cute_little_R_functions.R 195 KB
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fun_list_comp <- function(data1, data2){
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    # AIM:
    # compare two lists. Check and report in a list if the 2 datasets have:
    # same length
    # common names
    # common compartments
    # REQUIRED FUNCTIONS
    # none
    # 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)?
    # 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_list_comp(obs1, obs2)
    # obs1 = list(1:5, LETTERS[1:2]) ; obs2 = list(a = 1:5, b = LETTERS[1:2]) ; fun_list_comp(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_list_comp(obs1, obs2)
    # obs1 = list(b = 1:5, c = LETTERS[1:2]) ; obs2 = list(LETTERS[5:9], matrix(1:6), 1:5) ; fun_list_comp(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
    # argument checking
    # 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)) # activate this line and use the function to check arguments status and if they have been checked using fun_param_check()
    if( ! any(class(data1) %in% "list")){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_list_comp(): THE data1 ARGUMENT MUST BE A LIST\n\n================\n\n")
        stop(tempo.cat)
    }
    if( ! any(class(data2) %in% "list")){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_list_comp(): THE data2 ARGUMENT MUST BE A LIST\n\n================\n\n")
        stop(tempo.cat)
    }
    # end argument checking
    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)
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}


################ Object modification


######## fun_dataframe_remodeling() #### remodeling a data frame to have column name as a qualitative column and vice-versa


# Check OK: clear to go Apollo
fun_dataframe_remodeling <- function(data, quanti.col.name = "quanti", quali.col.name = "quali"){
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    # 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
    
    
    # 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
    
    
    
    # REQUIRED FUNCTIONS
    # fun_param_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_dataframe_remodeling(obs)
    # obs <- data.frame(col1 = (1:4)*10, col2 = 5:8) ; obs ; fun_dataframe_remodeling(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_dataframe_remodeling(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
    # required function checking
    if(length(find("fun_param_check", mode = "function")) == 0){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_dataframe_remodeling(): REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
        stop(tempo.cat)
    }
    # end required function checking
    arg.check <- NULL # for function debbuging
    checked.arg.names <- NULL # for function debbuging
    ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
    tempo <- fun_param_check(data = quanti.col.name, class = "character", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = quali.col.name, class = "character", length = 1) ; eval(ee)
    if(any(arg.check) == TRUE){
        stop() # nothing else because print = TRUE by default in fun_param_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_param_check_dev)) # activate this line and use the function to check arguments status and if they have been checked using fun_param_check()
    if( ! any(class(data) %in% "data.frame")){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_dataframe_remodeling(): THE data ARGUMENT MUST BE A DATA FRAME\n\n================\n\n")
        stop(tempo.cat)
    }
    # end argument checking
    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 fun_dataframe_remodeling(): 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)
        }
        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 fun_dataframe_remodeling(): 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)
        }
    }else{
        if( ! all(tempo.factor %in% "numeric")){
            tempo.cat <- paste0("\n\n================\n\nERROR IN fun_dataframe_remodeling(): 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)
        }
    }
    if(( ! any(tempo.factor %in% "character")) & is.null(names(data))){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_dataframe_remodeling(): NUMERIC DATA FRAME in the data ARGUMENT MUST HAVE COLUMN NAMES\n\n================\n\n")
        stop()
    }
    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)
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}


######## fun_refactorization() #### remove classes that are not anymore present in factors or factor columns in data frames


