R/getMDFR.FisheryQuantities.R

In wStockhausen/rTCSAM2013: Functions to run and plot output from TCSAM2013 models.

#'
#'@title Get estimated/predicted fishery-related quantities from several model runs
#'
#'@description Function to get estimated/predicted fishery-related quantities from 
#'several model runs.
#'
#'@param obj - object that can be converted into a list of tcsam2013.resLst objects
#'@param type - fishery-related quantity to retrieve
#'@param pdfType - type of error distribution for observations
#'@param ci - confidence interval for error bars on observations
#'@param verbose - flag (T/F) to print debug info
#'
#'@details Potential values for 'type' are:
#'\itemize{
#'  \item {'bio.retm' - retained catch mortality (1000's t)}
#'  \item {'bio.dscm' - discard catch mortality (1000's t) for males in directed fishery}
#'  \item {'bio.totm' - total catch mortality (1000's t)}
#'  \item {'prNatZ.ret' - annual retained catch proportions-at-size}
#'  \item {'prNatZ.tot' - annual total catch proportions-at-size}
#'  \item {'PRs.ret'      - pearsons residuals for retained catch proportions-at-size}
#'  \item {'PRs.tot'      - pearsons residuals for total catch proportions-at-size}
#'  \item {'mnPrNatZ.ret' - mean proportions-at-size for retained catch data}
#'  \item {'mnPrNatZ.tot' - mean proportions-at-size for total catch data}
#'  \item {'sel_cxz' - fishery selectivity and retention functions, by time period and sex}
#'  \item {'sel_yxz' - fishery selectivity functions, by year and sex}
#'  \item {'ret_yxz' - fishery retention functions, by year and sex}
#'  \item {'zscores.tot' - annual z-scores for fits to total catch biomass}
#'  \item {'zscores.ret' - annual z-scores for fits to retained catch biomass}
#'  \item {'effSS.tot' - effective (and input) sample sizes for total catch size comps}
#'  \item {'effSS.ret' - effective (and input) sample sizes for retained catch size comps}
#'  \item {'qFsh_xy' - annual fishery catchabilities}
#'  \item {'maxFc_xy' - annual max capture rates}
#'  \item {'max rates' - max fishing mortality, retained mortality, and capture rates}
#'  \item {'mean rates' - mean fishing mortality, retained mortality, and capture rates}
#'}
#'Requires sqldf package.
#'
#'@return dataframe in canonical format
#'
#'@export
#'
getMDFR.FisheryQuantities<-function(obj,
                                    type=c("bio.retm","bio.dscm","bio.totm",
                                           "prNatZ.ret","prNatZ.tot",
                                           "PRs.ret","PRs.tot",
                                           "mnPrNatZ.ret","mnPrNatZ.tot",
                                           "sel_cxz","sel_yxz","ret_yxz",
                                           "zscores.tot","zscores.ret",
                                           "effSS.ret","effSS.tot",
                                           "qFsh_xy","maxFc_xy",
                                           "max rates","mean rates"),
                                    ci=0.80,
                                    pdfType=c("norm2","normal","lognormal"),
                                    verbose=FALSE){
    options(stringsAsFactors=FALSE);
    
    lst<-convertToListOfResults(obj);
    cases<-names(lst);

    #set up time info
    tinfo<-getTimeInfo(obj);
    years    <-tinfo$years;
    years.m1 <-tinfo$years.m1;

    #----------------------------------
    # observed and predicted retained catch mortality from fisheries (1000's t)
    #----------------------------------
    if (type[1]=="bio.retm"){
        dfr<-NULL;
        for (fsh in c('TCF')){
            nmo<-gsub("&&fsh",fsh,"fsh.obs.ret.bio.&&fsh",fixed=TRUE);
            nmp<-gsub("&&fsh",fsh,"fsh.mod.ret.bio.&&fsh",fixed=TRUE);
            nmy<-gsub("&&fsh",fsh,"fsh.obs.ret.bio.yrs.&&fsh",fixed=TRUE);
            for (case in cases){
                    #observed
                    idx <- years.m1[[case]] %in% (lst[[case]]$rep)[[nmy]];
                    val <-(lst[[case]]$rep)[[paste0(nmo,".M")]];
                    dfrp<-data.frame(case=case,type='observed',fleet=fsh,
                                      y=(years.m1[[case]])[idx],x='male',m='all',s='all',val=val[idx]);
                    dfr<-rbind(dfr,dfrp);
                    #predicted
                    val <-(lst[[case]]$rep)[[paste0(nmp,".M")]];
                    dfrp<-data.frame(case=case,type='predicted',fleet=fsh,
                                      y=(years.m1[[case]]),x='male',m='all',s='all',val=val);
                    dfr<-rbind(dfr,dfrp);
            }#--case
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'retained';
        return(dfrp);
    }    

