2[same.element.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, common.levels = common.levels, same.name = same.name, name = name, any.id.name = any.id.name, same.name.pos1 = same.name.pos1, same.name.pos2 = same.name.pos2, common.names = common.names, any.id.element = any.id.element, same.element.pos1 = same.element.pos1, same.element.pos2 = same.element.pos2, common.elements = common.elements, same.order = same.order, order1 = order1, order2 = order2, identical.object = identical.object, identical.content = identical.content)
return(output)
}
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######## fun_comp_2d() #### comparison of two 2D datasets (row & col names, dimensions, etc.)
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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
# 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.name.pos1: position, in data1, of the row names identical in data2
# $same.row.name.pos2: position, in data2, of the row names identical in data1
# $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.name.pos1: position, in data1, of the column names identical in data2
# $same.col.name.pos2: position, in data2, of the column names identical in data1
# $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: position, 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: position, in data2, of the rows identical in data1 (not considering row names). Return "TOO BIG FOR EVALUATION" if nrow(data1) * nrow(data2) > 1e10
# $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
# $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)
# 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)
# 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)
# 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 ==
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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-v1.4/r_debugging_tools-v1.4.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.name.pos1 <- NULL
same.row.name.pos2 <- NULL
common.row.names <- NULL
same.col.name <- NULL
any.id.col.name <- NULL
same.col.name.pos1 <- NULL
same.col.name.pos2 <- NULL
common.col.names <- NULL
col.name <- NULL
any.id.row <- NULL
same.row.pos1 <- NULL
same.row.pos2 <- NULL
any.id.col <- NULL
same.col.pos1 <- NULL
same.col.pos2 <- 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.name.pos1 <- 1:row.nb
same.row.name.pos2 <- 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.name.pos1 <- 1:col.nb
same.col.name.pos2 <- 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
any.id.col <- TRUE
same.col.pos1 <- 1:col.nb
same.col.pos2 <- 1:col.nb
identical.object <- TRUE
identical.content <- TRUE
}else{
identical.object <- FALSE
if(all(class(data1) == "table") & length(dim(data1)) == 1){
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)) == 1){
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
same.col.name <- NULL
# row and col names 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
# row and col names remain NULL
}else{
if( ! identical(dimnames(data1)[[1]], dimnames(data2)[[1]])){
same.row.name <- FALSE
# row names remain NULL
}else{
same.row.name <- TRUE
row.name <- dimnames(data1)[[1]]
}
# row names
any.id.row.name <- FALSE
if(any(dimnames(data1)[[1]] %in% dimnames(data2)[[1]])){
any.id.row.name <- TRUE
same.row.name.pos1 <- which(dimnames(data1)[[1]] %in% dimnames(data2)[[1]])
}
if(any(dimnames(data2)[[1]] %in% dimnames(data1)[[1]])){
any.id.row.name <- TRUE
same.row.name.pos2 <- which(dimnames(data2)[[1]] %in% dimnames(data1)[[1]])
}
if(any.id.row.name == TRUE){
common.row.names <- unique(c(dimnames(data1)[[1]][same.row.name.pos1], dimnames(data2)[[1]][same.row.name.pos2]))
}
# col names
any.id.col.name <- FALSE
if(any(dimnames(data1)[[2]] %in% dimnames(data2)[[2]])){
any.id.col.name <- TRUE
same.col.name.pos1 <- which(dimnames(data1)[[2]] %in% dimnames(data2)[[2]])
}
if(any(dimnames(data2)[[2]] %in% dimnames(data1)[[2]])){
any.id.col.name <- TRUE
same.col.name.pos2 <- which(dimnames(data2)[[2]] %in% dimnames(data1)[[2]])
}
if(any.id.col.name == TRUE){
common.col.names <- unique(c(dimnames(data1)[[2]][same.col.name.pos1], dimnames(data2)[[2]][same.col.name.pos2]))
}
if( ! identical(dimnames(data1)[[2]], dimnames(data2)[[2]])){
