#'
#'@title Compare fits to size comps by fleet among several model runs
#'
#'@description Function to compare fits to size comps by fleet among
#'several model runs.
#'
#' @param objs - object that can be converted into a list of tcsam2013.resLst and/or tcsam02.resLst objects
#' @param mdfr - dataframe from call to [rCompTCMs::extractFits.SizeComps()] (as alternative to objs)
#' @param fleets - names of fleets to include (or "all")
#' @param fleet.type - fleet type ('fishery' or 'survey')
#' @param catch.type - catch type ('index','retained', or 'total')
#' @param years - years to plot, as numerical vector (or "all" to plot all years)
#' @param plot1stObs - flag (T/F) to plot observations only from first case, or character vector or cases from which to plot observations
#' @param nrow - number of rows per page for output plots
#' @param ncol - number of columns per page for output plots
#' @param useBars - flag to use bars for observations
#' @param usePins - flag to use pins for observations
#' @param usePinsAndPts - flag to add pts to observations when pins are used
#' @param useLines - flag to use lines for predictions
#' @param usePoints - flag to use points for predictions
#' @param pinSize - width of pin line
#' @param lineSize - prediction line size
#' @param pointSize - prediction point size
#' @param alpha - prediction transparency
#' @param stripText - [ggplot2::element_text()] object describing font and margin to use for panel strips
#' @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 [rCompTCMs::extractFits.SizeComps()] to extract results.
#'Also uses [wtsUtilities::printGGList()].
#'
#'If \code{years} is numeric, plots start with \code{min(years)}, otherwise they
#'start at the largest half-decade (e.g., 1980, 1985, 1990,...) les than or equal to the min
#'year with observations.
#'
#'@return Non-nested list of ggplot2 objects, with captions as names
#'
#'@import dplyr
#'@import ggplot2
#'
#'@md
#'
#'@export
#'
compareFits.SizeComps<-function(objs=NULL,
mdfr=NULL,
fleets="all",
fleet.type=c('survey','fishery'),
catch.type=c('index','retained','discard','total'),
years='all',
plot1stObs=TRUE,
nrow=5,
ncol=4,
useBars=TRUE,
usePins=FALSE,
usePinsAndPts=FALSE,
useLines=TRUE,
usePoints=TRUE,
pinSize=0.2,
lineSize=1,
pointSize=1,
alpha=0.5,
stripText=ggplot2::element_text(),
pdf=NULL,
showPlot=FALSE,
verbose=FALSE){
if (verbose) message("Starting rCompTCMs::compareFits.SizeComps().\n");
options(stringsAsFactors=FALSE);
fleet.type<-fleet.type[1];
catch.type<-catch.type[1];
if (fleet.type=='survey') catch.type<-'index';
#create pdf, if necessary
if(!is.null(pdf)){
pdf(file=pdf,width=11,height=8,onefile=TRUE);
on.exit(grDevices::dev.off());
showPlot<-TRUE;
}
if (is.null(mdfr)){
mdfr<-extractFits.SizeComps(objs,
fleets=fleets,
fleet.type=fleet.type,
catch.type=catch.type,
years=years,
plot1stObs=plot1stObs,
verbose=verbose);
if (is.character(plot1stObs)) plot1stObs = FALSE;#--
} else {
if (is.logical(plot1stObs)) {
#--do nothing
} else if (is.character(plot1stObs)){
#--filter for desired cases
mdfrp = mdfr |> dplyr::filter(type=="predicted");
mdfro = mdfr|> dplyr::filter((type=="observed")&(as.character(case) %in% plot1stObs));
mdfr = dplyr::bind_rows(mdfrp,mdfro);
plot1stObs = FALSE;
} else {
stop(paste0("Error: plot1stObs must be logical or a character vector. ",
"It was ",class(plot1stObs)));
}
}
#----------------------------------
# define output list of plots
#----------------------------------
plots<-list();
figno<-1;
std_theme = wtsPlots::getStdTheme();
#----------------------------------
# plot fits to size comps
#----------------------------------
if (verbose) message("Plotting",nrow(mdfr),"rows.\n")
ylab<-""; cap1<-"1";
if ((catch.type=="index")&&(fleet.type=="survey")) {
ylab<-"survey size comps";
