R/Plotntile.R

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

#' @title Plotntile
#' @description Plot of number of tiles in the Poisson-Voronoi tessellation
#'   along the MCMC run
#' @usage Plotntile(path.mcmc,burnin,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
#'  @param burnin An integer: number of saved iterations to discard for
#'     the representation of the histogram of the chain
#'  @export
Plotntile <- function(path.mcmc,burnin,printit=FALSE,file)
  {
    fileparam <- paste(path.mcmc,"parameters.txt",sep="/")
    param <- as.matrix(read.table(fileparam))
    thinning <- as.numeric(param[param[,1]=="thinning",3])
    
    filenpp <- paste(path.mcmc,"nuclei.numbers.txt",sep="")
    npp <- scan(filenpp)
    if(burnin >0)
      {
        sub <- -(1:burnin)
      }else
    {
      sub <- 1:length(npp)
    }
    if(printit==TRUE){
      postscript(file)
      par(mfrow=c(1,2))
      plot((1:length(npp))*thinning,npp,type="l",
           ylab="Number of Tiles",
           xlab=paste("Index of MCMC iteration"," \n Whole chain",sep=""))
      hist(npp[sub],plot=TRUE,prob=TRUE,
           xlab=paste("Number of tiles along the chain \n(after a burnin of ",burnin,"x",thinning," it.)",sep=""),
            main="Number of tiles along the chain  \n  after burnin")
      dev.off()
    }
    else{
      par(mfrow=c(1,2))
      plot((1:length(npp))*thinning,npp,type="l",ylab="Number of Tiles",
           xlab=paste("Index of MCMC iteration" ,"\n Whole chain",sep=""))
      hist(npp[sub],plot=TRUE,prob=TRUE,
           xlab=paste("Number of tiles along the chain \n(after a burnin of ",burnin,"x",thinning," it.)",sep=""),
            main="Number of tiles along the chain  \n  after burnin")
    }
  }