same.col.name <- FALSE
# col names remain NULL
}else{
same.col.name <- TRUE
col.name <- dimnames(data1)[[2]]
}
}
# identical row and col content
if(all(class(data1) == "table")){
as.data.frame(matrix(data1, ncol = ncol(data1)), stringsAsFactors = FALSE)
}else if(all(class(data1) %in% c("matrix", "array"))){
data1 <- as.data.frame(data1, stringsAsFactors = FALSE)
}else if(all(class(data1) == "data.frame")){
data1 <- data.frame(lapply(data1, as.character), stringsAsFactors = FALSE)
}
if(all(class(data2) == "table")){
as.data.frame(matrix(data2, ncol = ncol(data2)), stringsAsFactors = FALSE)
}else if(all(class(data2) %in% c("matrix", "array"))){
data2 <- as.data.frame(data2, stringsAsFactors = FALSE)
}else if(all(class(data2) == "data.frame")){
data2 <- data.frame(lapply(data2, as.character), stringsAsFactors = FALSE)
}
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){ # as.double(nrow(data1)) to prevent integer overflow because R is 32 bits for integers
same.row.pos1 <- which(c(as.data.frame(t(data1), stringsAsFactors = FALSE)) %in% c(as.data.frame(t(data2), stringsAsFactors = FALSE))) # this work fast with only integers (because 32 bits)
same.row.pos2 <- which(c(as.data.frame(t(data2), stringsAsFactors = FALSE)) %in% c(as.data.frame(t(data1), stringsAsFactors = FALSE)))
}else if(as.double(nrow(data1)) * nrow(data2) <= 1e6){ # as.double(nrow(data1)) to prevent integer overflow because R is 32 bits for integers
same.row.pos1 <- logical(length = nrow(data1)) # FALSE by default
same.row.pos1[] <- FALSE # security
for(i3 in 1:nrow(data1)){
for(i4 in 1:nrow(data2)){
same.row.pos1[i3] <- identical(data1[i3, ], data2[i4, ])
}
}
same.row.pos1 <- which(same.row.pos1)
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same.row.pos2 <- logical(length = nrow(data2)) # FALSE by default
same.row.pos2[] <- FALSE # security
for(i3 in 1:nrow(data2)){
for(i4 in 1:nrow(data1)){
same.row.pos2[i3] <- identical(data2[i3, ], data1[i4, ])
}
}
same.row.pos2 <- which(same.row.pos2)
}else{
same.row.pos1 <- "TOO BIG FOR EVALUATION"
same.row.pos2 <- "TOO BIG FOR EVALUATION"
}
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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) == 0 & length(same.row.pos2) == 0){
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(all(sapply(data1, FUN = typeof) == "integer") & all(sapply(data2, FUN = typeof) == "integer") & as.double(ncol(data1)) * ncol(data2) <= 1e10){ # as.double(ncol(data1)) to prevent integer overflow because R is 32 bits for integers
same.col.pos1 <- which(c(data1) %in% c(data2))
same.col.pos2 <- which(c(data2) %in% c(data1))
}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
for(i3 in 1:ncol(data1)){
for(i4 in 1:ncol(data2)){
same.col.pos1[i3] <- identical(data1[ , i3], data2[ ,i4])
}
}
same.col.pos1 <- which(same.col.pos1)
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same.col.pos2 <- logical(length = ncol(data2)) # FALSE by default
same.col.pos2[] <- FALSE # security
for(i3 in 1:ncol(data2)){
for(i4 in 1:ncol(data1)){
same.col.pos2[i3] <- identical(data2[ , i3], data1[ , i4])
}
}
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) == 0 & length(same.col.pos2) == 0){
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.name.pos1 = same.row.name.pos1, same.row.name.pos2 = same.row.name.pos2, 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.name.pos1 = same.col.name.pos1, same.col.name.pos2 = same.col.name.pos2, common.col.names = common.col.names, any.id.row = any.id.row, same.row.pos1 = same.row.pos1, same.row.pos2 = same.row.pos2, any.id.col = any.id.col, same.col.pos1 = same.col.pos1, same.col.pos2 = same.col.pos2, identical.object = identical.object, identical.content = identical.content)
return(output)
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tempo    
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}
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######## fun_comp_list() #### comparison of two lists
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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.name: 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.name.pos1: position, in data1, of the element names identical in data2
