R/multiplot.TL.R

In Zink-Antoine/TLpack: Analyse TL measurement using Bayesian approach, MCMC, Gibbs and slice samplers

#' multiplot.TL
#'
#' plot for TL measurements
#'
#' @param file [Risoe.BINfileData-class] (**required**) the BIN/BINX file(s)
#' @param nomFile [character] (**with default**) name of the BIN/BINX file
#' @param ech [numeric] (**with default**) the sample number
#' @param Doseb0 [numeric] (**with default**)  the reference of beta irradiation (in seconds)
#' @param Dosea0 [numeric] (**with default**)  the reference of alpha irradiation (in seconds)
#' @param supra [logical] (**with default**) TRUE if supra measurements are included. Based on the number of data files, the value is corrected
#' @param norm [logical] (**with default**) TRUE if the measurements are normalized.
#' @param plateau [numeric],[list] (**with default**) the plateau range for normalization
#' @param Temp [numeric],[list] (**with default**) the temperature range
#' @param Ib.max [numeric] (**with default**) the Y-axis range for beta curve (default value is the maximum of TL intensity between 175°C and 450°C increased by 25%)
#' @param Ia.max [numeric] (**with default**) the Y-axis range for alpha curve (default value is the maximum of TL intensity between 175°C and 450°C increased by 25%)
#' @param Isup.max [numeric] (**with default**) the Y-axis range for supralinearity curve (default value is the maximum of TL intensity between 175°C and 450°C increased by 25%)
#' @param NumInv [character] (**with default**) the inventory number
#' @param b.check [numeric],[list] (**with default**) list of beta curves to plot
#' @param a.check [numeric],[list] (**with default**) list of alpha curves to plot
#' @param sup.check [numeric],[list] (**with default**) list of supralinarity curves to plot
#' @param brate [numeric] (**with default**) dose rate of the beta source (default value 0.1 Gy/s)
#' @param arate [numeric] (**with default**) dose rate of the alpha source (default value 0.1 micro-2)
#'
#' @return plot figures
#'
#'
#' @export
#'
#' @examples
#'
#' \dontrun{
#' library(OSLpack)
#' file<-OSLpack::ReadFile(n=1)
#'
#' File<-file$FILE
#' NFile<-file$NFILE
#'
#' png("TLplot.png",width=720,height=960)
#' multiplot.TL(file=File,nomFile=NFile)
#' dev.off()
#' }
#'

'multiplot.TL'<-
function(file,nomFile="",ech=1,
         Doseb0=90,Dosea0=0,
         supra=FALSE,norm=FALSE,
         plateau=seq(200,500),Temp=seq(26,599),
         Ib.max=-1,Ia.max=-1,Isup.max=-1,
         NumInv="",
         b.check=rep(1,9),a.check=rep(1,4),sup.check=rep(1,9),
         brate=0.1, arate=0.1) {

	alpha<-Dosea0>1
	plateau.corr<-mapply(Canal,Temp=plateau,file=list(file[[1]]))
	if (supra) 	plateau.corr.sup<-mapply(Canal,Temp=plateau,file=list(file[[2]]))

	L<-Lum(file,ech=ech,Doseb0=Doseb0,Dosea0=Dosea0,alpha=alpha,supra=supra,Temp=Temp)

	par(mfrow=c(2,2),mar=c(3,3,2,2))

	Ib<-L$b
	if (alpha) Ia<-L$a
	if (supra) Isup<-L$bsup
	if (norm){
		for (i in 1:3){
			for (j in 1:3){
				Ib[,j,i]<-Ib[,j,i]/sum(L$n[plateau.corr,,(i-1)*3+j])
				if (supra) {Isup[,j,i]<-Isup[,j,i]/sum(L$nsup[plateau.corr.sup,,(i-1)*3+j])}
			}
		}
		if (alpha)
		{
			for (i in 1:2){
				for (j in 1:2){
					Ia[,j,i]<-Ia[,j,i]/sum(L$n[plateau.corr,,(i-1)*2+9+j])
				}
			}
		Ia[NaN]<-0
		}
		Ib[NaN]<-0
		if (supra) Isup[NaN]<-0
	}

