#'
#'@title Plot fits to size comps by fleet among several model runs from a dataframe
#'
#'@description Function to plot fits to size comps by fleet among
#'several model runs from a dataframe.
#'
#' @param mdfr - dataframe from call to \code{rCompTCMs::extractFits.SizeComps}
#' @param ylab - y axis label
#' @param cap1 - template for caption
#' @param plotObs - flag to plot observations
#' @param plotMod - flag to plot model predictions
#' @param plotObsAsBars - flag (T/F) to plot observations/predictions as bars/lines (T) or lines/bars (F)
#' @param nrow - number of rows per page for output plots
#' @param ncol - number of columns per page for output plots
#' @param pdf - name for output pdf file
#' @param showPlot - flag (T/F) to show plot
#' @param verbose - flag (T/F) to print diagnostic information
#'
#'@details Uses \code{wtsUtilities::printGGList}.
#'
#'@return Non-nested list of ggplot2 objects, with captions as names
#'
#'@import ggplot2
#'
#'@export
#'
plotMDFR.Fits.SizeComps<-function(mdfr=NULL,
ylab="",
cap1="1",
plotObs=TRUE,
plotMod=TRUE,
plotObsAsBars=TRUE,
nrow=5,
ncol=3,
pdf=NULL,
showPlot=FALSE,
verbose=FALSE){
if (verbose) cat("Starting rCompTCMs::plotMDFR.Fits.SizeComps().\n");
options(stringsAsFactors=FALSE);
#create pdf, if necessary
if(!is.null(pdf)){
cat("Creating pdf:",pdf,"\n");
pdf(file=pdf,width=11,height=8,onefile=TRUE);
on.exit(grDevices::dev.off());
showPlot<-TRUE;
}
#----------------------------------
# define output list of plots
#----------------------------------
plots<-list();
figno<-1;
std_theme = ggplot2::theme(plot.background =ggplot2::element_blank(),
panel.background=ggplot2::element_blank(),
panel.border =ggplot2::element_rect(colour="black",fill=NA),
panel.grid =ggplot2::element_blank(),
panel.spacing =unit(0,units="cm"));
idx<-mdfr$x=="all"; mdfr$x[idx]<-"all sex";
idm<-mdfr$m=="all"; mdfr$m[idm]<-"all maturity";
ids<-mdfr$s=="all"; mdfr$s[ids]<-"all shell";
mdfrp<-NULL;
if (plotObs) mdfrp<-rbind(mdfrp,mdfr[mdfr$type=="observed",]);
if (plotMod) mdfrp<-rbind(mdfrp,mdfr[mdfr$type=="predicted",]);
mdfr<-mdfrp;
#----------------------------------
# plot fits to size comps
#----------------------------------
if (verbose) cat("Plotting",nrow(mdfr),"rows.\n")
xs<-c("male","female","all sex");
ms<-c("immature","mature","all maturity");
ss<-c("new shell","old shell","all shell");
zs<-sort(unique(mdfr$z));
mxp<-nrow*ncol;
xlab<-'size (mm CW)';
for (fleet in unique(mdfr$fleet)){
if (verbose) cat("Plotting fleet '",fleet,"'.\n",sep='');
idf<-mdfr$fleet==fleet;
pxs<-list();
for (x in xs){
idx<-mdfr$x==x;
pms<-list();
for (m in ms){
idm<-mdfr$m==m;
pss<-list();
for (s in ss){
ids<-mdfr$s==s;
if (verbose) cat("Checking",x,m,s,"\n");
pgs<-list();
if (sum(idf&idx&idm&ids)==0){
if (verbose) cat("--Dropping",x,m,s,"\n");
} else {
if (verbose) cat("--Plotting",x,m,s,"size comps\n");
mdfrp<-mdfr[idf&idx&idm&ids,];#select results for fleet, sex, maturity state, and shell condition
if (verbose) cat("--Plotting",nrow(mdfrp),"rows.\n")
#add in missing years as size comps with 0's
ys<-sort(unique(mdfrp$y));
mny<-5*floor(min(ys)/5);
mxy<-mny+mxp*ceiling((max(ys)-mny+1)/mxp)-1;
mdfrpp<-mdfrp[1,];
mdfrpp$val<-0;
if (mny<min(ys)){
for (y in mny:(min(ys)-1)) {
mdfrpp$y<-y;
mdfrp<-rbind(mdfrp,mdfrpp);
}
}
if (mxy>max(ys)){
for (y in (max(ys)+1):mxy) {
mdfrpp$y<-y;
mdfrp<-rbind(mdfrp,mdfrpp);
}
}
ys<-mny:mxy;
npg<-ceiling(length(ys)/mxp);
if (verbose) cat("mny =",mny,",mxy =",mxy,", npg =",npg,'\n')
for (y in ys){
if (!any(mdfrp$y==y)) {
#year y is missing, so add in zero size comp for year y
mdfrpp$y<-y;
mdfrp<-rbind(mdfrp,mdfrpp);
}
}
rng<-range(mdfrp$val,na.rm=TRUE,finite=TRUE);
if (verbose) cat("rng = ",rng,'\n')
for (pg in 1:npg){ #loop over pages
dfrp<-mdfrp[(mdfrp$y %in% ys[(pg-1)*mxp+1:mxp]),]
#do plot
pd<-position_identity();
p <- ggplot(data=dfrp);
if (plotObsAsBars){
p <- p + geom_bar(aes(x=z,y=val,fill=case),data=dfrp[dfrp$type=='observed',],stat="identity",position='identity',alpha=0.5);
p <- p + geom_line(aes(x=z,y=val,colour=case),data=dfrp[(dfrp$type=='predicted'),],size=1);
p <- p + guides(fill=guide_legend('observed'),colour=guide_legend('predicted'));
} else {
p <- p + geom_bar(aes(x=z,y=val,fill=case),data=dfrp[dfrp$type=='predicted',],stat="identity",position='identity',alpha=0.5);
p <- p + geom_line(aes(x=z,y=val,colour=case),data=dfrp[(dfrp$type=='observed'),],size=1);
p <- p + guides(fill=guide_legend('predicted'),colour=guide_legend('observed'));
}
p <- p + ylim(0,rng[2])
p <- p + geom_hline(yintercept=0,colour='black',size=0.5)
p <- p + labs(x=xlab,y=ylab)
p <- p + facet_wrap(~y,ncol=ncol,dir='v')
ttl<-paste0(fleet,': ',x,", ",m,", ",s);
if (verbose) cat("Plotting '",ttl,"'.\n",sep='')
p <- p + ggtitle(ttl)
xms<-paste0(x,", ",m,", ",s);
cp1<-gsub("&&xms",xms,cap1,fixed=TRUE);
cp1<-gsub("&&fleet",fleet,cp1,fixed=TRUE);
cp1<-gsub("&&pg",paste0("Page ",pg," of ",npg),cp1,fixed=TRUE);
if (showPlot) figno<-wtsUtilities::printGGList(p,figno,cp1,showPlot)$figno;
plots[[cp1]]<-p+std_theme;
}#pg
}#if
}#ss
}#ms
}#xs
}#fleets
if (verbose) cat("Finished rCompTCMs::plotMDFR.Fits.SizeComps().\n");
return(plots);
}
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