# Check OK: clear to go Apollo
fun_refactorization <- function(data, also.ordered = TRUE){
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    # AIM:
    # refactorize a factor or the factor columns of a data frame, such as only the class present are in the levels (no empty levels). The class order in levels is kept
    # useful to remove the empty classes after row removing for instance
    # REQUIRED FUNCTIONS
    # fun_param_check()
    # ARGUMENTS
    # data: factor (ordered or not) or data frame
    # also.ordered: refactorize also ordered factors? This to deal with ordered factors that have class "ordered" "factor"
    # RETURN
    # a list containing:
    # $data: the modified object
    # $removed: the removed classes for a factor and a list of the removed classes for each factor class of the data frame
    # EXAMPLES
    # obs <- data.frame(a = LETTERS[1:6], b = paste0(letters[1.6], c(1,1,2,2,3,3)), c = ordered(LETTERS[7:12]), d = 1:6, e = "A")[-c(1:2),] ; sapply(obs, levels) ; fun_refactorization(obs, FALSE)
    # obs <- data.frame(a = LETTERS[1:6], b = paste0(letters[1.6], c(1,1,2,2,3,3)), c = ordered(LETTERS[7:12]), d = 1:6, e = "A")[-c(1:2),] ; sapply(obs, levels) ; fun_refactorization(obs, TRUE)
    # obs <- factor(LETTERS[1:6])[-c(1:2)] ; obs ; fun_refactorization(obs, TRUE)
    # obs <- ordered(LETTERS[1:6])[-c(1:2)] ; obs ; fun_refactorization(obs, TRUE)
    # obs <- factor(LETTERS[1:6], levels = rev(LETTERS[1:6]))[-c(1:2)] ; obs ; fun_refactorization(obs, FALSE)
    # DEBUGGING
    # data <- data.frame(a = LETTERS[1:6], b = paste0(letters[1.6], c(1,1,2,2,3,3)), c = ordered(LETTERS[7:12]), d = 1:6, e = "A") ; data <- data[-c(1:2),] ; also.ordered <- TRUE # for function debugging
    # data <- factor(LETTERS[1:6])[-c(1:2)] ; also.ordered <- TRUE # for function debugging
    # data <- ordered(LETTERS[1:6])[-c(1:2)] ; also.ordered <- TRUE # for function debugging
    # required function checking
    if(length(find("fun_param_check", mode = "function")) == 0){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_refactorization(): REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
        stop(tempo.cat)
    }
    # end required function checking
    # argument checking
    arg.check <- NULL # for function debbuging
    checked.arg.names <- NULL # for function debbuging
    ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
    tempo <- fun_param_check(data = also.ordered, class = "logical", length = 1) ; eval(ee)
    if(any(arg.check) == TRUE){
        stop() # nothing else because print = TRUE by default in fun_param_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_param_check_dev)) # activate this line and use the function to check arguments status and if they have been checked using fun_param_check()
    if(also.ordered == FALSE){
        if( ! (all(class(data) == "data.frame") | all(class(data) == "factor"))){
            tempo.cat <- paste0("\n\n================\n\nERROR IN fun_refactorization(): data ARGUMENT MUST BE A FACTOR (NON ORDERED BECAUSE THE also.ordered ARGUMENT IS SET TO FALSE) OR A DATA FRAME\n\n================\n\n")
            stop(tempo.cat)
        }
    }
    if(also.ordered == TRUE){
        if( ! (all(class(data) == "data.frame") | all(class(data) == "factor") | all(class(data) %in% c("ordered", "factor")))){
            tempo.cat <- paste0("\n\n================\n\nERROR IN fun_refactorization(): data ARGUMENT MUST BE A FACTOR OR A DATA FRAME\n\n================\n\n")
            stop(tempo.cat)
        }
    }
    # end argument checking
    text <- NULL
    if(all(class(data) == "factor")){
        tempo.keep.log <- levels(data) %in% unique(data)
        text <- levels(data)[ ! tempo.keep.log]
        data <- factor(data, levels = levels(data)[tempo.keep.log])
    }else if(all(class(data) %in% c("ordered", "factor"))){
        tempo.keep.log <- levels(data) %in% unique(data)
        text <- levels(data)[ ! tempo.keep.log]
        data <- ordered(data, levels = levels(data)[tempo.keep.log])
    }else if(all(class(data) == "data.frame")){
        text <- vector("list", length(data))
        names(text) <- names(data)
        tempo.factor.col <- sapply(sapply(lapply(data, class), FUN = "%in%", "factor"), FUN = "all") # get the factor column (logical)
        for(i in 1:length(tempo.factor.col)){
            if(tempo.factor.col[i] == TRUE){
                tempo.keep.log <- levels(data[[i]]) %in% unique(data[[i]])
                text[[i]] <- levels(data[[i]])[ ! tempo.keep.log]
                data[[i]] <- factor(data[[i]], levels = levels(data[[i]])[tempo.keep.log])
            }
        }
        tempo.ordered.col <- sapply(sapply(lapply(data, class), FUN = "%in%", "ordered"), FUN = "any") # get the ordered factor column (logical) if they exist
        if(also.ordered == TRUE){
            for(i in 1:length(tempo.ordered.col)){
                if(tempo.ordered.col[i] == TRUE){
                    tempo.keep.log <- levels(data[[i]]) %in% unique(data[[i]])
                    text[[i]] <- levels(data[[i]])[ ! tempo.keep.log]
                    data[[i]] <- ordered(data[[i]], levels = levels(data[[i]])[tempo.keep.log])
                }
            }
        }
        text <- text[(tempo.factor.col | tempo.ordered.col) & ! (sapply(text, FUN = length) == 0)] # remove the compartments of text that are not modified factors columns of data frame
    }
    output <- list(data = data, removed = text)
    return(output)
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}


