cute_little_R_functions.R 585 KB
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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-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# main code
ini <- NULL
post <- NULL
if(any(data1 %in% data2)){
tempo.names <- data1[data1 %in% data2]
ini <- NULL
post <- NULL
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for(i2 in 1:length(tempo.names)){
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count <- 0
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tempo <- tempo.names[i2]
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while(any(tempo %in% data2) | any(tempo %in% data1)){
count <- count + 1
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tempo <- paste0(tempo.names[i2], "_modif", count)
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}
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data1[data1 %in% tempo.names[i2]] <- paste0(tempo.names[i2], "_modif", count)
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if(count != 0){
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ini <- c(ini, tempo.names[i2])
post <- c(post, paste0(tempo.names[i2], "_modif", count))
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}
}
data <- data1
}else{
data <- data1
}
output <- list(data = data, ini = ini, post = post)
return(output)
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}


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######## fun_df_remod() #### remodeling a data frame to have column name as a qualitative values and vice-versa
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# Check OK: clear to go Apollo
fun_df_remod <- function(data, quanti.col.name = "quanti", quali.col.name = "quali"){
# AIM
# if the data frame is made of numeric columns, a new data frame is created, with the 1st column gathering all the numeric values, and the 2nd column being the name of the columns of the initial data frame. If row names were present in the initial data frame, then a new ini_rowname column is added with the names of the rows
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# If the data frame is made of one numeric column and one character or factor column, a new data frame is created, with the new columns corresponding to the split numeric values (according to the character column). NA are added a the end of each column to have the same number of rows. BEWARE: in such data frame, rows are not individuals. This means that in the example below, values 10 and 20 are associated on the same row but that means nothing in term of association
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# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# ARGUMENTS
# data: data frame to convert
# quanti.col.name: optional name for the quanti column of the new data frame
# quali.col.name: optional name for the quali column of the new data frame
# RETURN
# the modified data frame
# EXAMPLES
# obs <- data.frame(col1 = (1:4)*10, col2 = c("A", "B", "A", "A")) ; obs ; fun_df_remod(obs)
# obs <- data.frame(col1 = (1:4)*10, col2 = 5:8) ; obs ; fun_df_remod(obs, quanti.col.name = "quanti", quali.col.name = "quali")
# obs <- data.frame(col1 = (1:4)*10, col2 = 5:8) ; rownames(obs) <- paste0("row", 1:4) ; obs ; fun_df_remod(obs, quanti.col.name = "quanti", quali.col.name = "quali")
# DEBUGGING
# data = data.frame(a = 1:3, b = 4:6) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
# data = data.frame(a = 1:3, b = 4:6, c = 11:13) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
# data = data.frame(a = 1:3, b = letters[1:3]) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
# data = data.frame(a = 1:3, b = letters[1:3]) ; quanti.col.name = "TEST" ; quali.col.name = "quali" # for function debugging
# data = data.frame(b = letters[1:3], a = 1:3) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
# data = data.frame(b = c("e", "e", "h"), a = 1:3) ; quanti.col.name = "quanti" ; quali.col.name = "quali" # for function debugging
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end required function checking
# argument checking
# argument checking without fun_check()
if( ! any(class(data) %in% "data.frame")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THE data ARGUMENT MUST BE A DATA FRAME\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end argument checking without fun_check()
# argument checking with fun_check()
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = quanti.col.name, class = "character", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = quali.col.name, class = "character", length = 1, fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# end argument checking with fun_check()
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# main code
tempo.factor <- unlist(lapply(data, class))
for(i in 1:length(tempo.factor)){ # convert factor columns as character
if(all(tempo.factor[i] == "factor")){
data[, i] <- as.character(data[, i])
}
}
tempo.factor <- unlist(lapply(data, mode))
if(length(data) == 2){
if( ! ((mode(data[, 1]) == "character" & mode(data[, 2]) == "numeric") | mode(data[, 2]) == "character" & mode(data[, 1]) == "numeric" | mode(data[, 2]) == "numeric" & mode(data[, 1]) == "numeric") ){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": IF data ARGUMENT IS A DATA FRAME MADE OF 2 COLUMNS, EITHER A COLUMN MUST BE NUMERIC AND THE OTHER CHARACTER, OR THE TWO COLUMNS MUST BE NUMERIC\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if((mode(data[, 1]) == "character" | mode(data[, 2]) == "character") & (quanti.col.name != "quanti" | quali.col.name != "quali")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": IMPROPER quanti.col.name OR quali.col.name RESETTINGS. THESE ARGUMENTS ARE RESERVED FOR DATA FRAMES MADE OF n NUMERIC COLUMNS ONLY\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
}else{
if( ! all(tempo.factor %in% "numeric")){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": IF data ARGUMENT IS A DATA FRAME MADE OF ONE COLUMN, OR MORE THAN 2 COLUMNS, THESE COLUMNS MUST BE NUMERIC\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
}
if(( ! any(tempo.factor %in% "character")) & is.null(names(data))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": NUMERIC DATA FRAME in the data ARGUMENT MUST HAVE COLUMN NAMES\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if(all(tempo.factor %in% "numeric")){ # transfo 1
quanti <- NULL
for(i in 1:length(data)){
quanti <-c(quanti, data[, i])
}
quali <- rep(names(data), each = nrow(data))
output.data <- data.frame(quanti, quali)
names(output.data) <- c(quanti.col.name, quali.col.name)
# add the ini_rowname column
ini.rownames <- rownames(data)
tempo.data <- data
rownames(tempo.data) <- NULL
null.rownames <- (tempo.data)
if( ! identical(ini.rownames, null.rownames)){
ini_rowname <- rep(ini.rownames, times = ncol(data))
output.data <- cbind(output.data, ini_rowname)
}
}else{ # transfo 2
if(class(data[, 1]) == "character"){
data <- cbind(data[2], data[1])
}
nc.max <- max(table(data[, 2])) # effectif maximum des classes
nb.na <- nc.max - table(data[,2]) # nombre de NA à ajouter pour réaliser la data frame
tempo<-split(data[, 1], data[, 2])
for(i in 1:length(tempo)){tempo[[i]] <- append(tempo[[i]], rep(NA, nb.na[i]))} # des NA doivent être ajoutés lorsque les effectifs sont différents entre les classes. C'est uniquement pour que chaque colonne ait le même nombre de lignes
output.data<-data.frame(tempo)
}
return(output.data)
}