# $same.name.pos2: position, in data2, of the compartment names identical in data1
# $any.id.compartment: logical. is there any identical compartments ?
# $same.compartment.pos1: position, in data1, of the compartments identical in data2
# $same.compartment.pos2: position, 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-v1.4/r_debugging_tools-v1.4.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.name <- NULL
name <- NULL
any.id.name <- NULL
same.name.pos1 <- NULL
same.name.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.name <- TRUE
name <- names(data1)
any.id.name <- TRUE
same.name.pos1 <- 1:length(data1)
same.name.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.name <- FALSE
}else{
same.name <- TRUE
name <- names(data1)
}
any.id.name <- FALSE
if(any(names(data1) %in% names(data2))){
any.id.name <- TRUE
same.name.pos1 <- which(names(data1) %in% names(data2))
}
if(any(names(data2) %in% names(data1))){
any.id.name <- TRUE
same.name.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.name = same.name, name = name, any.id.name = any.id.name, same.name.pos1 = same.name.pos1, same.name.pos2 = same.name.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, 
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)
# 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
# thread.nb: numeric value indicating the number of available threads. Write NULL if no parallelization wanted
# 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 thread.nb is not NULL. 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 thread.nb is not NULL 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. Not considered if thread.nb is NULL
# REQUIRED PACKAGES
# lubridate
# parallel if thread.nb argument is not NULL (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
# $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
# $instruction: the initial instruction
# $sys.info: system and packages info
# 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)), 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)), 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"), 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))), 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)) ; 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 ; 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 ; 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 ; thread.nb = NULL ; plot.fun = TRUE ; export = TRUE ; res.path = "C:\\Users\\Gael\\Desktop\\" ; lib.path = NULL # for function debugging
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# fun = "unique" ; arg = "x" ; val = list(list(1:3, mean)) ; expect.error = NULL ; 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
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# function name
function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
instruction <- match.call()
# end function name
# required function checking
req.function <- c(
"fun_check", 
"fun_get_message", 
"fun_pack"
)
for(i1 in req.function){
if(length(find(i1, mode = "function")) == 0){
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
if(any(missing(fun) | missing(arg) | missing(val))){
tempo.cat <- paste0("ERROR IN ", function.name, ": ARGUMENTS fun, arg AND val HAVE NO DEFAULT VALUE AND REQUIRE ONE")
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 = fun, class = "vector", mode = "character", length = 1, fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
if(grepl(x = fun, pattern = "()$")){ # remove ()
fun <- sub(x = fun, pattern = "()$", replacement = "")
}
if( ! exists(fun)){
tempo.cat <- paste0("ERROR IN ", function.name, ": CHARACTER STRING IN fun ARGUMENT DOES NOT EXIST IN THE R WORKING ENVIRONMENT: ", paste(fun, collapse = "\n"))
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}else if( ! all(class(get(fun)) == "function")){ # here no env = sys.nframe(), inherit = FALSE for get() because fun is a function in the classical scope
tempo.cat <- paste0("ERROR IN ", function.name, ": fun ARGUMENT IS NOT CLASS \"function\" BUT: ", paste(class(get(fun)), collapse = "\n"), "\nCHECK IF ANY CREATED OBJECT WOULD HAVE THE NAME OF THE TESTED FUNCTION")
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
tempo <- fun_check(data = arg, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE & length(arg) == 0){
tempo.cat <- paste0("ERROR IN ", function.name, ": arg ARGUMENT CANNOT BE LENGTH 0")
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
tempo <- fun_check(data = val, class = "list", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
for(i2 in 1:length(val)){
tempo1 <- fun_check(data = val[[i2]], class = "vector", na.contain = TRUE, fun.name = function.name)
tempo2 <- fun_check(data = val[[i2]], class = "list", na.contain = TRUE, fun.name = function.name)
if(tempo1$problem == TRUE & tempo2$problem == TRUE){
tempo.cat <- paste0("ERROR IN ", function.name, ": COMPARTMENT ", i2, " OF val ARGUMENT MUST BE A VECTOR OR A LIST")
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}else if(tempo1$problem == FALSE){ # vector split into list compartments
val[[i2]] <- split(x = val[[i2]], f = 1:length(val[[i2]]))
}
}
}
if( ! is.null(expect.error)){
tempo <- fun_check(data = expect.error, class = "list", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
for(i3 in 1:length(expect.error)){
tempo1 <- fun_check(data = expect.error[[i3]], class = "vector",  mode = "logical", fun.name = function.name)
tempo2 <- fun_check(data =  expect.error[[i3]], class = "list", fun.name = function.name)
if(tempo1$problem == TRUE & tempo2$problem == TRUE){
tempo.cat <- paste0("ERROR IN ", function.name, ": COMPARTMENT ", i3, " OF expect.error ARGUMENT MUST BE TRUE OR FALSE")