######## fun_rounding() #### Rounding number if decimal present


# Check OK: clear to go Apollo
fun_rounding <- function(data, dec.nb = 2, after.lead.zero = TRUE){
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    # AIM:
    # round a vector of values, if decimal, with the desired number of decimal digits after the decimal leading zeros
    # BEWARE
    # 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
    # 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
    # fun_param_check()
    # RETURN
    # the modified vector
    # EXAMPLES
    # cat(fun_rounding(data = c(10, 100.001, 333.0001254, 12312.1235), dec.nb = 2, after.lead.zero = FALSE))
    # cat(fun_rounding(data = c("10", "100.001", "333.0001254", "12312.1235"), dec.nb = 2, after.lead.zero = FALSE))
    # 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
    # argument checking
    if( ! (all(typeof(data) == "character") | all(typeof(data) == "double") | all(typeof(data) == "integer"))){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_rounding(): data ARGUMENT MUST BE A VECTOR OF NUMBERS (IN NUMERIC OR CHARACTER MODE)\n\n================\n\n")
        stop(tempo.cat)
    }
    arg.check <- NULL # for function debbuging
    checked.arg.names <- NULL # for function debbuging
    ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
    tempo <- fun_param_check(data = dec.nb, typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = after.lead.zero, class = "logical", length = 1) ; eval(ee)
    if(any(arg.check) == TRUE){
        stop() # nothing else because print = TRUE by default in fun_param_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_param_check_dev)) # activate this line and use the function to check arguments status and if they have been checked using fun_param_check()
    # end argument checking
    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_90clock_matrix_rot() #### 90° clockwise matrix rotation
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# Check OK: clear to go Apollo
fun_90clock_matrix_rot <- function(data){
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    # AIM:
    # 90° clockwise matrix rotation
    # applied twice, the function provide the mirror matrix, according to vertical and horizontal symmetry
    # REQUIRED FUNCTIONS
    # fun_param_check()
    # ARGUMENTS
    # data: matrix (matrix class)
    # RETURN
    # the modified matrix
    # EXAMPLES
    # obs <- matrix(1:10, ncol = 1) ; obs ; fun_90clock_matrix_rot(obs)
    # obs <- matrix(LETTERS[1:10], ncol = 5) ; obs ; fun_90clock_matrix_rot(obs)
    # DEBUGGING
    # data = matrix(1:10, ncol = 1)
    # required function checking
    if(length(find("fun_param_check", mode = "function")) == 0){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_90clock_matrix_rot(): REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
        stop(tempo.cat)
    }
    # end required function checking
    # argument checking
    # 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)) # activate this line and use the function to check arguments status and if they have been checked using fun_param_check()
    if( ! any(class(data) %in% "matrix")){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_90clock_matrix_rot(): THE data ARGUMENT MUST BE A MATRIX\n\n================\n\n")
        stop(tempo.cat)
    }
    # end argument checking
    for (i in 1:ncol(data)){data[,i] <- rev(data[,i])}
    data <- t(data)
    return(data)
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}


######## fun_hexa_hsv_color_matrix() #### Conversion of a numeric matrix into hexadecimal color matrix


# Check OK: clear to go Apollo
fun_hexa_hsv_color_matrix <- function(mat1, mat.hsv.h = TRUE, notch = 1, s = 1, v = 1, forced.color = NULL){
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    # AIM:
    # convert a matrix made of numbers into a hexadecimal matrix for rgb colorization
    # REQUIRED FUNCTIONS
    # fun_param_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
    # $text.problem: text when overlapping colors. NULL if forced.color = NULL or problem == FALSE
    # EXAMPLES
    # mat1 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; dimnames(mat1) <- list(LETTERS[1:4], letters[1:2]) ; fun_hexa_hsv_color_matrix(mat1, mat.hsv.h = FALSE, notch = 1, s = 1, v = 1, forced.color = NULL)
    # DEBUGGING
    # mat1 = matrix(c(1,1,1,2,1,5,9,NA), ncol = 2) ; dimnames(mat1) <- list(LETTERS[1:4], letters[1:2]); mat.hsv.h = FALSE ; notch = 1 ; s = 1 ; v = 1 ; forced.color = c(hsv(1,1,1), hsv(0,0,0)) # for function debugging
    # required function checking
    if(length(find("fun_param_check", mode = "function")) == 0){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_hexa_hsv_color_matrix(): REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
        stop(tempo.cat)
    }
    # end required function checking
    # argument checking
    arg.check <- NULL # for function debbuging
    checked.arg.names <- NULL # for function debbuging
    ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
    tempo <- fun_param_check(data = mat1, mode = "numeric", class = "matrix", na.contain = TRUE, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = mat.hsv.h, class = "logical", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = notch, mode = "numeric", length = 1, prop = TRUE) ; eval(ee)
    tempo <- fun_param_check(data = s, mode = "numeric", length = 1, prop = TRUE) ; eval(ee)
    tempo <- fun_param_check(data = v, mode = "numeric", length = 1, prop = TRUE) ; eval(ee)
    if(any(arg.check) == TRUE){
        stop() # nothing else because print = TRUE by default in fun_param_check()
    }
    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_param_check_dev)) # activate this line and use the function to check arguments status and if they have been checked using fun_param_check()
    if(mat.hsv.h == TRUE & fun_param_check(data = mat1, mode = "numeric", prop = TRUE, print = FALSE)$problem == TRUE){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_hexa_hsv_color_matrix(): 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)
    }
    if( ! is.null(forced.color)){
        tempo <- fun_param_check(data = forced.color, class = "character")
        if(tempo$problem == TRUE){
            stop()
        }
        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 fun_hexa_hsv_color_matrix(): 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)
        }
    }
    # end argument checking
    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 fun_hexa_hsv_color_matrix(): 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)
        }
    }else{
        if(any(mat1 - floor(mat1) > 0, na.rm = TRUE) | any(mat1 == 0, na.rm = TRUE)){
            tempo.cat <- paste0("\n\n================\n\nERROR IN fun_hexa_hsv_color_matrix(): mat1 MUST BE MADE OF INTEGER VALUES WITHOUT 0 BECAUSE mat.hsv.h ARGUMENT SET TO FALSE\n\n================\n\n")
            stop(tempo.cat)
        }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 fun_hexa_hsv_color_matrix(): 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)
        }else if(length(different.color) != length(tempo.different.color)){
            tempo.cat <- paste0("\n\n================\n\nERROR IN fun_hexa_hsv_color_matrix(): 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)
        }else{
            for(i in 1:length(different.color)){
                mat1[mat1 == different.color[i]] <- tempo.different.color[i]
            }
        }
    }
    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)){
                tempo.cat <- paste0("\n\n================\n\nERROR IN fun_hexa_hsv_color_matrix(): 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)
            }else{
                mat1[which(mat1 == hexa.values.to.change[i])] <- forced.color[i]
            }
        }
    }
    output <- list(mat1.name = mat1.name, colored.mat = mat1, problem = problem, text.problem = text.problem)
    return(output)
}