cap1<-" \n \nFigure &&fno. Comparison of observed and predicted &&xms survey size comps for &&fleet. &&pg. \n \n";
}
if ((catch.type=="index")&&(fleet.type=="fishery")) {
ylab<-"fishery CPUE size comps";
cap1<-" \n \nFigure &&fno. Comparison of observed and predicted &&xms index catch (CPUE) size comps for &&fleet. &&pg. \n \n";
}
if (catch.type=="retained") {
ylab<-"retained catch size comps";
cap1<-" \n \nFigure &&fno. Comparison of observed and predicted &&xms retained catch size comps for &&fleet. &&pg. \n \n";
}
if (catch.type=="total") {
ylab<-"total catch size comps";
cap1<-" \n \nFigure &&fno. Comparison of observed and predicted &&xms total catch size comps for &&fleet. &&pg. \n \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$z));
mxp<-nrow*ncol;
xlab<-'size (mm CW)';
if (verbose) message(paste0("names(mdfr)= '",names(mdfr),"'.\n"));
for (fleet in unique(mdfr$fleet)){
if (verbose) message("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) message("Checking",x,m,s,"\n");
pgs<-list();
if (sum(idf&idx&idm&ids,na.rm=TRUE)==0){
if (verbose) message("--Dropping",x,m,s,"\n");
} else {
if (verbose) message("--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) message("--Plotting",nrow(mdfrp),"rows.\n")
#add in missing years as size comps with 0's
ys<-sort(unique(mdfrp$y));
if (is.numeric(years)){
mny = min(years);
} else {
mny<-5*floor(min(ys)/5);
}
mxy<-mny+mxp*ceiling((max(ys)-mny+1)/mxp)-1;
mdfrpp<-mdfrp[1,];
mdfrpp$val<-0;
if (mny<min(ys)){
for (y in mny:(min(ys)-1)) {
mdfrpp$y<-y;
mdfrp<-dplyr::bind_rows(mdfrp,mdfrpp);
}
}
if (mxy>max(ys)){
for (y in (max(ys)+1):mxy) {
mdfrpp$y<-y;
mdfrp<-dplyr::bind_rows(mdfrp,mdfrpp);
}
}
ys<-mny:mxy;
npg<-ceiling(length(ys)/mxp);
if (verbose) message("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<-dplyr::bind_rows(mdfrp,mdfrpp);
}
}
rng<-range(mdfrp$val,na.rm=TRUE,finite=TRUE);
if (verbose) message("rng = ",rng,'\n')
for (pg in 1:npg){ #loop over pages
dfrp = mdfrp |> dplyr::filter(y %in% ys[(pg-1)*mxp+1:mxp]);
dfrpo = dfrp |> dplyr::filter(type=='observed');
dfrpp = dfrp |> dplyr::filter(type=='predicted');
#do plot
pd = position_identity();
p = ggplot(data=dfrp)
if (useLines) p = p + geom_line(aes(x=z,y=val,colour=case),data=dfrpp,size=lineSize,alpha=alpha)
if (usePoints) p = p + geom_point(aes(x=z,y=val,colour=case,shape=case),data=dfrpp,size=pointSize)
if (plot1stObs) {
if (useBars) p = p + geom_bar(aes(x=z,y=val),fill="black",data=dfrpo,stat="identity",position='identity',alpha=0.5)
if (usePins) p = p + geom_linerange(aes(x=z,ymax=val),colour="black",data=dfrpo,stat="identity",position='identity',ymin=0.0,size=pinSize)
if (usePinsAndPts) p = p + geom_point(aes(x=z,y=val),colour="black",data=dfrpo,stat="identity",position='identity',size=0.5,alpha=1)
} else {
if (useBars) p = p + geom_bar(aes(x=z,y=val,fill=case),data=dfrpo,stat="identity",position=position_dodge2(0.2),alpha=0.5)
if (usePins) p = p + geom_linerange(aes(x=z,ymax=val,colour=case),data=dfrpo,stat="identity",position=position_dodge2(0.2),ymin=0.0,size=pinSize)
if (usePinsAndPts) p = p + geom_point(aes(x=z,y=val,colour=case),data=dfrpo,stat="identity",position=position_dodge2(0.2),size=0.5,alpha=1)
}
if (useLines) p = p + geom_line(aes(x=z,y=val,colour=case),data=dfrpp,size=lineSize,alpha=alpha)
if (usePoints) p = p + geom_point(aes(x=z,y=val,colour=case,shape=case),data=dfrpp,size=pointSize)
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) message("Plotting '",ttl,"'.\n",sep='')
p <- p + ggtitle(ttl)
p <- p + guides(fill=guide_legend('observed'),colour=guide_legend('predicted'),shape=guide_legend('predicted'))
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+theme(strip.text=stripText);
}#pg
}#if
}#ss
}#ms
}#xs
}#fleets
if (verbose) message("Finished rCompTCMs::compareFits.SizeComps().\n");
return(plots);
}
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