#'
#'@title Get model fits to size frequencies as z-scores for fleet data components
#'
#'@description Function to get model fits to size frequencies as z-scores for fleet data components.
#'
#'@param objs - single model report list object, or named list of them
#'@param fleet.type - fleet type ('fishery' or 'survey')
#'@param catch.type - catch type ('index','retained','discarded',or 'total')
#'@param residuals.type - residual type ('pearsons' or 'nlls')
#'@param verbose - flag (T/F) to print diagnostic info
#'
#'@return dataframe
#'
#'@details Uses \code{getMDFR.ZScores.PrNatZ1()}.
#' Returned dataframe is in canonical form.
#'
#'@export
#'
getMDFR.ZScores.PrNatZ<-function(objs,
fleet.type=c('survey','fishery'),
catch.type=c('index','retained','discarded','total'),
residuals.type=c('pearsons','nlls'),
verbose=FALSE){
if (verbose) cat("--Starting rTCSAM02::getMDFR.ZScores.PrNatZ.\n");
options(stringsAsFactors=FALSE);
fleet.type<-fleet.type[1];
catch.type<-catch.type[1];
residuals.type<-residuals.type[1];
data.type<-"n.at.z";
mdfr<-NULL;
if (inherits(objs,'tcsam02.resLst')){
#objs is a tcsam02 resLst object
mdfrp<-getMDFR.ZScores.PrNatZ(objs$rep,
fleet.type=fleet.type,
catch.type=catch.type,
residuals.type=residuals.type,
verbose=verbose);
if (!is.null(mdfrp)) mdfr<-rbind(mdfr,mdfrp);
} else if (inherits(objs,'tcsam02.rep')){
#objs is a single tcsam02 model report object
if (fleet.type=='fishery'){
flts<-objs$model.fits$fisheries;
fltNms<-names(flts);
} else if (fleet.type=='survey'){
flts<-objs$model.fits$surveys;
fltNms<-names(flts);
} else {
##throw error
}
ctNms<-catch.type;
for (fltNm in fltNms){
if (fltNm!=''){
fleet<-gsub("_"," ",fltNm,fixed=TRUE);
flt<-flts[[fltNm]];
for (ctNm in ctNms){
#catch.type<-gsub("."," ",ctNm,fixed=TRUE);
ctNm<-paste0(ctNm,".catch");
ct<-flt[[ctNm]];
if (!is.null(ct)){
if (verbose) cat("---Getting '",ctNm,"' for ",fltNm,"\n",sep='');
mdfrp<-NULL;
if ((data.type=="n.at.z")&&!is.null(ct$n.at.z)){
if (verbose) cat("---Getting n.at.z zscores\n")
mdfrp<-getMDFR.ZScores.PrNatZ1(ct$n.at.z,
objs$mc,
type=residuals.type,
verbose=verbose);
}
if (!is.null(mdfrp)){
if (verbose) cat("--created dataframe w/",nrow(mdfrp),"rows\n")
mdfrp$process<-fleet.type;
mdfrp$fleet<-fleet;
mdfrp$category<-catch.type;
mdfr<-rbind(mdfr,mdfrp);
}
} else {
if (verbose) cat(ctNm,"not found for",fltNm,"\n");
}
}##ctNms
}
}##fltNms
if (!is.null(mdfr)) mdfr$case<-"tcsam02";
} else if (inherits(objs,'list')){
#objs is a list of tcsam02.resLst objects
nl<-length(objs);
nms<-names(objs);
for (l in 1:nl){
obj1<-objs[[l]];
mdfrp<-getMDFR.ZScores.PrNatZ(obj1,
fleet.type=fleet.type,
catch.type=catch.type,
residuals.type=residuals.type,
verbose=verbose);
if (!is.null(mdfrp)){
if (!is.null(nms[l])) mdfrp$case<-nms[l];
mdfr<-rbind(mdfr,mdfrp);
}
}
} else {
#throw n error
}
if (!is.null(mdfr)) mdfr<-getMDFR.CanonicalFormat(mdfr);
if (verbose) cat("--Finished rTCSAM02::getMDFR.ZScores.PrNatZ().\n");
return(mdfr);
}
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