######## fun_merge() #### merge the columns of two 2D objects, by common rows


fun_merge <- function(data1, data2, name1, name2, factor.as = "numeric", warn.print = FALSE){
# AIM
# merge the columns of 2 data frames or 2 matrices or 2 tables, by associating the rows according to 1 or several common colums that must be strictly similar between the 2 objects
# contrary to the classical merge() function of R, fun_merge() orders the rows of the 2 objects according to the common columns, and merge only and only if the ordered common columns are strictly identical. Otherwise return an error
# keep row names of data1 in the merged object if they exist. Do not consider row names of data2
# keep the intial row order of data1 after merging
# BEWARE:
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# see: https://stackoverflow.com/questions/1299871/how-to-join-merge-data-frames-inner-outer-left-right
# see: https://en.wikipedia.org/wiki/Join_(SQL) and the french version
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# REQUIRED PACKAGES
# none
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_comp_2d()
# fun_check()
# ARGUMENTS
# data1: matrix or data frame or table
# data2: same class of object as data1 (data frame for data1 data frame, matrix for data1 matrix and table for data1 table) with same number of rows as in data1
# name1: either a vector of character strings or a vector of integer. If character strings, they must be the name of the columns in data1 that are common to the columns in data2. If integers, they must be the column numbers in data1 that are common to column numbers in data2. name1 can be strings and name2 (below) integers, and vice-versa. BEWARE: order of the elements in data1 are important as ordering is according to the first element, then the second, etc.
# name2: as in name1 but for data2. Order in name2 is not important as order in name1 is used for the ordering
# factor.as: either "numeric" (sort factors according to levels order, i.e., class number) or "character" (sort factors according to alphabetical order)
# warn.print: logical. Print warnings at the end of the execution? No print if no warning messages
# RETURN
# a list containing:
# $data: the merged data frame or matrix or table
# $warn: the warning messages. Use cat() for proper display. NULL if no warning
# EXAMPLES
# obs1 = matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5])) ; obs2 = as.data.frame(matrix(1:10, ncol = 5, dimnames = list(letters[1:2], LETTERS[1:5]))) ; obs1 ; obs2 ; fun_comp_2d(obs1, obs2)
# DEBUGGING
# data1 = matrix(1.0001:21, ncol = 4) ; dimnames(data1) <- list(LETTERS[1:5], letters[1:4]); data2 = matrix(1.0001:31, ncol = 6) ; dimnames(data2) <- list(NULL, c("a", "aa", "c", "d", "aaa", "aaaa")) ; set.seed(1) ; data2[, "c"] <- sample(data2[, "c"]) ; data2[, "d"] <- sample(data2[, "d"]) ; set.seed(NULL) ; data1 ; data2 ; name1 = c("c", "d") ; name2 = c("d", "c") ; factor.as = "numeric" # for function debugging
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end required function checking
# argument checking using fun_check()
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo1 <- fun_check(data = data1, class = "matrix", print = FALSE)
tempo2 <- fun_check(data = data1, class = "data.frame", print = FALSE)
tempo3 <- fun_check(data = data1, class = "table", print = FALSE)
if(tempo1$problem == TRUE & tempo2$problem == TRUE & tempo3$problem == TRUE){
tempo.cat <- paste0("ERROR IN ", function.name, ":\ndata1 ARGUMENT MUST BE A 2D OBJECT (MATRIX, DATA FRAME OR TABLE)\nHERE IT IS: ", paste(class(data1), collapse = " ")) #
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
tempo1 <- fun_check(data = data2, class = "matrix", print = FALSE)
tempo2 <- fun_check(data = data2, class = "data.frame", print = FALSE)
tempo3 <- fun_check(data = data2, class = "table", print = FALSE)
if(tempo1$problem == TRUE & tempo2$problem == TRUE & tempo3$problem == TRUE){
tempo.cat <- paste0("ERROR IN ", function.name, ":\ndata2 ARGUMENT MUST BE A 2D OBJECT (MATRIX, DATA FRAME OR TABLE)\nHERE IT IS: ", paste(class(data2), collapse = " ")) #
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
if( ! identical(class(data1), class(data2))){
tempo.cat <- paste0("ERROR IN ", function.name, ":\ndata1 and data2 ARGUMENTS MUST BE A 2D OBJECT (MATRIX, DATA FRAME OR TABLE) OF SAME CLASS\nHERE IT IS RESPECTIVELY: ", paste(class(data1), collapse = " "), " AND ", paste(class(data2), collapse = " ")) #
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
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tempo1 <- fun_check(data = name1, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, print = FALSE)
tempo2 <- fun_check(data = name1, class = "vector", typeof = "character", print = FALSE)
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if(tempo1$problem == TRUE & tempo2$problem == TRUE){
tempo.cat <- paste0("ERROR IN ", function.name, ":\nname1 ARGUMENT MUST BE A UNIQUE CHARACTER STRING OR INTEGER\nHERE IT IS: ", paste(name1, collapse = " ")) #
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
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tempo1 <- fun_check(data = name2, class = "vector", typeof = "integer", double.as.integer.allowed = TRUE, print = FALSE)
tempo2 <- fun_check(data = name2, class = "vector", typeof = "character", print = FALSE)
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if(tempo1$problem == TRUE & tempo2$problem == TRUE){
tempo.cat <- paste0("ERROR IN ", function.name, ":\nname2 ARGUMENT MUST BE A UNIQUE CHARACTER STRING OR INTEGER\nHERE IT IS: ", paste(name2, collapse = " ")) #
text.check <- c(text.check, tempo.cat)
arg.check <- c(arg.check, TRUE)
}
tempo <- fun_check(data = factor.as, options = c("numeric", "character"), length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = warn.print, class = "vector", mode = "logical", length = 1, fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.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 using fun_check()
# other argument checking
# column existence
if(mode(name1) == "character"){
if( ! all(name1 %in% colnames(data1))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ":\nTHE CHARACTER STRINGS IN name1 ARGUMENT ARE NOT ALL COLUMN NAMES OF data1:\n", paste(name1, collapse = " "), "\n", colnames(data1), "\n\n================\n\n") #
stop(tempo.cat, call. = FALSE)
}
}else if(mode(name1) == "numeric"){
if( ! all((name1 > ncol(data1) & name1 <= 0))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ":\nINTEGERS IN name1 ARGUMENT ARE NOT ALL COLUMN NUMBERS OF data1:\n", paste(name1, collapse = " "), "\n1:", ncol(data1), "\n\n================\n\n") #
stop(tempo.cat, call. = FALSE)
}
}else{
tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 1\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}
if(mode(name2) == "character"){
if( ! all(name2 %in% colnames(data2))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ":\nTHE CHARACTER STRINGS IN name2 ARGUMENT ARE NOT ALL COLUMN NAMES OF data2:\n", paste(name2, collapse = " "), "\n", colnames(data2), "\n\n================\n\n") #
stop(tempo.cat, call. = FALSE)
}
}else if(mode(name2) == "numeric"){
if( ! all((name2 > ncol(data2) & name2 <= 0))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ":\nINTEGERS IN name2 ARGUMENT ARE NOT ALL COLUMN NUMBERS OF data2:\n", paste(name2, collapse = " "), "\n1:", ncol(data2), "\n\n================\n\n") #
stop(tempo.cat, call. = FALSE)
}
}else{
tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ": CODE INCONSISTENCY 2\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}
if(length(name1) != length(name2)){
tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ":\nLENGTH OF name1 ARGUMENT (", length(name1), ") IS NOT THE SAME AS LENGTH OF name2 ARGUMENT (", length(name2), "):\n", paste(name1, collapse = " "), "\n", paste(name2, collapse = " "), "\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}
# end column existence
# end other argument checking
# main code
# definition of set1 and set2: common columns
set1 <- data1[, name1, drop = FALSE] # set1 will be the reference for merging, drop = FALSE to keep the 2D structure
if(any(apply(set1, 2, FUN = "%in%", "factor"))){
if(factor.as == "numeric"){
set1[, apply(set1, 2, FUN = "%in%", "factor")] <- as.numeric(set1[, apply(set1, 2, FUN = "%in%", "factor")])
}
}
set2 <- data2[, name2, drop = FALSE] # set2 will be the reference for merging, drop = FALSE to keep the 2D structure
if(any(apply(set2, 2, FUN = "%in%", "factor"))){
if(factor.as == "numeric"){
set2[, apply(set2, 2, FUN = "%in%", "factor")] <- as.numeric(set2[, apply(set2, 2, FUN = "%in%", "factor")])
}
}
# end definition of set1 and set2: common columns
# conversion as character to avoid floating point problems
options.ini <- options()$digits
options(digits = 22)
set1 <- as.matrix(set1)
set2 <- as.matrix(set2)
mode(set1) <- "character"
mode(set2) <- "character"
options(digits = options.ini)
# end conversion as character to avoid floating point problems
# recovering initial order of set1
ini.set1.order <- eval(parse(text = paste("order(", paste("set1[, ", 1:ncol(set1), "]", sep = "", collapse = ", "), ")")))
set1 <- set1[ini.set1.order, ]
ini.set2.order <- eval(parse(text = paste("order(", paste("set2[, ", 1:ncol(set2), "]", sep = "", collapse = ", "), ")")))
set2 <- set2[ini.set2.order, ]
# end recovering initial order of set1
# check non identical columns
if(length(name1) > 1){
for(i2 in 1:(length(name1) - 1)){
for(i3 in (i2 + 1):length(name1)){
if(identical(set1[, i2], set1[, i3])){
tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ":\nCOLUMN ", i2, " OF data1 CORRESPONDING TO ELEMENT ", name1[i2], " OF name1 ARGUMENT IS IDENTICAL TO COLUMN ", i3, " OF data1 CORRESPONDING TO ELEMENT ", name1[i3], " OF name1 ARGUMENT\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}
}
}
}
if(length(name2) > 1){
for(i2 in 1:(length(name2) - 1)){
for(i3 in (i2 + 1):length(name2)){
if(identical(set2[, i2], set2[, i3])){
tempo.cat <- paste0("\n\n============\n\nERROR IN ", function.name, ":\nCOLUMN ", i2, " OF data2 CORRESPONDING TO ELEMENT ", name2[i2], " OF name2 ARGUMENT IS IDENTICAL TO COLUMN ", i3, " OF data2 CORRESPONDING TO ELEMENT ", name2[i3], " OF name2 ARGUMENT\n\n============\n\n")
stop(tempo.cat, call. = FALSE)
}
}
}
}
# end check non identical columns
# warning duplicates
# repositioning of the column in set2 as in set1 by comparing the two sorted column
#deal with identical col names when merging -> .x for data1, .y for data2