    #----------------------------------
    # observed and predicted total catch mortality from fisheries (1000's t)
    #----------------------------------
    if (type[1]=="bio.totm"){
        dfr<-NULL;
        for (fsh in c('TCF','SCF','RKF','GTF')){
            nmo<-gsub("&&fsh",fsh,"fsh.obs.totm.bio.&&fsh",fixed=TRUE);
            nmp<-gsub("&&fsh",fsh,"fsh.mod.totm.bio.&&fsh",fixed=TRUE);
            nmy<-gsub("&&fsh",fsh,"fsh.obs.totm.bio.yrs.&&fsh",fixed=TRUE);
            for (case in cases){
                if (fsh!='GTF'){
                        #observed females
                        val <-(lst[[case]]$rep)[[paste0(nmo,".F")]];
                        dfrp<-data.frame(case=case,type='observed',fleet=fsh,
                                          y=(lst[[case]]$rep)[[nmy]],x='female',m='all',s='all',val=val);
                        dfr<-rbind(dfr,dfrp);
                        #observed males
                        val <-(lst[[case]]$rep)[[paste0(nmo,".M")]];
                        dfrp<-data.frame(case=case,type='observed',fleet=fsh,
                                          y=(lst[[case]]$rep)[[nmy]],x='male',m='all',s='all',val=val);
                        dfr<-rbind(dfr,dfrp);
                        #predicted females
                        val <-(lst[[case]]$rep)[[paste0(nmp,".F")]];
                        dfrp<-data.frame(case=case,type='predicted',fleet=fsh,
                                          y=(years.m1[[case]]),x='female',m='all',s='all',val=val);
                        dfr<-rbind(dfr,dfrp);
                        #predicted males
                        val <-(lst[[case]]$rep)[[paste0(nmp,".M")]];
                        dfrp<-data.frame(case=case,type='predicted',fleet=fsh,
                                          y=(years.m1[[case]]),x='male',m='all',s='all',val=val);
                        dfr<-rbind(dfr,dfrp);
                } else {
                    #observed for GTF is males+females
                    val <-(lst[[case]]$rep)[[paste0(nmo,"")]];
                    dfrp<-data.frame(case=case,type='observed',fleet=fsh,
                                      y=(lst[[case]]$rep)[[nmy]],x='all',m='all',s='all',val=val);
                    dfr<-rbind(dfr,dfrp);
                    #predicted
                    val <-(lst[[case]]$rep)[[paste0(nmp,"")]];
                    dfrp<-data.frame(case=case,type='predicted',fleet=fsh,
                                      y=(years.m1[[case]]),x='all',m='all',s='all',val=val);
                    dfr<-rbind(dfr,dfrp);
                }
            }#--case
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-"total mortality";
        return(dfrp);
    }    

    #----------------------------------
    # observed and predicted discard catch mortality from fisheries (1000's t)
    #----------------------------------
    if (type[1]=="bio.dscm"){
        dfr<-NULL;
        for (fsh in c('TCF')){
            nmo<-gsub("&&fsh",fsh,"fsh.obs.dscm.bio.&&fsh",fixed=TRUE);
            nmp<-gsub("&&fsh",fsh,"fsh.mod.dscm.bio.&&fsh",fixed=TRUE);
            nmy<-gsub("&&fsh",fsh,"fsh.obs.totm.bio.yrs.&&fsh",fixed=TRUE);
            for (case in cases){
                    #observed
                    val <-(lst[[case]]$rep)[[paste0(nmo,".M")]];
                    dfrp<-data.frame(case=case,type='observed',fleet=fsh,
                                      y=(lst[[case]]$rep)[[nmy]],x='male',m='all',s='all',val=val);
                    dfr<-rbind(dfr,dfrp);
                    #predicted
                    val <-(lst[[case]]$rep)[[paste0(nmp,".M")]];
                    dfrp<-data.frame(case=case,type='predicted',fleet=fsh,
                                      y=(years.m1[[case]]),x='male',m='all',s='all',val=val);
                    dfr<-rbind(dfr,dfrp);
            }#--case
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'discard mortality';
        return(dfrp);
    }    

