R/PlotDrift.R

In gilles-guillot/Geneland: Clustering of living organisms from geo-referenced genetic and/or morphometrics data

#' @title PlotDrift
#' @description Gives a plot of the trace of the drift factors along the
#'   MCMC run 
#' @usage PlotDrift(path.mcmc,printit=FALSE,file)
#'   @param path.mcmc  Path to output files directory 
#'   @param printit Logical : if TRUE, figures are also printed
#'   @param file Character : Path to file where figures
#'     should be printed
#' @export
PlotDrift <- function(path.mcmc,printit=FALSE,file)
  {
    fileparam <- paste(path.mcmc,"parameters.txt",sep="/")
    param <- as.matrix(read.table(fileparam))
    thinning <- as.numeric(param[param[,1]=="thinning",3])
    
    filedrift <-  paste(path.mcmc,"drifts.txt",sep="")
    drift <- as.matrix(read.table(filedrift))
    npopmax <- ncol(drift)
    if(printit == TRUE){
      postscript(file=file)
      par(mfrow=c(ceiling(sqrt(npopmax)),ceiling(sqrt(npopmax))))
      for(iclass in 1:npopmax)
        {
          plot(drift[,iclass],
               xlab=paste("Index of MCMC iteration"," (x ",thinning,")",sep=""),
               ylab=paste("Drift of population",iclass),type="l")
        }
      dev.off()
    }
    dev.new()
    par(mfrow=c(ceiling(sqrt(npopmax)),ceiling(sqrt(npopmax))))
    for(iclass in 1:npopmax)
      {
        plot(drift[,iclass],
             xlab=paste("Index of MCMC iteration"," (x ",thinning,")",sep=""),
             ylab=paste("Drift of population",iclass),
             type="l",ylim=c(0,max(drift))) 
      }
  }