R/LT_RegenDose.R

In R-Lum/BayLum: Chronological Bayesian Models Integrating Optically Stimulated Luminescence and Radiocarbon Age Dating

#' @title Plots Lx/Tx as a function of the regenerative dose (DEPRECATED)
#'
#' @description This function plots `Lx/Tx` values as a function of regenerative dose,
#' for every selected aliquot and for each sample.
#'
#' @param DATA [list] (**required**): list of objects `LT`, `sLT`, `ITimes`, `dLab`, `ddot_env`, `regDose`, `J`, `K`, `Nb_measurement`, #' provided by [Generate_DataFile] or [Generate_DataFile_MG] or [combine_DataFiles].`DATA` can contain information from more than one sample.
#'
#' @param Path [character] (**required**): path to the project folder
#' (the same as the one used in [Generate_DataFile]  or [Generate_DataFile_MG] to provide \code{DATA})
#'
#' @param FolderNames [character] (**required**): vector of names of the sub-folders
#' containing the BIN-files, which were used by [Generate_DataFile] or [Generate_DataFile_MG]
#' to generate the `DATA` object.
#'
#' @param Nb_sample [integer] (**required**): ID number (in `[1,Nb_sample]`) of the
#' sample selected for plotting L/T as a function of regenerative doses.
#' Required if the `DATA` object contains information for more than one sample.
#'
#' @param BinPerSample [integer] (with default): integer vector (with default):
#' vector with the number of BIN files per sample, which was used in [Generate_DataFile] or
#' [Generate_DataFile_MG] to generate the `DATA` object.
#'
#' @param SampleNames [character] (with default): Names of samples. To use if there is more than one bin file per sample.
#'
#' @param SG [logical] (with default): vector to set the type of measurement for
#' each sample `length(SG)=Nb_sample`.If the sample of number ID equal to `i`, `SG[i]=TRUE`
#' if it is a Single-grain OSL measurements,
#' `SG[i]=FALSE` if it is a Multi-grain OSL measurements.
#'
#' @param sepDP [character] (with default): column separator in the `DiscPos.csv`
#' file or in Disc.csv file. It must be the same separator for all samples,
#' for single-grain OSL measurements or multi-grain OSL measurements.
#'
#' @param nrow [integer] (with default): controls the arrangement of the plots,
#' here the number of rows. Can be set to `NULL`.
#'
#' @param ncol [integer] (with default): controls the arrangement of the plots,
#' here the number of columns. Can be set to `NULL`.
#'
#' @details
#' To fill `FolderNames` and `BinPerSample`, we refer to the \bold{Detail} section from the
#' [Generate_DataFile] or [Generate_DataFile_MG] function.
#' As well for a precise description of input `DATA`.
#'
#' @return Lx/Tx plots; there are as many plots as selected aliquots in the `DiscPos.csv` file.
#' There are 9 plots per page.
#' There is not interpolation.
#'
#' @author Claire Christophe, Sebastian Kreutzer, Anne Philippe, Guillaume Guérin
#'
#' @seealso [Generate_DataFile], [Generate_DataFile_MG]
#'
#' @examples
#' \dontrun{
#' ## load data file generated by the function Generate_DataFile
#' data(DATA3,envir = environment())
#' path<- system.file("extdata/FER1", "", package="BayLum")
#' folder=""
#' samplename <- "FER1"
#' LT_RegenDose(
#'  DATA = DATA3,
#'  Path = path,
#'  FolderNames = folder,
#'  SampleNames = samplename,
#'  Nb_sample = 1,
#'  SG = FALSE)
#' }
#'
#' @name LT_RegenDose-deprecated
#' @md
#' @export
LT_RegenDose<-function(
  DATA,
  Path,
  FolderNames,
  SampleNames = FolderNames,
  Nb_sample,
  BinPerSample = rep(1,Nb_sample),
  SG = rep(TRUE, Nb_sample),sepDP=c(","),
  nrow = 3L,
  ncol = nrow
){

  .Deprecated("plot_RegDosePoints()")

  ##get number of samples
  CSBinPerSample <- cumsum(BinPerSample)

  ##loop to generate the plots
  for(I in 1:Nb_sample){
    ##plot setting per sample ... if wanted and make sure that we clean up the mess afterwards
    if(!is.null(nrow) & !is.null(ncol)){
      par_default <- par()$mfrow
      on.exit(par(mfrow = par_default))
      par(mfrow = c(nrow, ncol))

    }

    if(BinPerSample[I]==1){
      index <- 0

    }else{
      index <- rep(0,BinPerSample[I])
      index[2:BinPerSample[I]] <- cumsum(DATA$J[(CSBinPerSample[I]-BinPerSample[I]+1):(CSBinPerSample[I]-1)])
    }
    for(bf in 1:BinPerSample[I]){
      for(j in 1:DATA$J[bf+CSBinPerSample[I]-BinPerSample[I]]){
        if(SG[I]){
          DP <- read.csv(file=paste(Path,FolderNames[(CSBinPerSample[I]-BinPerSample[I]+bf)],"/DiscPos.csv",sep=""),sep=sepDP)
          plot(
            x = DATA$regDose[[I]][(index[bf]+j),(1:(DATA$K[(CSBinPerSample[I]-BinPerSample[I]+bf)]))],
            y = DATA$LT[[I]][(index[bf]+j),2:(DATA$K[(CSBinPerSample[I]-BinPerSample[I]+bf)]+1)],
            main = paste('sample:',SampleNames[I]),
            xlab = "Dose (Gy)",
            ylab = expression(L[x]/T[x]))

          ##add information on position and disc
          mtext(side = 3, c(paste("Disc = ",DP[j,1],', Pos =',DP[j,2])))

        }else{
          DP <- read.csv(file=paste(Path,FolderNames[(CSBinPerSample[I]-BinPerSample[I]+bf)],"/Disc.csv",sep=""),sep=sepDP)
          plot(
            x = DATA$regDose[[I]][(index[bf]+j),(1:(DATA$K[(CSBinPerSample[I]-BinPerSample[I]+bf)]))],
            y = DATA$LT[[I]][(index[bf]+j),2:(DATA$K[(CSBinPerSample[I]-BinPerSample[I]+bf)]+1)],
            main = paste('sample:',SampleNames[I]),
            xlab = "Dose (Gy)",
            ylab = expression(L[x]/T[x]))

          ##add information on the disc
          mtext(side = 3, c(paste("Disc = ",DP[j,1])))
        }
      }
    }
  }
}