if(warn.print == TRUE & ! is.null(warn)){
Gael  MILLOT's avatar
Gael MILLOT committed
2335
warning(warn, call. = FALSE)
Gael  MILLOT's avatar
Gael MILLOT committed
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}
# output <- list()
return(output)
}


######## fun_round() #### rounding number if decimal present


# Check OK: clear to go Apollo
fun_round <- function(data, dec.nb = 2, after.lead.zero = TRUE){
# AIM
# round a vector of values, if decimal, with the desired number of decimal digits after the decimal leading zeros
# WARNINGS
# Work well with numbers as character strings, but not always with numerical numbers because of the floating point
# Numeric values are really truncated from a part of their decimal digits, whatever options(digits) settings
# See ?.Machine or https://stackoverflow.com/questions/5173692/how-to-return-number-of-decimal-places-in-r, with the interexting formula: abs(x - round(x)) > .Machine$double.eps^0.5
# ARGUMENTS
# data: a vector of numbers (numeric or character mode)
# dec.nb: number of required decimal digits
# after.lead.zero: logical. If FALSE, rounding is performed for all the decimal numbers, whatever the leading zeros (e.g., 0.123 -> 0.12 and 0.00128 -> 0.00). If TRUE, dec.nb are taken after the leading zeros (e.g., 0.123 -> 0.12 and 0.00128 -> 0.0013)
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# RETURN
# the modified vector
# EXAMPLES
# ini.options <- options()$digits ; options(digits = 8) ; cat(fun_round(data = c(NA, 10, 100.001, 333.0001254, 12312.1235), dec.nb = 2, after.lead.zero = FALSE), "\n\n") ; options(digits = ini.options)
# ini.options <- options()$digits ; options(digits = 8) ; cat(fun_round(data = c(NA, 10, 100.001, 333.0001254, 12312.1235), dec.nb = 2, after.lead.zero = TRUE), "\n\n") ; options(digits = ini.options)
# ini.options <- options()$digits ; options(digits = 8) ; cat(fun_round(data = c(NA, "10", "100.001", "333.0001254", "12312.1235"), dec.nb = 2, after.lead.zero = FALSE), "\n\n") ; options(digits = ini.options)
# ini.options <- options()$digits ; options(digits = 8) ; cat(fun_round(data = c(NA, "10", "100.001", "333.0001254", "12312.1235"), dec.nb = 2, after.lead.zero = TRUE), "\n\n") ; options(digits = ini.options)
# DEBUGGING
# data = data = c(10, 100.001, 333.0001254, 12312.1235) ; dec.nb = 2 ; after.lead.zero = FALSE # # for function debugging
# data = data = c("10", "100.001", "333.0001254", "12312.1235") ; dec.nb = 2 ; after.lead.zero = TRUE # # for function debugging
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end required function checking
# argument checking
# argument checking without fun_check()
if( ! (all(typeof(data) == "character") | all(typeof(data) == "double") | all(typeof(data) == "integer"))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": data ARGUMENT MUST BE A VECTOR OF NUMBERS (IN NUMERIC OR CHARACTER MODE)\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end argument checking without fun_check()
# argument checking with fun_check()
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = data, class = "vector", na.contain = TRUE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = dec.nb, class = "vector", typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = after.lead.zero, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# end argument checking with fun_check()
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# main code
tempo <- grepl(x = data, pattern = "\\.") # detection of decimal numbers
ini.mode <- mode(data)
data <- as.character(data) # to really truncate decimal digits
for(i in 1:length(data)){ # scan all the numbers of the vector
if(tempo[i] == TRUE){ # means decimal number
if(after.lead.zero == TRUE){
zero.pos <- unlist(gregexpr(text=data[i], pattern = 0)) # recover all the position of the zeros in the number. -1 if no zeros (do not record the leading and trailing zeros)
}else{
zero.pos <- -1 # -1 as if no zero
}
dot.pos <- unlist(gregexpr(text=data[i], pattern = "\\.")) # recover all the position of the zeros in the number
digit.pos <- unlist(gregexpr(text=data[i], pattern = "[[:digit:]]")) # recover all the position of the digits in the number
dec.pos <- digit.pos[digit.pos > dot.pos]
count <- 0
while((dot.pos + count + 1) %in% zero.pos & (dot.pos + count + 1) <= max(dec.pos) & (count + dec.nb) < length(dec.pos)){ # count the number of leading zeros in the decimal part
count <- count + 1
}
data[i] <- formatC(as.numeric(data[i]), digits = (count + dec.nb), format = "f")
}
}
if(ini.mode != "character"){
data <- as.numeric(data)
}
return(data)
}


######## fun_mat_rotate() #### 90° clockwise matrix rotation


# Check OK: clear to go Apollo
fun_mat_rotate <- function(data){
# AIM
# 90° clockwise matrix rotation
# applied twice, the function provide the mirror matrix, according to vertical and horizontal symmetry
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# ARGUMENTS
# data: matrix (matrix class)
# RETURN
# the modified matrix
# EXAMPLES
# obs <- matrix(1:10, ncol = 1) ; obs ; fun_mat_rotate(obs)
# obs <- matrix(LETTERS[1:10], ncol = 5) ; obs ; fun_mat_rotate(obs)
# DEBUGGING
# data = matrix(1:10, ncol = 1)
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# 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$fun.name))
tempo <- fun_check(data = data, class = "matrix", fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# main code
for (i in 1:ncol(data)){data[,i] <- rev(data[,i])}
data <- t(data)
return(data)
}


######## fun_mat_num2color() #### convert a numeric matrix into hexadecimal color matrix


# Check OK: clear to go Apollo
fun_mat_num2color <- function(mat1, mat.hsv.h = TRUE, notch = 1, s = 1, v = 1, forced.color = NULL){
# AIM
# convert a matrix made of numbers into a hexadecimal matrix for rgb colorization
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# ARGUMENTS:
# mat1: matrix 1 of non negative numerical values that has to be colored (matrix class). NA allowed
# mat.hsv.h: logical. Is mat1 the h of hsv colors ? (if TRUE, mat1 must be between zero and 1)
# notch: single value between 0 and 1 to shift the successive colors on the hsv circle by + notch
# s: s argument of hsv(). Must be between 0 and 1
# v: v argument of hsv(). Must be between 0 and 1
# forced.color: Must be NULL or hexadecimal color code or name given by colors(). The first minimal values of mat1 will be these colors. All the color of mat1 can be forced using this argument
# RETURN
# a list containing:
# $mat1.name: name of mat1
# $colored.mat: colors of mat1 in hexa
# $problem: logical. Is any colors of forced.color overlap the colors designed by the function. NULL if forced.color = NULL
# $text.problem: text when overlapping colors. NULL if forced.color = NULL or problem == FALSE
# EXAMPLES
# mat1 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; dimnames(mat1) <- list(LETTERS[1:4], letters[1:2]) ; fun_mat_num2color(mat1, mat.hsv.h = FALSE, notch = 1, s = 1, v = 1, forced.color = NULL)
# DEBUGGING
# mat1 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; dimnames(mat1) <- list(LETTERS[1:4], letters[1:2]); mat.hsv.h = FALSE ; notch = 1 ; s = 1 ; v = 1 ; forced.color = c(hsv(1,1,1), hsv(0,0,0)) # for function debugging
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end required function checking
# argument checking
# argument checking with fun_check()
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = mat1, mode = "numeric", class = "matrix", na.contain = TRUE, neg.values = FALSE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = mat.hsv.h, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = notch, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = s, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = v, class = "vector", mode = "numeric", length = 1, prop = TRUE, fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# end argument checking with fun_check()
# argument checking without fun_check()
if(mat.hsv.h == TRUE & fun_check(data = mat1, mode = "numeric", prop = TRUE, print = FALSE)$problem == TRUE){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": mat1 ARGUMENT MUST BE A MATRIX OF PROPORTIONS SINCE THE mat.hsv.h ARGUMENT IS SET TO TRUE\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if( ! is.null(forced.color)){
tempo <- fun_check(data = forced.color, class = "character")
if(any(tempo$problem == TRUE)){
paste0("\n\n================\n\n", paste(tempo$text[tempo$problem], collapse = "\n"), "\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if( ! all(forced.color %in% colors() | grepl(pattern = "^#", forced.color))){ # check that all strings of forced.color start by #
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": forced.color ARGUMENT MUST BE A HEXADECIMAL COLOR VECTOR STARTING BY # AND/OR COLOR NAMES GIVEN BY colors()\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
}
# end argument checking without fun_check()
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# main code
problem <- NULL
text.problem <- NULL
mat1.name <- deparse(substitute(mat1))
# change the scale of the plotted matrix
if(mat.hsv.h == TRUE){
if(any(min(mat1, na.rm = TRUE) < 0 | max(mat1, na.rm = TRUE) > 1, na.rm = TRUE)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": mat1 MUST BE MADE OF VALUES BETWEEN 0 AND 1 BECAUSE mat.hsv.h ARGUMENT SET TO TRUE\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
}else{
if(any(mat1 - floor(mat1) > 0, na.rm = TRUE) | any(mat1 == 0, na.rm = TRUE)){ # no need of isTRUE(all.equal()) because we do not require approx here but strictly 0, thus == is ok
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": mat1 MUST BE MADE OF INTEGER VALUES WITHOUT 0 BECAUSE mat.hsv.h ARGUMENT SET TO FALSE\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}else{
mat1 <- mat1 / max(mat1, na.rm = TRUE)
}
}
if(notch != 1){
different.color <- unique(as.vector(mat1))
different.color <- different.color[ ! is.na(different.color)]
tempo.different.color <- different.color + c(0, cumsum(rep(notch, length(different.color) - 1)))
tempo.different.color <- tempo.different.color - floor(tempo.different.color)
if(any(duplicated(tempo.different.color) == TRUE)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": DUPLICATED VALUES AFTER USING notch (", paste(tempo.different.color[duplicated(tempo.different.color)], collapse = " "), "). TRY ANOTHER notch VALUE\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}else if(length(different.color) != length(tempo.different.color)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": LENGTH OF different.color (", paste(different.color, collapse = " "), ") DIFFERENT FROM LENGTH OF tempo.different.color (", paste(tempo.different.color, collapse = " "), ")\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}else{
for(i in 1:length(different.color)){
mat1[mat1 == different.color[i]] <- tempo.different.color[i] # no need of isTRUE(all.equal()) because different.color comes from mat1
}
}
}
if( ! is.null(forced.color)){
hexa.values.to.change <- hsv(unique(sort(mat1))[1:length(forced.color)], s, v)
}
mat1[ ! is.na(mat1)] <- hsv(mat1[ ! is.na(mat1)], s, v)
if( ! is.null(forced.color)){
if(any(forced.color %in% mat1, na.rm = TRUE)){
problem <- TRUE
text.problem <- paste0("THE FOLLOWING COLORS WHERE INTRODUCED USING forced.color BUT WHERE ALREADY PRESENT IN THE COLORED MATRIX :", paste(forced.color[forced.color %in% mat1], collapse = " "))
}else{
problem <- FALSE
}
for(i in 1:length(hexa.values.to.change)){
if( ! any(mat1 == hexa.values.to.change[i], na.rm = TRUE)){# no need of isTRUE(all.equal()) because character
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THE ", hexa.values.to.change[i], " VALUE FROM hexa.values.to.change IS NOT REPRESENTED IN mat1 : ", paste(unique(as.vector(mat1)), collapse = " "), "\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}else{
mat1[which(mat1 == hexa.values.to.change[i])] <- forced.color[i] # no need of isTRUE(all.equal()) because character
}
}
}
output <- list(mat1.name = mat1.name, colored.mat = mat1, problem = problem, text.problem = text.problem)
return(output)
}