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}else if(tempo1$problem == FALSE){ # vector split into list compartments
expect.error[[i3]] <- split(x = expect.error[[i3]], f = 1:length(expect.error[[i3]]))
}
}
}
}
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$problem == FALSE & thread.nb < 1){
tempo.cat <- paste0("ERROR IN ", function.name, ": thread.nb PARAMETER MUST EQUAL OR GREATER THAN 1: ", thread.nb)
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
tempo <- fun_check(data = print.count, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = plot.fun, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = export, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
if( ! is.null(res.path)){
tempo <- fun_check(data = res.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
if( ! all(dir.exists(res.path))){ # separation to avoid the problem of tempo$problem == FALSE and res.path == NA
tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE res.path ARGUMENT DOES NOT EXISTS:\n", paste(res.path, collapse = "\n"))
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
}
if( ! is.null(lib.path)){
tempo <- fun_check(data = lib.path, class = "vector", mode = "character", fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
if( ! all(dir.exists(lib.path))){ # separation to avoid the problem of tempo$problem == FALSE and lib.path == NA
tempo.cat <- paste0("ERROR IN ", function.name, ": DIRECTORY PATH INDICATED IN THE lib.path ARGUMENT DOES NOT EXISTS:\n", paste(lib.path, collapse = "\n"))
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
}
}
if( ! is.null(thread.nb)){
tempo <- fun_check(data = cute.path, class = "vector", typeof = "character", length = 1, fun.name = function.name) ; eval(ee)
if(tempo$problem == FALSE){
if( ! file.exists(cute.path)){
tempo.cat <- paste0("ERROR IN ", function.name, ": 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)
}
}
}
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-v1.4/r_debugging_tools-v1.4.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(fun)) | any(is.na(arg)) | any(is.na(expect.error)) | any(is.na(thread.nb)) | any(is.na(print.count)) | any(is.na(plot.fun)) | any(is.na(export)) | any(is.na(res.path)) | any(is.na(lib.path))){
tempo.cat <- paste0("ERROR IN ", function.name, ": NO ARGUMENT EXCEPT val 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(fun) | is.null(arg) | is.null(val) | is.null(print.count) | is.null(plot.fun) | is.null(export)){
tempo.cat <- paste0("ERROR IN ", function.name, ": THESE ARGUMENTS\nfun\narg\nval\nprint.count\nplot.fun\nexport\nCANNOT BE NULL") #problematic arguments are -> put everywhere
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(length(arg) != length(val)){
tempo.cat <- paste0("ERROR IN ", function.name, ": LENGTH OF arg ARGUMENT MUST BE IDENTICAL TO LENGTH OF val ARGUMENT:\nHERE IT IS: ", length(arg), " VERSUS ", 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(length(val) != 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: ", length(val), " VERSUS ", length(expect.error))
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE)
}
}
if( ! is.null(thread.nb) & is.null(res.path)){
tempo.cat <- paste0("ERROR IN ", function.name, ": res.path ARGUMENT MUST BE SPECIFIED IF thread.nb ARGUMENT IS NOT NULL")
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( ! is.null(thread.nb) & 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)
}
# end second round of checking and data preparation
# package checking
fun_pack(req.package = c("lubridate"), lib.path = lib.path)
if( ! is.null(thread.nb)){
fun_pack(req.package = c("parallel"), 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 <- options()$warning.length
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:length(arg)){
if(is.null(thread.nb)){
if(length(val[[i1]]) > 1){ # loop only if more than one value in length(val[[i1]])
loop.string <- paste0(loop.string, "for(i", i1, " in 1:", 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 == 1, "", ", "), 
arg[i1], 
" = val[[", 
i1, 
"]][[", 
if(is.null(thread.nb)){
if(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 == 1, "", ", "), 
arg[i1], 
" = val[[", 
i1, 
"]][[', ", 
if(is.null(thread.nb)){
if(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(is.null(thread.nb)){
if(length(val[[i1]]) > 1){
paste0("i", i1)
}else{
"1" # a unique element in val[[i1]]
}
}else{
paste0("i.list[[", i1, "]][i]")
}, 
"]]", 
ifelse(i1 == length(arg), "", ", ")
)
error.values <- paste0(
error.values, 
ifelse(i1 == 1, "", " | "), 
"expect.error[[", i1, "]][[", 
if(is.null(thread.nb)){
if(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(length(arg) == 1){
data <- data.frame()
}else{ # length(arg) == 0 already tested above
data <- data.frame(t(vector("character", length(arg))), stringsAsFactors = FALSE)[-1, ] # -1 to remove the single row created and to have an empty data frame with length(arg) columns
}
code <- paste(
loop.string, '
count <- count + 1
print.count.loop <- print.count.loop + 1
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arg.values.print <- eval(parse(text = arg.values)) # recover the list of the i1 compartment
for(i3 in 1:length(arg.values.print)){
tempo.error <- fun_get_message(data =  paste0("paste(arg.values.print[[", i3, "]])"), 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[[i3]] <- paste0("SPECIAL VALUE OF CLASS ", class(arg.values.print[[i3]]), " AND TYPE ", typeof(arg.values.print[[i3]]))
}
}
data <- rbind(data, as.character(sapply(arg.values.print, FUN = "paste", collapse = " ")), stringsAsFactors = FALSE) # each colum is a test
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