#'
#'@title Function to plot TCSAM2013 input data from a .R file
#'
#'@description This function plots input data to TCSAM2013 from a .R output file
#'
#'@details Creates a set of plots (in a pdf file, if desired) from a TCSAM2013 .R
#'output file.
#'
#'@param lst - the data list object
#'@param fn - the file
#'@param out.dir - directory to write pdf output to
#'@param pdfFile - (base) filename for output pdf file (if not NULL)
#'
#'@import graphics
#'
#'@export
#'
plotData<-function(lst=NULL,
fn=NULL,
out.dir=NULL,
pdfFile=NULL){
if (is.null(lst)) {
if (is.null(fn)) fn<-choose.files(default=getwd(),caption="Select TCSAM output .R file",index=1);
if (length(fn)<1) {cat("No file chosen. canceled.\n"); return;}
if (is.null(out.dir)) out.dir<-dirname(fn);
source(fn,local=TRUE);
lst<-res$model.data;
}
if (!is.null(pdfFile)){
pdf(file=file.path(out.dir,pdfFile),width=8.5,height=11);
on.exit(dev.off(),add=TRUE);
}
#biological info
#surveys
surveys<-lst[["surveys"]]
for (survey in names(surveys)){
#--abundance
#--size comps
plotData.Survey.NatZ(surveys[[survey]]$nAtZ$data,
label="trawl survey")
}
#fisheries
fisheries<-lst[["fisheries"]]
for (fishery in names(fisheries)){
#--abundance
#--size comps
if (fishery=="tcf.r") {
plotData.Fishery.Retained.NatZ(fisheries[[fishery]]$nAtZ$data,
label="directed fishery: retained males");
} else {
plotData.Fishery.Discarded.NatZ(fisheries[[fishery]]$nAtZ$data,
label=fisheries[[fishery]]$name);
}
}
}
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