######## fun_mat_op() #### assemble several matrices with operation


# Check OK: clear to go Apollo
fun_mat_op <- function(mat.list, kind.of.operation = "+"){
# AIM
# assemble several matrices of same dimensions by performing by case operation. For instance add the value of all the case 1 (row1 & column1) of the matrices and put it in the case 1 of a new matrix M, add the value of all the case 2 (row2 & column1) of the matrices and put it in the case 2 of a new matrix M, etc.
 
# c: case
# i: row number
# j: column number
# k: matrix number
# z: number of matrices
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# fun_comp_2d()
# ARGUMENTS:
# mat.list: list of matrices
# kind.of.operation: either "+" (by case addition), "-" (by case subtraction) or "*" (by case multiplication)
# RETURN
# the assembled matrix, with row and/or column names only if all the matrices have identical row/column names
# EXAMPLES
# mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; fun_mat_op(mat.list = list(mat1, mat2), kind.of.operation = "+")
# mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; fun_mat_op(mat.list = list(mat1, mat2), kind.of.operation = "*")
# mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2, dimnames = list(LETTERS[1:4], c(NA, NA))) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; fun_mat_op(mat.list = list(mat1, mat2), kind.of.operation = "-")
# mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2, dimnames = list(c("A1", "A2", "A3", "A4"), letters[1:2])) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; mat3 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; fun_mat_op(mat.list = list(mat1, mat2, mat3), kind.of.operation = "+")
# DEBUGGING
# mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; mat.list = list(mat1, mat2) ; kind.of.operation = "+" # for function debugging
# mat1 = matrix(c(1,1,1,2,1,5,9,8), ncol = 2, dimnames = list(LETTERS[1:4], c(NA, NA))) ; mat2 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2, dimnames = list(LETTERS[1:4], letters[1:2])) ; mat.list = list(mat1, mat2) ; kind.of.operation = "*" # for function debugging
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if(length(utils::find("fun_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_comp_2d() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end required function checking
# argument checking
# argument checking with fun_check()
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = mat.list, class = "list", fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = kind.of.operation, options = c("+", "-", "*"), length = 1, fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# end argument checking with fun_check()
# argument checking without fun_check()
if(length(mat.list) < 2){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": mat.list ARGUMENT MUST BE A LIST CONTAINING AT LEAST 2 MATRICES\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
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for(i1 in 1:length(mat.list)){
tempo <- fun_check(data = mat.list[[i1]], class = "matrix", mode = "numeric", na.contain = TRUE)
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if(tempo$problem == TRUE){
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tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ELEMENT ", i1, " OF mat.list ARGUMENT MUST BE A NUMERIC MATRIX\n\n================\n\n")
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stop(tempo.cat, call. = FALSE)
}
}
ident.row.names <- TRUE
ident.col.names <- TRUE
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for(i1 in 2:length(mat.list)){
tempo <- fun_comp_2d(data1 = mat.list[[1]], data2 = mat.list[[i1]])
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if(tempo$same.dim == FALSE){
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tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": MATRIX ", i1, " OF mat.list ARGUMENT MUST HAVE THE SAME DIMENSION (", paste(dim(mat.list[[i1]]), collapse = " "), ") THAN THE MATRIX 1 IN mat.list (", paste(dim(mat.list[[1]]), collapse = " "), ")\n\n================\n\n")
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stop(tempo.cat, call. = FALSE)
}
if( ! is.null(tempo$same.row.name)){
if(tempo$same.row.name != TRUE){ # != TRUE to deal with NA
ident.row.names <- FALSE
}
}
if( ! is.null(tempo$same.col.name)){
if(tempo$same.col.name != TRUE){ # != TRUE to deal with NA
ident.col.names <- FALSE
}
}
}
# end argument checking without fun_check()
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# main code
output <- mat.list[[1]]
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for(i1 in 2:length(mat.list)){
output <- get(kind.of.operation)(output, mat.list[[i1]])
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}
dimnames(output) <- NULL
if(ident.row.names == TRUE){
rownames(output) <- rownames(mat.list[[1]])
}
if(ident.col.names == TRUE){
colnames(output) <- colnames(mat.list[[1]])
}
return(output)
}


