R/plotZScoresForFisheries.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 fishery data components.
#'
#'@param repObj - model report list object
#'@param showPlot - flag to show plots immediately
#'@param verbose - flag (T/F) to print dagnostic info
#'
#'@return list by fishery of lists with ggplot objects
#'
#'@details Superseded by \code{plotZScoresForFleets()}.
#'
#'@export
#'
plotZScoresForFisheries<-function(repObj,
                                  showPlot=TRUE,
                                  verbose=FALSE){
    plots.fsh<-list();
    fshs<-names(repObj$model.fits$fisheries)
    for (fsh in fshs){
        if (fsh!=''){
            plots.ret<-list();
            fit<-repObj$model.fits$fisheries[[fsh]]$retained.catch;
            if (!is.null(fit)){
                if (!is.null(fit$abundance)){
                    if (verbose) cat("Plotting retained catch abundance zscores for",fsh,"\n")
                    afits<-fit$abundance$fits;
                    plots.ret$abund<-plotZScoresGG(afits,ylab='abundance',label=paste(fsh,": ","retained catch abundance",sep=''),showPlot=showPlot);
                }
                if (!is.null(fit$biomass)){
                    if (verbose) cat("Plotting retained catch biomass zscores for",fsh,"\n")
                    afits<-fit$biomass$fits;
                    plots.ret$biom<-plotZScoresGG(afits,ylab='biomass',label=paste(fsh,": ","retained catch biomass",sep=''),showPlot=showPlot);
                }
                if (!is.null(fit$n.at.z)){
                    if (verbose) cat("Plotting fits for total catch size frequencies.\n")
                    plots.ret$zfs <-plotFitsGG.SizeComps(    fit$n.at.z,repObj$mc,label=paste(fsh,": ","retained catch",sep=''),showPlot=showPlot)
                    plots.ret$mzfs<-plotFitsGG.MeanSizeComps(fit$n.at.z,repObj$mc,label=paste(fsh,": ","retained catch",sep=''),showPlot=showPlot)
                    cat("Plotting retained catch size frequency zscores for",fsh,"\n")
                    plots.ret$zrs<-plotZScoresGG1.SizeFreqs(fit$n.at.z,repObj$mc,label=paste(fsh,": ","retained catch",sep=''))
                    cat("Plotting ESSs for size frequencies.\n")
                    plots.ret$effn<-plotEffNsGG(fit$n.at.z,repObj$mc,label=paste(fsh,": ","retained catch",sep=''),showPlot=showPlot)
                }
            }
            plots.dsc<-list();
            fit<-repObj$model.fits$fisheries[[fsh]]$discard.catch;
            if (!is.null(fit)){
                if (!is.null(fit$abundance)){
                    if (verbose) cat("Plotting discard catch abundance zscores for",fsh,"\n")
                    afits<-fit$abundance$fits;
                    plots.dsc$abund<-plotZScoresGG(afits,ylab='abundance',label=paste(fsh,": ","discard catch abundance",sep=''),showPlot=showPlot);
                }
                if (!is.null(fit$biomass)){
                    if (verbose) cat("PLotting discard catch biomass zscores for",fsh,"\n")
                    afits<-fit$biomass$fits;
                    plots.dsc$biom<-plotZScoresGG(afits,ylab='biomass',label=paste(fsh,": ","discard catch biomass",sep=''),showPlot=showPlot);
                }
                if (!is.null(fit$n.at.z)){
                    if (verbose) cat("Plotting fits for discard catch size frequencies.\n")
                    plots.tot$zfs <-plotFitsGG.SizeComps(    fit$n.at.z,repObj$mc,label=paste(fsh,": ","discard catch",sep=''),showPlot=showPlot)
                    plots.tot$mzfs<-plotFitsGG.MeanSizeComps(fit$n.at.z,repObj$mc,label=paste(fsh,": ","discard catch",sep=''),showPlot=showPlot)
                    if (verbose) cat("Plotting discard catch size frequency zscores for",fsh,"\n")
                    plots.dsc$zrs<-plotZScoresGG1.SizeFreqs(fit$n.at.z,repObj$mc,label=paste(fsh,": ","discard catch",sep=''),showPlot=showPlot)
                    if (verbose) cat("Plotting ESSs for size frequencies.\n")
                    plots.dsc$effn<-plotEffNsGG(fit$n.at.z,repObj$mc,label=paste(fsh,": ","discard catch",sep=''),showPlot=showPlot)
                }
            }
            plots.tot<-list();
            fit<-repObj$model.fits$fisheries[[fsh]]$total.catch;
            if (!is.null(fit)){
                if (!is.null(fit$abundance)){
                    if (verbose) cat("Plotting total catch abundance zscores for",fsh,"\n")
                    afits<-fit$abundance$fits;
                    plots.tot$abund<-plotZScoresGG(afits,ylab='abundance',label=paste(fsh,": ","total catch abundance",sep=''),showPlot=showPlot);
                }
                if (!is.null(fit$biomass)){
                    if (verbose) cat("Plotting total catch biomass zscores for",fsh,"\n")
                    afits<-fit$biomass$fits;
                    plots.tot$biom<-plotZScoresGG(afits,ylab='biomass',label=paste(fsh,": ","total catch biomass",sep=''),showPlot=showPlot);
                }
                if (!is.null(fit$n.at.z)){
                    cat("Plotting fits for total catch size frequencies.\n")
                    plots.tot$zfs <-plotFitsGG.SizeComps(    fit$n.at.z,repObj$mc,label=paste(fsh,": ","total catch",sep=''),showPlot=showPlot)
                    plots.tot$mzfs<-plotFitsGG.MeanSizeComps(fit$n.at.z,repObj$mc,label=paste(fsh,": ","discard catch",sep=''),showPlot=showPlot)
                    cat("Plotting total catch size frequencies for",fsh,"\n")
                    plots.tot$zrs<-plotZScoresGG1.SizeFreqs(fit$n.at.z,repObj$mc,label=paste(fsh,": ","total catch",sep=''),showPlot=showPlot)
                    cat("Plotting ESSs for size frequencies.\n")
                    plots.tot$effn<-plotEffNsGG(fit$n.at.z,repObj$mc,label=paste(fsh,": ","total catch",sep=''),showPlot=showPlot)
                }
            }
            plots.fsh[[fsh]]<-list(ret=plots.ret,dsc=plots.dsc,tot=plots.tot);
        }
    }#fsh
    return(invisible(plots.fsh));
}