    #----------------------------------
    # observed and predicted fishery total catch size comps
    #----------------------------------
    if (type[1]=="prNatZ.tot"){
        dfr<-NULL;
        for (fsh in c('TCF','SCF','RKF','GTF')){
            nmo<-gsub("&&fsh",fsh,"fsh.obs.tot.PrNatZ.&&fsh",fixed=TRUE);
            nmp<-gsub("&&fsh",fsh,"fsh.mod.tot.PrNatZ.&&fsh",fixed=TRUE);
            nmc<-gsub("&&fsh",fsh,"fsh.mod.cap.PrNatZ.&&fsh",fixed=TRUE);
            nmy<-gsub("&&fsh",fsh,"fsh.obs.tot.PrNatZ.yrs.&&fsh",fixed=TRUE);
            for (case in cases){
                for (x in c('female','male')){
                    #observed
                    vals_yz<-(lst[[case]]$rep)[[paste0(nmo,".",toupper(substr(x,1,1)))]];
                    obsy<-as.character((lst[[case]]$rep)[[nmy]]);
                    dimnames(vals_yz)<-list(y=obsy,
                                            z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(vals_yz,value.name='val');
                    dfrp<-cbind(case=case,type='observed',fleet=fsh,
                                x=x,m="all",s="all",dfrp);
                    dfr<-rbind(dfr,dfrp[,c("case","type","fleet","y","x","m","s","z","val")]);
                    #predicted
                    nmm<-paste0(nmp,".",toupper(substr(x,1,1)));
                    if (lst[[case]]$rep$mod.optFMFit>0) nmm<-paste0(nmc,".",toupper(substr(x,1,1)))
                    vals_yz<-(lst[[case]]$rep)[[nmm]];
                    dimnames(vals_yz)<-list(y=as.character(years.m1[[case]]),
                                            z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(vals_yz,value.name='val');
                    dfrp<-cbind(case=case,type='predicted',fleet=fsh,
                                x=x,m="all",s="all",dfrp[dfrp$y %in% obsy,]);
                    dfr<-rbind(dfr,dfrp[,c("case","type","fleet","y","x","m","s","z","val")]);
                    rm(obsy);
                }#--x
            }#--cases
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'total catch size comps';
        return(dfrp);
    }    

    #----------------------------------
    # observed and predicted fishery retained catch size comps
    #----------------------------------
    if (type[1]=="prNatZ.ret"){
        dfr<-NULL;
        for (fsh in c('TCF')){
            nmo<-gsub("&&fsh",fsh,"fsh.obs.ret.PrNatZ.&&fsh",fixed=TRUE);
            nmp<-gsub("&&fsh",fsh,"fsh.mod.ret.PrNatZ.&&fsh",fixed=TRUE);
            nmy<-gsub("&&fsh",fsh,"fsh.obs.ret.PrNatZ.yrs.&&fsh",fixed=TRUE);
            for (case in cases){
                for (x in c('male')){
                    #observed
                    vals_yz<-(lst[[case]]$rep)[[paste0(nmo,".",toupper(substr(x,1,1)))]];
                    obsy<-as.character((lst[[case]]$rep)[[nmy]]);
                    dimnames(vals_yz)<-list(y=obsy,
                                            z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(vals_yz,value.name='val');
                    dfrp<-cbind(case=case,type='observed',fleet=fsh,
                                x=x,m="all",s="all",dfrp);
                    dfr<-rbind(dfr,dfrp[,c("case","type","fleet","y","x","m","s","z","val")]);
                    #predicted
                    vals_yz<-(lst[[case]]$rep)[[paste0(nmp,".",toupper(substr(x,1,1)))]];
                    dimnames(vals_yz)<-list(y=as.character(years.m1[[case]]),
                                            z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(vals_yz,value.name='val');
                    dfrp<-cbind(case=case,type='predicted',fleet=fsh,
                                x=x,m="all",s="all",dfrp[dfrp$y %in% obsy,]);
                    dfr<-rbind(dfr,dfrp[,c("case","type","fleet","y","x","m","s","z","val")]);
                    rm(obsy);
                }#--x
            }#--cases
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'retained catch size comps';
        return(dfrp);
    }    