######## fun_mat_inv() #### return the inverse of a square matrix


# Check OK: clear to go Apollo
fun_mat_inv <- function(mat){
# AIM
# return the inverse of a square matrix when solve() cannot
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# ARGUMENTS:
# mat: a square numeric matrix without NULL, NA, Inf or single case (dimension 1, 1) of 0
# RETURN
# the inversed matrix
# EXAMPLES
# mat1 = matrix(c(1,1,1,2,1,5,9,8,9), ncol = 3) ; fun_mat_inv(mat = mat1) # use solve()
# mat1 = matrix(c(0,0,0,0,0,0,0,0,0), ncol = 3) ; fun_mat_inv(mat = mat1) # use the trick
# mat1 = matrix(c(1,1,1,2,Inf,5,9,8,9), ncol = 3) ; fun_mat_inv(mat = mat1)
# mat1 = matrix(c(1,1,1,2,NA,5,9,8,9), ncol = 3) ; fun_mat_inv(mat = mat1)
# mat1 = matrix(c(1,2), ncol = 1) ; fun_mat_inv(mat = mat1)
# mat1 = matrix(0, ncol = 1) ; fun_mat_inv(mat = mat1)
# mat1 = matrix(2, ncol = 1) ; fun_mat_inv(mat = mat1)
# DEBUGGING
# mat = matrix(c(1,1,1,2,1,5,9,8,9), ncol = 3) # for function debugging
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end required function checking
# argument checking
# argument checking with fun_check()
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = mat, class = "matrix", mode = "numeric", fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# end argument checking with fun_check()
# argument checking without fun_check()
if(ncol(mat) != nrow(mat)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": mat ARGUMENT MUST BE A SQUARE MATRIX\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if(any(mat %in% c(Inf, -Inf, NA))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": mat ARGUMENT MUST BE A MATRIX WITHOUT Inf, -Inf OR NA\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if(all(mat == 0) & ncol(mat) == 1){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": mat ARGUMENT CANNOT BE A SQUARE MATRIX MADE OF A SINGLE CASE OF 0\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end argument checking without fun_check()
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# main code
if(any(grepl(x = try(solve(mat), silent = TRUE)[], pattern = "[Ee]rror"))){
tempo <- svd(mat)
val.critique <- which(tempo$d < 10^-8)
Diag.mod <- diag(1 / tempo$d)
for(i in val.critique){
Diag.mod[i, i] <- 0
}
return(tempo$v %*% Diag.mod %*% t(tempo$u))
}else{
return(solve(mat))
}
}


######## fun_mat_fill() #### fill the empty half part of a symmetric square matrix