######## fun_by_case_matrix_op() #### assembling of several matrices with operation


# Check OK: clear to go Apollo
fun_by_case_matrix_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
    # fun_param_check()
    # fun_2D_comp()
    # 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_by_case_matrix_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_by_case_matrix_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_by_case_matrix_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_by_case_matrix_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
    # required function checking
    if(length(find("fun_param_check", mode = "function")) == 0){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_by_case_matrix_op(): REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
        stop(tempo.cat)
    }
    if(length(find("fun_param_check", mode = "function")) == 0){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_by_case_matrix_op(): REQUIRED fun_2D_comp() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
        stop(tempo.cat)
    }
    # end required function checking
    # argument checking
    arg.check <- NULL # for function debbuging
    checked.arg.names <- NULL # for function debbuging
    ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
    tempo <- fun_param_check(data = mat.list, class = "list") ; eval(ee)
    tempo <- fun_param_check(data = kind.of.operation, options = c("+", "-", "*"), length = 1) ; eval(ee)
    if(any(arg.check) == TRUE){
        stop() # nothing else because print = TRUE by default in fun_param_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_param_check_dev)) # activate this line and use the function to check arguments status and if they have been checked using fun_param_check()
    if(length(mat.list) < 2){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_by_case_matrix_op(): mat.list ARGUMENT MUST BE A LIST CONTAINING AT LEAST 2 MATRICES\n\n================\n\n")
        stop(tempo.cat)
    }
    for(i0 in 1:length(mat.list)){
        tempo <- fun_param_check(data = mat.list[[i0]], class = "matrix", mode = "numeric", na.contain = TRUE)
        if(tempo$problem == TRUE){
            tempo.cat <- paste0("\n\n================\n\nERROR IN fun_by_case_matrix_op(): ELEMENT ", i0, " OF mat.list ARGUMENT MUST BE A NUMERIC MATRIX\n\n================\n\n")
            stop(tempo.cat)
        }
    }
    ident.row.names <- TRUE
    ident.col.names <- TRUE
    for(i0 in 2:length(mat.list)){
        tempo <- fun_2D_comp(data1 =  mat.list[[1]], data2 =  mat.list[[i0]])
        if(tempo$same.dim == FALSE){
            tempo.cat <- paste0("\n\n================\n\nERROR IN fun_by_case_matrix_op(): MATRIX ", i0, " OF mat.list ARGUMENT MUST HAVE THE SAME DIMENSION (", paste(dim(mat.list[[i0]]), collapse = " "), ") THAN THE MATRIX 1 IN mat.list (", paste(dim(mat.list[[1]]), collapse = " "), ")\n\n================\n\n")
            stop(tempo.cat)
        }
        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
    output <- mat.list[[1]]
    for(i0 in 2:length(mat.list)){
        output <- get(kind.of.operation)(output, mat.list[[i0]])
    }
    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)
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}


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######## 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
    # fun_param_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
    # required function checking
    if(length(find("fun_param_check", mode = "function")) == 0){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_mat_inv(): REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
        stop(tempo.cat)
    }
    # end required function checking
    # argument checking
    arg.check <- NULL # for function debbuging
    checked.arg.names <- NULL # for function debbuging
    ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
    tempo <- fun_param_check(data = mat, class = "matrix", mode = "numeric") ; eval(ee)
    if(any(arg.check) == TRUE){
        stop() # nothing else because print = TRUE by default in fun_param_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_param_check_dev)) # activate this line and use the function to check arguments status and if they have been checked using fun_param_check()
    if(ncol(mat) != nrow(mat)){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_mat_inv(): mat ARGUMENT MUST BE A SQUARE MATRIX\n\n================\n\n")
        stop(tempo.cat)
    }
    if(any(mat %in% c(Inf, -Inf, NA))){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_mat_inv(): mat ARGUMENT MUST BE A MATRIX WITHOUT Inf, -Inf OR NA\n\n================\n\n")
        stop(tempo.cat)
    }
    if(all(mat == 0) & ncol(mat) == 1){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_mat_inv(): mat ARGUMENT CANNOT BE A SQUARE MATRIX MADE OF A SINGLE CASE OF 0\n\n================\n\n")
        stop(tempo.cat)
    }
    # end argument checking
    if(any(grepl(x = try(solve(mat), silent = TRUE)[], pattern = "Error"))){
        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))
    }
}


