R/compareResults.Fisheries.Catchability.R

In wStockhausen/rCompTCMs: Package to compare TCSAM02, rsimTCSAM, and TCSAM2013 model runs

#'
#'@title Function to plot fishery catchabilities by year using ggplot2
#'
#'@description This function plots fishery catchability estimates by year,
#'   sex and maturity state.
#'
#' @param objs - list of resLst objects
#' @param fleets - vector of fisheries to plot, or "all"
#' @param years - vector of years to show, or 'all' to show all years
#' @param cast - formula to exclude factors from "averaging" over
#' @param dodge - width to dodge overlapping series
#' @param facet_grid - ggplot2 formula to produce figure with gridded facets
#' @param scales - parameter passed to ggplot2::facet_grid()
#' @param plotPoints - flag to plot points
#' @param colour_scale - ggplot2 colour scale to substitute for default (if not NULL)
#' @param fill_scale - ggplot2 fill scale to substitute for default (if not NULL)
#' @param pdf - creates pdf, if not NULL
#' @param showPlot - flag (T/F) to show plot
#' @param verbose - flag (T/F) to print diagnostic information
#'
#'@return lists ofggplot2 objects, nested by fishery or an empty list if year is NULL
#'
#'@details None.
#'
#'@import ggplot2
#'
#'@export
#'
compareResults.Fisheries.Catchability<-function(objs,
                                                fleets="all",
                                                years='all',
                                                cast='x',
                                                dodge=0.2,
                                                facet_grid="x~.",
                                                scales="free_y",
                                                plotPoints=TRUE,
                                                colour_scale=NULL,
                                                fill_scale=NULL,
                                                pdf=NULL,
                                                showPlot=FALSE,
                                                verbose=FALSE){
    if (verbose) cat("Starting rCompTCMs::compareResults.Fisheries.Catchability().\n");
    options(stringsAsFactors=FALSE);

    if (is.null(years)) return(list());

    cases<-names(objs);

    #create pdf, if necessary
    if(!is.null(pdf)){
        pdf(file=pdf,width=11,height=8,onefile=TRUE);
        on.exit(grDevices::dev.off());
        showPlot<-TRUE;
    }

    mdfr<-extractMDFR.Fisheries.Catchability(objs,fleets=fleets,years=years,cast=cast,verbose=verbose);

    #----------------------------------
    # plot fishery catchability by year
    #----------------------------------
    std_theme = wtsPlots::getStdTheme();
    uF<-unique(mdfr$fleet);
    if (fleets[1]!="all") uF<-fleets;
    plots<-list();
    pd<-position_dodge(width=dodge);
    for (f in uF){
        if (verbose) cat("Plotting fleet",f,"\n")
        mdfrp<-mdfr[mdfr$fleet==f,];
        p <- ggplot(mdfrp,aes_string(x='y',y='val',colour='case'));
        p <- p + geom_line(position=pd);
        if (plotPoints) p <- p + geom_point(position=pd);
        if (any(!is.na(mdfr$lci))) p <- p + geom_errorbar(aes_string(ymin='lci',ymax='uci'),position=pd);
        p <- p + labs(x='year',y="fishery catchability");
        p <- p + ggtitle(f);
        p <- p + facet_grid(facet_grid,scales=scales);
        p <- p + ylim(c(0,NA));
        if (!is.null(colour_scale)) p = p + colour_scale;
        if (!is.null(fill_scale))   p = p + fill_scale;
        if (showPlot) print(p);
        cap<-paste0("\n  \nFigure &&figno. Fishery catchabilities for ",f,".\n   \n");
        plots[[cap]]<-p+std_theme;
    }

    # p <- ggplot(mdfr,aes_string(x='y',y='val',colour='case'));
    # p <- p + geom_line(position=pd);
    # p <- p + geom_point(position=pd);
    # if (any(!is.na(mdfr$lci))) p <- p + geom_errorbar(aes_string(ymin='lci',ymax='uci'),position=pd);
    # p <- p + labs(x='year',y="fishery catchability");
    # p <- p + facet_grid(facet_grid,scales="free_y");
    # p <- p + ylim(c(0,max(1.0,1.05*max(mdfr$val,mdfr$uci,rm.na=TRUE))));
    # if (showPlot) print(p);
    # cap<-paste0("\n  \nFig. &&figno. Fishery catchabilities.\n   \n");
    # plots[[cap]]<-p;

    if (verbose) cat("Finished rCompTCMs::compareResults.Fisheries.Catchability().\n");
    return(plots)
}