# Check OK: clear to go Apollo
fun_mat_fill <- function(mat, empty.cell.string = 0, warn.print = FALSE){
# AIM
# detect the empty half part of a symmetric square matrix (either topleft, topright, bottomleft or bottomright)
# fill this empty half part using the other symmetric half part of the matrix
# WARNINGS
# a plot verification using fun_gg_heatmap() is recommanded
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# ARGUMENTS:
# mat: a numeric or character square matrix with the half part (according to the grand diagonal) filled with NA (any kind of matrix), "0" (character matrix) or 0 (numeric matrix) exclusively (not a mix of 0 and NA in the empty part)
# empty.cell.string: a numeric, character or NA (no quotes) indicating what empty cells are filled with
# warn.print: logical. Print warnings at the end of the execution? No print if no warning messages
# RETURN
# a list containing:
# $mat: the filled matrix
# $warn: the warning messages. Use cat() for proper display. NULL if no warning
# EXAMPLES
# mat1 = matrix(c(1,NA,NA,NA, 0,2,NA,NA, NA,3,4,NA, 5,6,7,8), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = NA, warn.print = TRUE) # bottomleft example
# mat1 = matrix(c(1,1,1,2, 0,2,3,0, NA,3,0,0, 5,0,0,0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = NA, warn.print = TRUE) # error example
# mat1 = matrix(c(1,1,1,2, 0,2,3,0, NA,3,0,0, 5,0,0,0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = 0, warn.print = TRUE) # bottomright example
# mat1 = matrix(c(1,1,1,2, "a",2,3,NA, "a","a",0,0, "a","a","a",0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = "a", warn.print = TRUE) # topright example
# mat1 = matrix(c(0,0,0,2, 0,0,3,0, 0,3,0,NA, 5,0,0,0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = 0, warn.print = TRUE) # topleft example
# mat1 = matrix(c(0,0,0,2, 0,0,3,0, 0,3,0,0, 5,0,0,0), ncol = 4) ; mat1 ; fun_mat_fill(mat = mat1, empty.cell.string = 0, warn.print = TRUE) # error example
# DEBUGGING
# mat = matrix(c(1,NA,NA,NA, 0,2,NA,NA, NA,3,4,NA, 5,6,7,8), ncol = 4) ; empty.cell.string = NA ; warn.print = TRUE # for function debugging
# mat = matrix(c(0,0,0,2, 0,0,3,0, 0,3,0,NA, 5,0,0,0), ncol = 4) ; empty.cell.string = 0 ; warn.print = TRUE # for function debugging # topleft example
# mat = matrix(c(0,0,0,2, 0,0,3,0, 0,3,0,NA, 5,0,0,0), ncol = 4) ; empty.cell.string = NA ; warn.print = TRUE # for function debugging # topleft example
# function name
function.name <- paste0(as.list(match.call(expand.dots=FALSE))[[1]], "()")
# end function name
# required function checking
if(length(utils::find("fun_check", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end required function checking
# argument checking
# argument checking with fun_check()
arg.check <- NULL #
text.check <- NULL #
checked.arg.names <- NULL # for function debbuging: used by r_debugging_tools
ee <- expression(arg.check <- c(arg.check, tempo$problem) , text.check <- c(text.check, tempo$text) , checked.arg.names <- c(checked.arg.names, tempo$fun.name))
tempo <- fun_check(data = mat, class = "matrix", na.contain = TRUE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = empty.cell.string, class = "vector", na.contain = TRUE, fun.name = function.name) ; eval(ee)
tempo <- fun_check(data = warn.print, class = "logical", length = 1, fun.name = function.name) ; eval(ee)
if(any(arg.check) == TRUE){
stop(paste0("\n\n================\n\n", paste(text.check[arg.check], collapse = "\n"), "\n\n================\n\n"), call. = FALSE) #
}
# end argument checking with fun_check()
# argument checking without fun_check()
if(ncol(mat) != nrow(mat)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": mat ARGUMENT MUST BE A SQUARE MATRIX\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if( ! (mode(mat) %in% c("numeric", "character"))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": mat ARGUMENT MUST BE A NUMERIC OR CHARACTER MATRIX\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if(nrow(mat) == 1 & ncol(mat) == 1){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": mat ARGUMENT CANNOT BE A SQUARE MATRIX MADE OF A SINGLE CASE\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if(ifelse(is.na(empty.cell.string), ! any(is.na(mat)), ! any(mat == empty.cell.string, na.rm = TRUE))){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": mat ARGUMENT MATRIX MUST HAVE CELLS WITH THE EMPTY STRING SPECIFIED IN empty.cell.string ARGUMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
# end argument checking without fun_check()
# source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_check_dev)) # activate this line and use the function (with no arguments left as NULL) to check arguments status and if they have been checked using fun_check()
# end argument checking
# main code
list.diag <- vector("list", length = nrow(mat) - 1)
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for(i1 in 1:(nrow(mat) - 1)){
list.diag[[i1]] <- numeric(length = nrow(mat) - i1)
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}
sector <- c("topleft", "topright", "bottomright", "bottomleft")
diag.scan <-c( # same order as sector. Recover each diag from center to corner
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"mat[as.matrix(as.data.frame(list(1:(nrow(mat) - i2), (ncol(mat) -i2):1)))]", # topleft part
"mat[as.matrix(as.data.frame(list(1:(nrow(mat) - i2), (1:ncol(mat))[-(1:i2)])))]", # topright part
"mat[as.matrix(as.data.frame(list((1 + i2):nrow(mat), ncol(mat):(1 + i2))))]", # bottomright part
"mat[as.matrix(as.data.frame(list((1 + i2):nrow(mat), 1:(ncol(mat) -i2))))]" # bottomleft part
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)
# empty part detection
tempo.list.diag <- list.diag
empty.sector <- NULL
full.sector <- NULL
warn <- NULL
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warn.count <- 0
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for(i1 in 1:length(sector)){
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tempo.list.diag <- list.diag
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for(i2 in 1:(nrow(mat) - 1)){
tempo.list.diag[[i2]] <- eval(parse(text = diag.scan[i1]))
if(ifelse(is.na(empty.cell.string), ! all(is.na(tempo.list.diag[[i2]])), ! (all(tempo.list.diag[[i2]] == empty.cell.string, na.rm = TRUE) & ! (is.na(all(tempo.list.diag[[i2]] == empty.cell.string, na.rm = FALSE)))))){ # I had to add this ! (is.na(all(tempo.list.diag[[i2]] == empty.cell.string, na.rm = FALSE))) because all(tempo.list.diag[[i2]] == empty.cell.string, na.rm = FALSE) gives NA and not FALSE if one NA in tempo.list.diag[[i2]] -> not good for if()
full.sector <- c(full.sector, sector[i1])
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break
}
}
if(i1 == nrow(mat) - 1){
if(all(unlist(lapply(tempo.list.diag, FUN = function(x){if(is.na(empty.cell.string)){is.na(x)}else{x == empty.cell.string}})), na.rm = TRUE)){
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empty.sector <- c(empty.sector, sector[i1])
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warn.count <- warn.count + 1
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tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": EMPTY SECTOR DETECTED ON THE ", toupper(sector[i1]), " CORNER, FULL OF ", empty.cell.string)
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warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
}else{
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tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THE ", toupper(sector[i1]), " SECTOR, DETECTED AS EMPTY, IS NOT? DIFFERENT VALUES IN THIS SECTOR:\n", paste(names(table(unlist(tempo.list.diag), useNA = "ifany")), collapse = " "), "\n\n================\n\n")
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stop(tempo.cat, call. = FALSE)
}
}
}
# end empty part detection
if(length(empty.sector) == 0){
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warn.count <- warn.count + 1
tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": ACCORDING TO empty.cell.string ARGUMENT (", empty.cell.string, "), mat ARGUMENT MATRIX HAS ZERO EMPTY HALF PART")
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warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
}else{
if(length(empty.sector) > 1){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": ACCORDING TO empty.cell.string ARGUMENT (", empty.cell.string, "), mat ARGUMENT MATRIX HAS MORE THAN ONE EMPTY HALF PART (ACCORDING TO THE GRAND DIAGONAL): ", paste(empty.sector, collapse = " "), "\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}else if(any(full.sector %in% empty.sector, na.rm = TRUE)){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THE FUNCTION HAS DETECTED EMPTY AND NON EMPTY HALF PART IN THE SAME SECTOR: ", paste(full.sector[full.sector %in% empty.sector], collapse = " "), "\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}else if(length(empty.sector) + length(full.sector)!= 4){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": THE FUNCTION HAS DETECTED MORE OR LESS SECTORS THAN 4:\nHALF SECTORS:", paste(empty.sector, collapse = " "), "\nFULL SECTORS:", paste(full.sector, collapse = " "), "\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}else{
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warn.count <- warn.count + 1
tempo.warn <- paste0("(", warn.count,") FROM FUNCTION ", function.name, ": ", toupper(empty.sector), " SECTOR HAS BEEN COMPLETED TO BECOME SYMMETRICAL")
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warn <- paste0(ifelse(is.null(warn), tempo.warn, paste0(warn, "\n\n", tempo.warn)))
}
# matrix filling
for(i1 in 1:(nrow(mat) - 1)){
if(empty.sector == "topleft"){
eval(parse(text = paste0(diag.scan[1], " <- ", diag.scan[3])))
}else if(empty.sector == "topright"){
eval(parse(text = paste0(diag.scan[2], " <- ", diag.scan[4])))
}else if(empty.sector == "bottomright"){
eval(parse(text = paste0(diag.scan[3], " <- ", diag.scan[1])))
}else if(empty.sector == "bottomleft"){
eval(parse(text = paste0(diag.scan[4], " <- ", diag.scan[2])))
}
}
# end matrix filling
}
if(warn.print == TRUE & ! is.null(warn)){
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warning(warn, call. = FALSE)
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}
return(list(mat = mat, warn = warn))
}


