R/plotZScoresForSurveys.R

In wStockhausen/rTCSAM2015: A set of tools to set up input for, and interact with output from, a TCSAM2015 model run, as well as to compare TCSAM2015 and rsimTCSAM runs.

#'
#'@title Plot model fits to abundance, biomass and size frequencies as z-scores for surveys.
#'
#'@param repObj - model report list object
#'
#'@return list by survey of lists with ggplot objects
#'
#'@details Superseded by \code{plotZScoresForFleets()}.
#'
#'@export
#'
plotZScoresForSurveys<-function(repObj,showPlot=FALSE){
    cat("---Running plotZScoresForSurveys(...)\n");
    plots.srv<-list();
    srvs<-names(repObj$model.fits$surveys)
    for (srv in srvs){
        if (srv!=''){
            plots<-list();
            cat("Plotting fits for survey '",srv,"'.\n",sep='')
            sfit<-repObj$model.fits$surveys[[srv]];
            if (!is.null(sfit$abundance)){
                cat("Plotting zscores for abundance time series.\n")
                afits<-sfit$abundance$fits;
                plots$abund<-plotZScoresGG(afits,ylab='abundance',label=srv,showPlot=showPlot)
            }
            if (!is.null(sfit$biomass)){
                cat("Plotting zscores for biomass time series.\n")
                afits<-sfit$biomass$fits;
                plots$biom<-plotZScoresGG(afits,ylab='biomass',label=srv,showPlot=showPlot)
            }
            if (!is.null(sfit$n.at.z)){
                plots$zfs<-plotFitsGG.SizeComps(    sfit$n.at.z,repObj$mc,label=srv,showPlot=showPlot)
                plots$mzfs<-plotFitsGG.MeanSizeComps(sfit$n.at.z,repObj$mc,label=srv,showPlot=showPlot)
                cat("Plotting zscores for size frequencies.\n")
                plots$zrs<-plotZScoresGG1.SizeFreqs(sfit$n.at.z,repObj$mc,label=srv,showPlot=showPlot)
                cat("Plotting ESSs for size frequencies.\n")
                plots$effn<-plotEffNsGG(sfit$n.at.z,repObj$mc,label=srv,showPlot=showPlot)
            }
            plots.srv[[srv]]<-plots;
        }
    }
    cat("---Done running plotZScoresForSurveys(...)\n");
    return(invisible(plots.srv));
}