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################ Graphics


# this order can be used:
# fun_window_width_resizing()
# fun_open_window()
# fun_graph_param_prior_plot() # not for ggplot2
# plot() or any other plotting
# fun_feature_post_plot() if fun_graph_param_prior_plot() has been used # not for ggplot2
# fun_close_specif_window()


######## fun_window_width_resizing() #### window width depending on classes to plot


# Check OK: clear to go Apollo
fun_window_width_resizing <- function(class.nb, inches.per.class.nb = 1, ini.window.width = 7, inch.left.space, inch.right.space, boundarie.space = 0.5){
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    # AIM:
    # rescale the width of a window to open depending on the number of classes to plot
    # can be used for height, considering that it is as if it was a width
    # this order can be used:
    # fun_window_width_resizing()
    # fun_open_window()
    # fun_graph_param_prior_plot() # not for ggplot2
    # plot() or any other plotting
    # fun_feature_post_plot() if fun_graph_param_prior_plot() has been used # not for ggplot2
    # fun_close_specif_window()
    # REQUIRED FUNCTIONS
    # fun_param_check()
    # ARGUMENTS
    # class.nb: number of class to plot
    # inches.per.class.nb: number of inches per unit of class.nb. 2 means 2 inches for each boxplot for instance
    # ini.window.width:initial window width in inches
    # inch.left.space: left horizontal margin of the figure region (in inches)
    # inch.right.space: right horizontal margin of the figure region (in inches)
    # boundarie.space: space between the right and left limits of the plotting region and the plot (0.5 means half a class width)
    # RETURN
    # the new window width in inches
    # EXAMPLES
    # fun_window_width_resizing(class.nb = 10, inches.per.class.nb = 0.2, ini.window.width = 7, inch.left.space = 1, inch.right.space = 1, boundarie.space = 0.5)
    # DEBUGGING
    # class.nb = 10 ; inches.per.class.nb = 0.2 ; ini.window.width = 7 ; inch.left.space = 1 ; inch.right.space = 1 ; boundarie.space = 0.5 # for function debugging
    # required function checking
    if(length(find("fun_param_check", mode = "function")) == 0){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_window_width_resizing(): REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
        stop(tempo.cat)
    }
    # end required function checking
    # argument checking
    arg.check <- NULL # for function debbuging
    checked.arg.names <- NULL # for function debbuging
    ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
    tempo <- fun_param_check(data = class.nb, typeof = "integer", length = 1, double.as.integer.allowed = TRUE, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = inches.per.class.nb, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = ini.window.width, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = inch.left.space, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = inch.right.space, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = boundarie.space, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    if(any(arg.check) == TRUE){
        stop() # nothing else because print = TRUE by default in fun_param_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_param_check_dev)) # activate this line and use the function to check arguments status and if they have been checked using fun_param_check()
    # end argument checking
    range.max <- class.nb + boundarie.space # the max range of the future plot
    range.min <- boundarie.space # the min range of the future plot
    window.width <- inch.left.space + inch.right.space + inches.per.class.nb * (range.max - range.min)
    return(window.width)
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}


