#'
#'@title Function to compare initial/final population abundance estimates among several models
#'
#'@description This function compares initial/final population abundance estimates
#' among several models.
#'
#'@param objs - list of resLst objects
#'@param type - type of abuundance ("iN_xmsz","fN_xmsz")
#'@param dodge - width to dodge overlapping series
#'@param showPlot - flag (T/F) to show plot
#'@param pdf - creates pdf, if not NULL
#'@param verbose - flag (T/F) to print diagnostic information
#'
#'@return ggplot2 object
#'
#'@details uses \code{rTCSAM2013::getMDFR.PopQuantities},
#'\code{rsimTCSAM::getMDFR.Pop.Quantities}, \code{rsimTCSAM::getMDFR.Pop.Quantities}, and
#'\code{plotMDFR.XY}.
#'
#'@import ggplot2
#'
#'@export
#'
compareResults.Pop.IF.NatZ<-function(objs,
type=c("iN_xmsz","fN_xmsz"),
dodge=0.2,
showPlot=FALSE,
pdf=NULL,
verbose=FALSE){
if (verbose) cat("Strating rCompTCMs::compareResults.Pop.IF.NatZ().\n");
options(stringsAsFactors=FALSE);
type<-type[1];
types<-c("iN_xmsz","fN_xmsz");
if (!(type %in% types)){
cat("rCompTCMs::compareResults.Pop.IF.NatZ: Unknown type requested: '",type[1],"'.\n",sep='');
return(NULL);
}
cases<-names(objs);
#create pdf, if necessary
if(!is.null(pdf)){
pdf(file=pdf,width=11,height=8,onefile=TRUE);
on.exit(grDevices::dev.off());
showPlot<-TRUE;
}
mdfr<-NULL;
for (case in cases){
obj<-objs[[case]];
if (verbose) cat("Processing '",case,"', a ",class(obj)[1]," object.\n",sep='');
if (inherits(obj,"tcsam2013.resLst")) mdfr1<-rTCSAM2013::getMDFR.Pop.Quantities(obj,type=type,verbose=verbose);
if (inherits(obj,"rsimTCSAM.resLst")) mdfr1<-rsimTCSAM::getMDFR.Pop.Quantities(obj,type=type,verbose=verbose);
if (inherits(obj,"tcsam02.resLst")) mdfr1<-rTCSAM02::getMDFR.Pop.Quantities(obj,type=type,verbose=verbose);
mdfr1$case<-case;
mdfr<-rbind(mdfr,mdfr1);
}
mdfr$y<-as.numeric(mdfr$y);
mdfr$z<-as.numeric(mdfr$z);
mdfr$case<-factor(mdfr$case,levels=cases);
#plot size comps by year
if (verbose) cat("Plotting size comps\n")
if (type=='iN_xmsz') ylab<-'Initial Population Abundance\n';
if (type=='fN_xmsz') ylab<-'Final Population Abundance\n';
p<-plotMDFR.XY(mdfr,x='z',value.var='val',agg.formula=NULL,
facet_grid=formula(m+s~x),
xlab='size (mm CW)',ylab=ylab,units='millions',lnscale=FALSE,
colour='case',guideTitleColor='',
shape='case',guideTitleShape='',
showPlot=FALSE);
if (showPlot||!is.null(pdf)) print(p);
if (verbose) cat("rCompTCMs::compareResults.Pop.IF.NatZ(): Done!\n");
return(p)
}
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