Nothing
#' Script for the plateau test
#'
#' This script calls a series of data pretreatment functions before performing the plateau test.
#' It just requires the name of the file with the TL curves and the relative error on the measurements.
#'
#' @param file.name
#' \link{character} (\bold{required}): Name of the file containing the luminescence data.
#' @param k
#' \link{numeric} (with default): Corrective factor for estimating the uncertainties using a poisson distribution.
#' @param remove.discs
#' \link{numeric} (with default): list containing the position of the aliquots that shall be removed.
#' @param file.parameters
#' \link{list} (with default): list containing the file parameters. See details.
#' @param aligning.parameters
#' \link{list} (with default): list containing the aligning parameters. See details.
#' @param plotting.parameters
#' \link{list} (with default): list containing the plotting parameters. See details.
#'
#' @details
#' \bold{Aligning parameters} \cr
#' The aligning parameters are: \cr
#' \describe{
#' \item{\code{peak.Tmin}}{
#' \link{numeric}: Lower boundary for looking for the peak maximum position.}
#' \item{\code{peak.Tmax}}{
#' \link{numeric}: Upper boundary for looking for the peak maximum position.}
#' \item{\code{no.testdose}}{
#' \link{logical}: If \code{TRUE}, the function will use the Lx curves rather than the Tx curves as reference for the peak maximum position.}
#' }
#'
#' \bold{File parameters} \cr
#' The file parameters are: \cr
#' \describe{
#' \item{\code{file.extension}}{
#' \link{character} (with default): extension of the file containing the luminescence data (.bin or .binx)}
#' \item{\code{folder.in}}{
#' \link{character} (with default): Folder containing the file with the luminescene data.}
#' \item{\code{folder.out}}{
#' \link{character} (with default): Folder containing the file with the new luminescene data.}
#' }
#' see also \link{script_TL.pretreatment}.
#'
#' \bold{Plotting parameters} \cr
#' The plotting parameters are: \cr
#' \describe{
#' \item{\code{plot.Tmin}}{
#' \link{numeric}: Lowest temperature plotted.}
#' \item{\code{plot.Tmax}}{
#' \link{numeric}: Highest temperature plotted.}
#' \item{\code{no.plot}}{
#' \link{logical}: If \code{TRUE}, the results will not be plotted.}
#' }
#' See also \link{plot_TL.MAAD}. \cr
#'
#'
#' @return
#' This function plots the results from the differents functions called using:
#' \link{plot_extract.TL},
#' \link{plot_remove.preheat}
#' \link{plot_substract.background}
#' \link{plot_align.peaks} and
#' \link{plot_TL.plateau}. \cr
#'
#'
#' @seealso
#' \link{read_BIN2R},
#' \link{Risoe.BINfileData2TLum.BIN.File},
#' \link{mod_extract.TL},
#' \link{mod_update.dType},
#' \link{mod_remove.aliquot},
#' \link{mod_remove.preheat},
#' \link{mod_substract.background},
#' \link{mod_align.peaks},
#' \link{write_R2BIN},
#' \link{TLum.BIN.File2TLum.Analysis} and
#' \link{analyse_TL.plateau}.
#'
#' @author David Strebler, University of Cologne (Germany).
#'
#' @export script_TL.plateau
script_TL.plateau <- function(
file.name,
k= 1,
remove.discs=NULL,
file.parameters=list(file.extension =".binx",
folder.in = "./",
folder.out = "./"),
aligning.parameters=list(peak.Tmin=NULL,
peak.Tmax=NULL,
no.testdose=FALSE),
plotting.parameters=list(plot.Tmin=0,
plot.Tmax=NA,
plateau.Tmin=0,
plateau.Tmax=0,
no.plot=FALSE)
){
# ------------------------------------------------------------------------------
# Integrity Check
# ------------------------------------------------------------------------------
if(missing(file.name)){
stop("[script_TL.plateau] Error: Input 'file.name' is missing.")
}else if(!is.character(file.name)){
stop("[script_TL.plateau] Error: Input 'file.name' is not of type 'character'.")
}
if(!is.numeric(k)){
stop("[script_TL.plateau] Error: Input 'k' is not of type 'numeric'.")
}
if(!is.list(file.parameters)){
stop("[script_TL.plateau] Error: Input 'file.parameters' is not of type 'list'.")
}
if(!is.list(aligning.parameters)){
stop("[script_TL.plateau] Error: Input 'aligning.parameters' is not of type 'list'.")
}
if(!is.list(plotting.parameters)){
stop("[script_TL.plateau] Error: Input 'plotting.parameters' is not of type 'list'.")
}
# ------------------------------------------------------------------------------
data <- script_TL.pretreatment(file.name = file.name,
k = k,
remove.discs = remove.discs,
file.parameters = file.parameters,
aligning.parameters = aligning.parameters,
plotting.parameters = plotting.parameters)
# MAAD analysis
temp.res <- analyse_TL.plateau(object = data,
plotting.parameters=plotting.parameters)
return(temp.res)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.