######## fun_open_window() #### Open a GUI or pdf graphic window


# Check OK: clear to go Apollo
fun_open_window <- function(pdf.disp = TRUE, path.fun = "working.dir", pdf.name.file = "graph", width.fun = 7, height.fun = 7, paper = "special", no.pdf.overwrite = TRUE, return.output = FALSE){
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    # AIM:
    # open a pdf or screen (GUI) graphic window
    # BEWARE: on Linux, use pdf.disp = TRUE, if (GUI) graphic window is not always available, meaning that X is not installed (clusters for instance). Use X11() in R to test if available
    # this order can be used:
    # fun_window_width_resizing()
    # fun_open_window()
    # fun_graph_param_prior_plot() # not for ggplot2
    # plot() or any other plotting
    # fun_feature_post_plot() if fun_graph_param_prior_plot() has been used # not for ggplot2
    # fun_close_specif_window()
    # REQUIRED FUNCTIONS
    # fun_param_check()
    # ARGUMENTS:
    # pdf.disp: use pdf or not
    # path.fun: where the pdf is saved. Write "working.dir" if working directory is required (default)
    # pdf.name.file: name of the pdf file containing the graphs (the .pdf extension is added by the function)
    # width.fun: width of the windows (in inches)
    # height.fun: height of the windows (in inches)
    # paper: paper argument of the pdf function (paper format). Only used for pdf(). Either "a4", "letter", "legal", "us", "executive", "a4r", "USr" or "special". If "special", means that width.fun and height.fun specify the paper size
    # no.pdf.overwrite: existing pdf can be overwritten ? Only used if pdf.disp = TRUE
    # return.output: return output ? If TRUE but function not assigned, the output list is displayed
    # RETURN
    # a list containing:
    # $pdf.loc: path of the pdf created
    # $ini.par: initial par() parameters (to reset in a new graph)
    # $zone.ini: initial window spliting (to reset in a new graph)
    # EXAMPLES
    # fun_open_window(pdf.disp = FALSE, path.fun = "C:/Users/Gael/Desktop", pdf.name.file = "graph", width.fun = 7, height.fun = 7, paper = "special", no.pdf.overwrite = TRUE, return.output = TRUE)
    # DEBUGGING
    # pdf.disp = TRUE ; path.fun = "C:/Users/Gael/Desktop" ; pdf.name.file = "graphs" ; width.fun = 7 ; height.fun = 7 ; paper = "special" ; no.pdf.overwrite = TRUE ; return.output = TRUE # for function debugging
    # pdf.disp = TRUE ; path.fun = "/pasteur/homes/gmillot/" ; pdf.name.file = "graphs" ; width.fun = 7 ; height.fun = 7 ; paper = "special" ; no.pdf.overwrite = TRUE ; return.output = TRUE # for function debugging
    # required function checking
    if(length(find("fun_param_check", mode = "function")) == 0){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_open_window(): REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
        stop(tempo.cat)
    }
    # end required function checking
    # argument checking
    arg.check <- NULL # for function debbuging
    checked.arg.names <- NULL # for function debbuging
    ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
    tempo <- fun_param_check(data = pdf.disp, class = "logical", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = path.fun, class = "character", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = pdf.name.file, class = "character", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = width.fun, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = height.fun, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = path.fun, class = "character", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = paper, options = c("a4", "letter", "legal", "us", "executive", "a4r", "USr", "special", "A4", "LETTER", "LEGAL", "US"), length = 1) ; eval(ee)
    tempo <- fun_param_check(data =no.pdf.overwrite, class = "logical", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = return.output, class = "logical", length = 1) ; eval(ee)
    if(any(arg.check) == TRUE){
        stop() # nothing else because print = TRUE by default in fun_param_check()
    }
    # source("C:/Users/Gael/Documents/Git_versions_to_use/debugging_tools_for_r_dev-v1.2/r_debugging_tools-v1.2.R") ; eval(parse(text = str_basic_arg_check_dev)) ; eval(parse(text = str_arg_check_with_fun_param_check_dev)) # activate this line and use the function to check arguments status and if they have been checked using fun_param_check()
    # end argument checking
    if(path.fun == "working.dir"){
        path.fun <- getwd()
    }else{
        if(grepl(x = path.fun, pattern = ".+/$")){
            path.fun <- substr(path.fun, 1, nchar(path.fun) - 1) # remove the last /
        }
        if(dir.exists(path.fun) == FALSE){