	if (Ib.max<0){Ib.max=max(Ib[seq(175,450),,])*1.25}

	plot(Temp,xlim=c(20,500),ylim=c(0,Ib.max),col=1,type="l",axes=FALSE)
	axis(1,tcl=-0.2,padj=-2,cex.axis=0.7)
	axis(2,tcl=-0.2,padj=2,cex.axis=0.7)
	box()
	title(xlab=paste("Temperature (\u00B0","C)",sep=""),ylab="Luminescence (ua)",cex.lab=0.7,line=1)
	text(50,max(Ib[seq(200,450),,])*1.05,"Irradiation beta",cex=1,adj=0)
	for (i in 1:3){
		for (j in 1:3){
	   lines(Temp,Ib[,j,i],col=j*b.check[3*(i-1)+j])
		}
	}

	if (alpha)
	{
	  if (Ia.max<0){Ia.max=max(Ia[seq(175,450),,])*1.25}
		plot(Temp,xlim=c(20,500),ylim=c(0,Ia.max),col=1,type="l",axes=FALSE)
		axis(1,tcl=-0.2,padj=-2,cex.axis=0.7)
		axis(2,tcl=-0.2,padj=2,cex.axis=0.7)
		box()
		title(xlab=paste("Temperature (\u00B0","C)",sep=""),ylab="Luminescence (ua)",cex.lab=0.7,line=1)
		text(50,max(Ia[seq(200,450),,])*1.05,"Irradiation alpha",cex=1,adj=0)
		for (i in 1:3){
			lines(Temp,Ib[,1,i],col=1*b.check(i))
		}
		for (i in 1:2){
			lines(Temp,Ia[,1,i],col=2*a.check[i])
			lines(Temp,Ia[,2,i],col=3*a.check[2+i])
		}
	}

	if (supra)
	{
	  if (Isup.max<0){Isup.max=max(Isup[seq(175,450),,])*1.25}
		plot(Temp,xlim=c(20,500),ylim=c(0,Isup.max),col=1,type="l",axes=FALSE)
		axis(1,tcl=-0.2,padj=-2,cex.axis=0.7)
		axis(2,tcl=-0.2,padj=2,cex.axis=0.7)
		box()
		title(xlab=paste("Temperature (\u00B0","C)",sep=""),ylab="Luminescence (ua)",cex.lab=0.7,line=1)
		text(50,max(Isup[seq(200,450),,])*1.05,paste("Supralin\u00e9","arit\u00e9",sep=""),cex=1,adj=0)
		for (j in 1:3){
			for (i in 1:3){
				lines(Temp,Isup[,j,i],col=i*sup.check[3*(i-1)+j])
			}
		}
	}

	plot.default(c(0,100), c(0,100), type="n", axes=FALSE,ylab="", xlab="")

	position<-c(-5,35,75)
	couleur<-c("black","red","green")
	beta.text<-c("beta : Nat",paste("Nat+",Doseb0*brate,"Gy",sep=""),paste("Nat+",2*Doseb0*brate,"Gy",sep=""))
	alpha.text<-c("alpha : Nat",paste("Nat+",Dosea0*arate,"\u00b5","m-2",sep=""),paste("Nat+",2*Dosea0*arate,"\u00b5","m-2",sep=""))
	supra.text<-c(paste("supra :",Doseb0*brate,"Gy  ",sep=""),paste(2*Doseb0*brate,"Gy  ",sep=""),paste(3*Doseb0*brate,"Gy",sep=""))

	text(50,90,paste("n. inv. ",NumInv[ech]))
	text(50,80,"Thermoluminescence")
	text(50,70,paste("1re chauffe : fichier ",nomFile[[1]][1]))
	text(position,60,beta.text,col=couleur,pos=4,cex=0.9)
	if (alpha) text(position,50,alpha.text,col=couleur,pos=4,cex=0.9)
	if (supra) {text(50,40,paste("2nde chauffe : fichier ",nomFile[[1]][2]))
	text(position,30,supra.text,col=couleur,pos=4,cex=0.9)}

}