######## fun_permut() #### progressively breaks a vector order


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fun_permut <- function(data1, data2 = NULL, n = NULL, seed = NULL, print.count = 10, text.print = "", cor.method = "spearman", cor.limit = 0.2, warn.print = FALSE, lib.path = NULL){
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# AIM
# reorder the elements of the data1 vector by flipping 2 randomly selected  consecutive positions either:
# 1) n times (when n is precised) or
# 2) until the correlation between data1 and data2 decreases down to the cor.limit (0.2 by default). See cor.limit below to deal with negative correlations
# Example of consecutive position flipping: ABCD -> BACD -> BADC, etc.
# WARNINGS
# see # https://www.r-bloggers.com/strategies-to-speedup-r-code/ for code speedup
# the random switch of non consecutive positions (ABCD -> DBCA for instance) does not work very well as the correaltion is quickly obtained but the initial vector structure is mainly kept (no much order). Ths code would be: pos <- ini.pos[1:2] ; pos <- sample.int(n = n , size = 2, replace = FALSE) ; tempo.pos[pos] <- tempo.pos[rev(pos)]
# ARGUMENTS
# data1: a vector of at least 2 elements. Must be numeric if data2 is specified
# data2: a numeric vector of same length as data1
# n: number of times "flipping 2 randomly selected consecutive positions". Ignored if data2 is specified
# seed: integer number used by set.seed(). Write NULL if random result is required, an integer otherwise. BEWARE: if not NULL, fun_permut() will systematically return the same result when the other parameters keep the same settings
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# print.count: interger value. Print a working progress message every print.count during loops. BEWARE: can increase substentially the time to complete the process using a small value, like 10 for instance. Use Inf is no loop message desired
# text.print: optional message to add to the working progress message every print.count loop
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# cor.method: correlation method. Either "pearson", "kendall" or "spearman". Ignored if data2 is not specified
# cor.limit: a correlation limit (between 0 and 1). Ignored if data2 is not specified. Compute the correlation between data1 and data2, permute the data1 values, and stop the permutation process when the correlation between data1 and data2 decreases down below the cor limit value (0.2 by default). If cor(data1, data2) is negative, then -cor.limit is used and the process stops until the correlation between data1 and data2 increases up over cor.limit (-0.2 by default). BEWARE: write a positive cor.limit even if cor(data1, data2) is known to be negative. The function will automatically uses -cor.limit. If the initial correlation is already below cor.limit (positive correlation) or over -cor.limit (negative correlation), then the data1 value positions are completely randomized (correlation between data1 and data2 is expected to be 0)
# warn.print: logical. Print warnings at the end of the execution? No print if no warning messages
# lib.path: absolute path of the required packages, if not in the default folders
# REQUIRED PACKAGES
# lubridate
# REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
# fun_check()
# fun_pack()
# fun_round()
# RETURN
# a list containing:
# $data: the modified vector
# $warn: potential warning messages (in case of negative correlation when data2 is specified). NULL if non warning message
# $cor: a spearman correlation between the initial positions (1:length(data1) and the final positions if data2 is not specified and the final correlation between data1 and data2 otherwise, according to cor.method
# $count: the number of loops used
# EXAMPLES
# example (1) showing that for loop, used in fun_permut(), is faster than while loop
# ini.time <- as.numeric(Sys.time()) ; count <- 0 ; for(i0 in 1:1e9){count <- count + 1} ; tempo.time <- as.numeric(Sys.time()) ; tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time)) ; tempo.lapse
# example (2) showing that for loop, used in fun_permut(), is faster than while loop
# ini.time <- as.numeric(Sys.time()) ; count <- 0 ; while(count < 1e9){count <- count + 1} ; tempo.time <- as.numeric(Sys.time()) ; tempo.lapse <- round(lubridate::seconds_to_period(tempo.time - ini.time)) ; tempo.lapse
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# fun_permut(data1 = LETTERS[1:5], data2 = NULL, n = 100, seed = 1, print.count = 10, text.print = "CPU NB 4")
# fun_permut(data1 = 101:110, data2 = 21:30, seed = 1, print.count = 1e4, text.print = "", cor.method = "spearman", cor.limit = 0.2)
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# a way to use the cor.limit argument just considering data1
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# obs1 <- 101:110 ; fun_permut(data1 = obs1, data2 = obs1, seed = 1, print.count = 10, cor.method = "spearman", cor.limit = 0.2)
# fun_permut(data1 = 1:1e3, data2 = 1e3:1, seed = 1, print.count = 1e6, text.print = "", cor.method = "spearman", cor.limit = 0.7)
# fun_permut(data1 = 1:1e2, data2 = 1e2:1, seed = 1, print.count = 1e3, cor.limit = 0.5)
# fun_permut(data1 = c(0,0,0,0,0), n = 5, data2 = NULL, seed = 1, print.count = 1e3, cor.limit = 0.5)
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# DEBUGGING
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# data1 = LETTERS[1:5] ; data2 = NULL ; n = 1e6 ; seed = NULL ; print.count = 1e3 ; text.print = "" ; cor.method = "spearman" ; cor.limit = 0.2 ; warn.print = TRUE ; lib.path = NULL
# data1 = LETTERS[1:5] ; data2 = NULL ; n = 10 ; seed = 22 ; print.count = 10 ; text.print = "" ; cor.method = "spearman" ; cor.limit = 0.2 ; warn.print = TRUE ; lib.path = NULL
# data1 = 101:110 ; data2 = 21:30 ; n = 10 ; seed = 22 ; print.count = 10 ; text.print = "" ; cor.method = "spearman" ; cor.limit = 0.2 ; warn.print = TRUE ; lib.path = NULL
# data1 = 1:1e3 ; data2 = 1e3:1 ; n = 20 ; seed = 22 ; print.count = 1e6 ; text.print = "" ; cor.method = "spearman" ; cor.limit = 0.5 ; warn.print = TRUE ; lib.path = NULL
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# 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("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if(length(utils::find("fun_pack", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}
if(length(utils::find("fun_round", mode = "function")) == 0){
tempo.cat <- paste0("\n\n================\n\nERROR IN ", function.name, ": REQUIRED fun_pack() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
stop(tempo.cat, call. = FALSE)
}