            tempo.cat <- paste0("\n\n================\n\nERROR IN fun_open_window(): path.fun ARGUMENT DOES NOT CORRESPOND TO EXISTING DIRECTORY\n\n================\n\n")
            stop(tempo.cat)
        }
    }
    if(Sys.info()["sysname"] == "Windows"){ # Note that .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
        open.fail <- NULL
        windows()
        ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code bacause always a tempo window opened
        invisible(dev.off()) # close the new window
    }else if(Sys.info()["sysname"] == "Linux"){
        if(pdf.disp == TRUE){
            if(file.exists(paste0(path.fun, "/recover_ini_par.pdf"))){
                tempo.cat <- paste0("\n\n================\n\nPROBLEM IN fun_open_window(): THIS FUNCTION CANNOT BE USED ON LINUX IF A recover_ini_par.pdf FILE ALREADY EXISTS HERE: ", paste(path.fun, collapse = " "), "\n\n================\n\n")
                stop(tempo.cat)
            }else{
                pdf(width = width.fun, height = height.fun, file=paste0(path.fun, "/recover_ini_par.pdf"), paper = paper)
                ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code bacause always a tempo window opened
                invisible(dev.off()) # close the pdf windows
                file.remove(paste0(path.fun, "/recover_ini_par.pdf")) # remove the pdf file
            }
        }else{
            # test if X11 can be opened
            if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
                tempo.cat <- paste0("\n\n================\n\nERROR IN fun_open_window(): THIS FUNCTION CANNOT BE USED ON LINUX IF A Rplots.pdf FILE ALREADY EXISTS HERE: ", getwd(), "\n\n================\n\n")
                stop(tempo.cat)
            }else{
                open.fail <- suppressWarnings(try(X11(), silent = TRUE))[] # try to open a X11 window. If open.fail == NULL, no problem, meaning that the X11 window is opened. If open.fail != NULL, a pdf can be opened here paste0(getwd(), "/Rplots.pdf")
                if(is.null(open.fail)){
                    ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code bacause always a tempo window opened
                    invisible(dev.off()) # close the new window
                }else if(file.exists(paste0(getwd(), "/Rplots.pdf"))){
                    file.remove(paste0(getwd(), "/Rplots.pdf")) # remove the pdf file
                    tempo.cat <- ("\n\n================\n\nPROBLEM IN fun_open_window(): THIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM (X GRAPHIC INTERFACE HAS TO BE SET).\nTO OVERCOME THIS, PLEASE SET pdf.disp ARGUMENT TO TRUE AND RERUN\n\n================\n\n")
                    stop(tempo.cat)
                }
            }
        }
    }else{
        open.fail <- NULL
        quartz()
        ini.par <- par(no.readonly = TRUE) # to recover the initial graphical parameters if required (reset). BEWARE: this command alone opens a pdf of GUI window if no window already opened. But here, protected with the code bacause always a tempo window opened
        invisible(dev.off()) # close the new window
    }
    zone.ini <- matrix(1, ncol=1) # to recover the initial parameters for next figure region when device region split into several figure regions
    if(pdf.disp == TRUE){
        pdf.loc <- paste0(path.fun, "/", pdf.name.file, ".pdf")
        if(file.exists(pdf.loc) == TRUE & no.pdf.overwrite == TRUE){
            tempo.cat <- paste0("\n\n================\n\nERROR IN fun_open_window(): pdf.loc FILE ALREADY EXISTS AND CANNOT BE OVERWRITTEN DUE TO no.pdf.overwrite ARGUMENT SET TO TRUE: ", pdf.loc, "\n\n================\n\n")
            stop(tempo.cat)
        }else{
            pdf(width = width.fun, height = height.fun, file=pdf.loc, paper = paper)
        }
    }else if(pdf.disp == FALSE){
        pdf.loc <- NULL
        if(Sys.info()["sysname"] == "Windows"){ # .Platform$OS.type() only says "unix" for macOS and Linux and "Windows" for Windows
            windows(width = width.fun, height = height.fun, rescale="fixed")
        }else if(Sys.info()["sysname"] == "Linux"){
            if( ! is.null(open.fail)){
                stop("\n\n================\n\nPROBLEM IN fun_open_window(): THIS FUNCTION CANNOT OPEN GUI ON LINUX OR NON MACOS UNIX SYSTEM (X GRAPHIC INTERFACE HAS TO BE SET).\nTO OVERCOME THIS, PLEASE SET pdf.disp ARGUMENT TO TRUE AND RERUN\n\n================\n\n")
            }else{
                X11(width = width.fun, height = height.fun)
            }
        }else{
            quartz(width = width.fun, height = height.fun)
        }
    }
    if(return.output == TRUE){
        output <- list(pdf.loc = pdf.loc, ini.par = ini.par, zone.ini = zone.ini)
        return(output)
    }
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}


