#'
#'@title Compare estimated/predicted fishery capture/mortality rates among several model runs
#'
#'@description Function to compare estimated/predicted fishery capture/mortality rates among
#'several model runs.
#'
#'@param obj - object that can be converted into a list of tcsam2013.resLst objects
#'@param numRecent - number of recent years to plot
#'@param showPlot - flag (T/F) to show plot
#'@param pdf - name for output pdf file
#'
#'@details Uses \code{getMDFR.FisheryQuantities}.
#'
#'@return list of ggplot2 objects
#'
#'@importFrom wtsUtilities printGGList
#'@import ggplot2
#'
#'@export
#'
compareModelResults.FisheryRates<-function(obj,
numRecent=15,
showPlot=FALSE,
pdf=NULL){
#create pdf, if necessary
if(!is.null(pdf)){
pdf(file=pdf,width=11,height=8,onefile=TRUE);
on.exit(dev.off());
showPlot<-TRUE;
}
plots<-list();#output list
#----------------------------------
# convert to list of ResLst objects
#----------------------------------
obj<-convertToListOfResults(obj);
#----------------------------------
# pull out generic info
#----------------------------------
cases<-names(obj);
tinfo<-getTimeInfo(obj);
endyr<-tinfo$endyr;
#----------------------------------
# define output list of plots
#----------------------------------
plots<-list();
figno<-1;
#----------------------------------
# plot max fishing mortality/capture rates
#----------------------------------
dfrp<-getMDFR.FisheryQuantities(obj,'max rates');
dfrp$case<-factor(dfrp$case,levels=cases);
for (fsh in c('TCF','SCF','RKF','GTF')){
idx<-(dfrp$fleet==fsh);
dfrpp<-dfrp[idx,];
p <- ggplot(data=dfrpp,mapping=aes_string(x='y',y='val',colour="case",shape="category",linetype="category"));
p <- p + geom_line();
p <- p + geom_point();
p <- p + labs(y="max rate",x="year");
p <- p + guides(colour=guide_legend("case"),
shape=guide_legend("category"),
linetype=guide_legend("category"));
p <- p + facet_grid(x~fleet);
cap<-paste0(" \n \nFigure &&fno. Estimated max fishery rates in ",fsh,". \n \n");
if (showPlot) figno<-(wtsUtilities::printGGList(p,figno=figno,cap=cap))$figno;
plots[[cap]]<-p; p<-NULL;
#zoomed to recent
dfrpp<-dfrp[idx&(dfrp$y>=(max(dfrp$y)-15)-numRecent),];
p <- ggplot(data=dfrpp,mapping=aes_string(x='y',y='val',colour="case",shape="category",linetype="category"));
p <- p + geom_line();
p <- p + geom_point();
p <- p + labs(y="max rate",x="year");
p <- p + guides(colour=guide_legend("case"),
shape=guide_legend("category"),
linetype=guide_legend("category"));
p <- p + facet_grid(x~fleet);
cap<-paste0(" \n \nFigure &&fno. Estimated max fishery rates in ",fsh," (zoomed to recent years). \n \n");
if (showPlot) figno<-(wtsUtilities::printGGList(p,figno=figno,cap=cap))$figno;
plots[[cap]]<-p; p<-NULL;
}
#----------------------------------
# plot max fishing mortality/capture rates w/ different scales
#----------------------------------
dfrp<-getMDFR.FisheryQuantities(obj,'max rates');
dfrp$case<-factor(dfrp$case,levels=cases);
for (fsh in c('TCF','SCF','RKF','GTF')){
idx<-(dfrp$fleet==fsh);
dfrpp<-dfrp[idx,];
p <- ggplot(data=dfrpp,mapping=aes_string(x='y',y='val',colour="case",shape="category",linetype="category"));
p <- p + geom_line();
p <- p + geom_point();
p <- p + labs(y="max rate",x="year");
p <- p + guides(colour=guide_legend("case"),
shape=guide_legend("category"),
linetype=guide_legend("category"));
p <- p + facet_grid(x~fleet,scales="free_y");
cap<-paste0(" \n \nFigure &&fno. Estimated max fishery rates in ",fsh,". Y-axis scales differ. \n \n");
if (showPlot) figno<-(wtsUtilities::printGGList(p,figno=figno,cap=cap))$figno;
plots[[cap]]<-p; p<-NULL;
#zoomed to recent
dfrpp<-dfrp[idx&(dfrp$y>=(max(dfrp$y)-15)-numRecent),];
p <- ggplot(data=dfrpp,mapping=aes_string(x='y',y='val',colour="case",shape="category",linetype="category"));
p <- p + geom_line();
p <- p + geom_point();
p <- p + labs(y="max rate",x="year");
p <- p + guides(colour=guide_legend("case"),
shape=guide_legend("category"),
linetype=guide_legend("category"));
p <- p + facet_grid(x~fleet,scales="free_y");
cap<-paste0(" \n \nFigure &&fno. Estimated max fishery rates in ",fsh," (zoomed to recent years). Y-axis scales differ. \n \n");
if (showPlot) figno<-(wtsUtilities::printGGList(p,figno=figno,cap=cap))$figno;
plots[[cap]]<-p; p<-NULL;
}
#----------------------------------
# plot mean fishing mortality/capture rates
#----------------------------------
dfrp<-getMDFR.FisheryQuantities(obj,'mean rates');
dfrp$case<-factor(dfrp$case,levels=cases);
for (fsh in c('TCF','SCF','RKF','GTF')){
idx<-(dfrp$fleet==fsh);
dfrpp<-dfrp[idx,];
p <- ggplot(data=dfrpp,mapping=aes_string(x='y',y='val',colour="case",shape="category",linetype="category"));
p <- p + geom_line();
p <- p + geom_point();
p <- p + labs(y="mean rate",x="year");
p <- p + guides(colour=guide_legend("case"),
shape=guide_legend("category"),
linetype=guide_legend("category"));
p <- p + facet_grid(x~fleet);
cap<-paste0(" \n \nFigure &&fno. Estimated mean fishery rates in ",fsh,". \n \n");
if (showPlot) figno<-(wtsUtilities::printGGList(p,figno=figno,cap=cap))$figno;
plots[[cap]]<-p; p<-NULL;
#zoom to recent
dfrpp<-dfrp[idx&(dfrp$y>=(max(dfrp$y)-15)-numRecent),];
p <- ggplot(data=dfrpp,mapping=aes_string(x='y',y='val',colour="case",shape="category",linetype="category"));
p <- p + geom_line();
p <- p + geom_point();
p <- p + labs(y="mean rate",x="year");
p <- p + guides(colour=guide_legend("case"),
shape=guide_legend("category"),
linetype=guide_legend("category"));
p <- p + facet_grid(x~fleet);
cap<-paste0(" \n \nFigure &&fno. Estimated mean fishery rates in ",fsh," (zoomed to recent years). \n \n");
if (showPlot) figno<-(wtsUtilities::printGGList(p,figno=figno,cap=cap))$figno;
plots[[cap]]<-p; p<-NULL;
}
return(invisible(plots));
}
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