R/DDgrowth.R

In NZRLIC/RLPlots: Graphical outputs for New Zealand rock lobster stock assessment

#' DDgrowth plots
#'
#' @param run the directory where the outputs for a run are sitting
#' @param stock the name of the stock (e.g. CRA1)
#' @export
#' 
DDgrowth <- function(stock, source.dir, target.dir = source.dir)
{
    dat<-read.table(paste(source.dir,"/",stock,"DDgrowth.out",sep=""),header=T,as.is=T)
    size <- unique(dat$Size)
    if(length(size)>1) stop('>1 size \n')
    x<-dat$Year
    #Set graphics parameters
    PlotType(paste(target.dir, "/", stock, "DDgrowth", sep = ""), width = 270, height = 200)
    par(las=1,oma=c(1,1,1,1),mar=c(4,4,1,1),mgp=c(3,1,0)) 
    plot(dat$B.Bo,dat$maleinc,type="b",pch=21,ylim=range(dat$maleinc,dat$feminc),ylab="Growth increment",xlab="Depletion relative to total equilibrium biomass")
    #text(dat$B.Bo,dat$maleinc,labels=substring(x,3))
    points(dat$B.Bo,dat$feminc,type="b",pch=19)
    legend('topright',c('Female','Male'),lty=2,pch=c(19,21),bty='n')
    if(PlotOptions$Captions)
    {
        mtext(paste(source.dir," ",stock,": Growth increments at size",size),side=1,line=0,outer=TRUE,cex=0.7)
    }
    dev.off()
}