######## fun_graph_param_prior_plot() #### Graph param before plotting


# Check OK: clear to go Apollo
fun_graph_param_prior_plot <- function(param.reinitial = FALSE, xlog.scale = FALSE, ylog.scale = FALSE, remove.label = TRUE, remove.x.axis = TRUE, remove.y.axis = TRUE, std.x.range = TRUE, std.y.range = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 3.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = FALSE){
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    # AIM:
    # very convenient to erase the axes for post plot axis redrawing using fun_feature_post_plot()
    # reinitialize and set the graphic parameters before plotting
    # CANNOT be used if no graphic device already opened
    # REQUIRED FUNCTIONS
    # fun_param_check()
    # ARGUMENTS
    # param.reinitial: reinitialize graphic parameters before applying the new ones, as defined by the other arguments? Either TRUE or FALSE
    # xlog.scale: Log scale for the x-axis? Either TRUE or FALSE. If TRUE, erases the x-axis, except legend, for further drawing by fun_feature_post_plot()(xlog argument of par())
    # ylog.scale: Log scale for the y-axis? Either TRUE or FALSE. If TRUE, erases the y-axis, except legend, for further drawing by fun_feature_post_plot()(ylog argument of par())
    # remove.label: remove labels (axis legend) of the two axes? Either TRUE or FALSE (ann argument of par())
    # remove.x.axis: remove x-axis except legend? Either TRUE or FALSE (control the xaxt argument of par()). Automately set to TRUE if xlog.scale == TRUE
    # remove.y.axis: remove y-axis except legend? Either TRUE or FALSE (control the yaxt argument of par()). Automately set to TRUE if ylog.scale == TRUE
    # std.x.range: standard range on the x-axis? TRUE (no range extend) or FALSE (4% range extend). Controls xaxs argument of par() (TRUE is xaxs = "i", FALSE is xaxs = "r")
    # std.y.range: standard range on the y-axis? TRUE (no range extend) or FALSE (4% range extend). Controls yaxs argument of par() (TRUE is yaxs = "i", FALSE is yaxs = "r")
    # down.space: lower vertical margin (in inches, mai argument of par())
    # left.space: left horizontal margin (in inches, mai argument of par())
    # up.space: upper vertical margin between plot region and grapical window (in inches, mai argument of par())
    # right.space: right horizontal margin (in inches, mai argument of par())
    # orient: scale number orientation (las argument of par()). 0, always parallel to the axis; 1, always horizontal; 2, always perpendicular to the axis; 3, always vertical
    # dist.legend: numeric value that moves axis legends away in inches (first number of mgp argument of par() but in inches thus / 0.2)
    # tick.length: length of the ticks (1 means complete the distance between the plot region and the axis numbers, 0.5 means half the length, etc. 0 means no tick
    # box.type: bty argument of par(). Either "o", "l", "7", "c", "u", "]", the resulting box resembles the corresponding upper case letter. A value of "n" suppresses the box
    # amplif.label: increase or decrease the size of the text in legends
    # amplif.axis: increase or decrease the size of the scale numbers in axis
    # display.extend: extend display beyond plotting region? Either TRUE or FALSE (xpd argument of par() without NA)
    # return.par: return graphic parameter modification?
    # RETURN
    # return graphic parameter modification
    # EXAMPLES
    # fun_graph_param_prior_plot(param.reinitial = FALSE, xlog.scale = FALSE, ylog.scale = FALSE, remove.label = TRUE, remove.x.axis = TRUE, remove.y.axis = TRUE, std.x.range = TRUE, std.y.range = TRUE, down.space = 1, left.space = 1, up.space = 1, right.space = 1, orient = 1, dist.legend = 4.5, tick.length = 0.5, box.type = "n", amplif.label = 1, amplif.axis = 1, display.extend = FALSE, return.par = FALSE)
    # DEBUGGING
    # param.reinitial = FALSE ; xlog.scale = FALSE ; ylog.scale = FALSE ; remove.label = TRUE ; remove.x.axis = TRUE ; remove.y.axis = TRUE ; std.x.range = TRUE ; std.y.range = TRUE ; down.space = 1 ; left.space = 1 ; up.space = 1 ; right.space = 1 ; orient = 1 ; dist.legend = 4.5 ; tick.length = 0.5 ; box.type = "n" ; amplif.label = 1 ; amplif.axis = 1 ; display.extend = FALSE ; return.par = FALSE # for function debugging
    # required function checking
    if(length(find("fun_param_check", mode = "function")) == 0){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_graph_param_prior_plot(): REQUIRED fun_param_check() FUNCTION IS MISSING IN THE R ENVIRONMENT\n\n================\n\n")
        stop(tempo.cat)
    }
    # end required function checking
    # argument checking
    arg.check <- NULL # for function debbuging
    checked.arg.names <- NULL # for function debbuging
    ee <- expression(arg.check <- c(arg.check, tempo$problem) , checked.arg.names <- c(checked.arg.names, tempo$param.name))
    tempo <- fun_param_check(data = param.reinitial, class = "logical", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = xlog.scale, class = "logical", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = ylog.scale, class = "logical", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = remove.label, class = "logical", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = remove.x.axis, class = "logical", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = remove.y.axis, class = "logical", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = std.x.range, class = "logical", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = std.y.range, class = "logical", length = 1) ; eval(ee)
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    tempo <- fun_param_check(data = down.space, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = left.space, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = up.space, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = right.space, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = orient, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = dist.legend, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = tick.length, mode = "numeric", length = 1, prop = TRUE) ; eval(ee)
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    tempo <- fun_param_check(data = box.type, options = c("o", "l", "7", "c", "u", "]", "n"), length = 1) ; eval(ee)
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    tempo <- fun_param_check(data = amplif.label, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
    tempo <- fun_param_check(data = amplif.axis, mode = "numeric", length = 1, neg.values = FALSE) ; eval(ee)
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    tempo <- fun_param_check(data = display.extend, class = "logical", length = 1) ; eval(ee)
    tempo <- fun_param_check(data = return.par, class = "logical", length = 1) ; eval(ee)
    if(any(arg.check) == TRUE){
        stop() # nothing else because print = TRUE by default in fun_param_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_param_check_dev)) # activate this line and use the function to check arguments status and if they have been checked using fun_param_check()
    # end argument checking
    if(is.null(dev.list())){
        tempo.cat <- paste0("\n\n================\n\nERROR IN fun_graph_param_prior_plot(): THIS FUNCTION CANNOT BE USED IF NO GRAPHIC DEVICE ALREADY OPENED (dev.list() IS CURRENTLY NULL)\n\n================\n\n")
        stop(tempo.cat)
    }
    if(param.reinitial == TRUE){
        if( ! all(names(dev.cur()) == "null device")){
            active.wind.nb <- dev.cur()
        }else{