    #----------------------------------
    # mean total catch size comps from fisheries
    #----------------------------------
    if (type[1]=="mnPrNatZ.tot"){
        #--take mean only over years w/ non-zero observations
        dfrp<-getMDFR.FisheryQuantities(obj,type="prNatZ.tot");
        dfrpp<-reshape2::dcast(dfrp[dfrp$type=='observed',],formula="case+fleet+y~.",fun.aggregate=sum,value.var='val');
        names(dfrpp)[4]<-'val';
        qry<-'select p."case",p.type,p.fleet,p.y,p.x,p.m,p.s,p.z,p.val
              from dfrp p, dfrpp pp
              where p."case"=pp."case" and p.fleet=pp.fleet and p.y=pp.y and pp.val>0;';
        dfrp<-sqldf::sqldf(qry);
        #--
        dfrp1<-reshape2::dcast(dfrp,formula="case+type+fleet+x+m+z~.",fun.aggregate=mean,value.var='val');
        names(dfrp1)[7]<-'val';
        dfrp2<-reshape2::dcast(dfrp,formula="case+type+fleet+x+m+z~.",fun.aggregate=sd,value.var='val');
        names(dfrp2)[7]<-'stdv';
        dfrp3<-reshape2::dcast(dfrp,formula="case+type+fleet+x+m+z~.",fun.aggregate=length,value.var='val');
        names(dfrp3)[7]<-'N';
        cis<-calcCIs(dfrp1$val,sdvs=dfrp2$stdv/sqrt(dfrp3$N),pdfType='normal',ci=0.80)
        dfrp<-cbind(dfrp1,lci=cis$lci,uci=cis$uci);
        
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfrp);
        dfrp$process<-'fishery';
        dfrp$category<-'total catch mean size comps';
         return(dfrp);
    }

    #----------------------------------
    # mean retained catch size comps from fisheries
    #----------------------------------
    if (type[1]=="mnPrNatZ.ret"){
        #--take mean only over years w/ non-zero observations
        dfrp<-getMDFR.FisheryQuantities(obj,type="prNatZ.ret");
        dfrpp<-reshape2::dcast(dfrp[dfrp$type=='observed',],formula="case+fleet+y~.",fun.aggregate=sum,value.var='val');
        names(dfrpp)[4]<-'val';
        qry<-'select p."case",p.type,p.fleet,p.y,p.x,p.m,p.s,p.z,p.val
              from dfrp p, dfrpp pp
              where p."case"=pp."case" and p.fleet=pp.fleet and p.y=pp.y and pp.val>0;';
        dfrp<-sqldf::sqldf(qry);
        #--
        dfrp1<-reshape2::dcast(dfrp,formula="case+type+fleet+x+m+z~.",fun.aggregate=mean,value.var='val');
        names(dfrp1)[7]<-'val';
        dfrp2<-reshape2::dcast(dfrp,formula="case+type+fleet+x+m+z~.",fun.aggregate=sd,value.var='val');
        names(dfrp2)[7]<-'stdv';
        dfrp3<-reshape2::dcast(dfrp,formula="case+type+fleet+x+m+z~.",fun.aggregate=length,value.var='val');
        names(dfrp3)[7]<-'N';
        cis<-calcCIs(dfrp1$val,sdvs=dfrp2$stdv/sqrt(dfrp3$N),pdfType='normal',ci=0.80)
        dfrp<-cbind(dfrp1,lci=cis$lci,uci=cis$uci);
        
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfrp);
        dfrp$process<-'fishery';
        dfrp$category<-'retained catch mean size comps';
        return(dfrp);
    }

    #----------------------------------
    # Pearson's residuals for total catch size comps from fisheries
    #----------------------------------
    if (type[1]=="PRs.tot"){
        dfrp1<-getMDFR.FisheryQuantities(obj,type="prNatZ.tot")
        dfrp1<-reshape2::dcast(dfrp1,formula="case+fleet+y+x+m+s+z~type",fun.aggregate=sum,value.var='val')
        dfrp1$val<-(dfrp1$observed-dfrp1$predicted)/sqrt((dfrp1$predicted+1.0e-5)*(1-dfrp1$predicted));
        dfrp2<-getMDFR.FisheryQuantities(obj,type="effSS.tot");
        #--TCF, SCF, RKF fit proportions by sex
        fsh<-c('TCF','SCF','RKF');
        dfrpp1<-dfrp1[dfrp1$fleet %in% fsh,];
        dfrpp2<-dfrp2[dfrp2$fleet %in% fsh,];
        qry<-'select
                p."case", "Pearsons Residuals" as type, p.fleet,
                p.y, p.x, p.m, p.s, p.z, sqrt(s.val)*p.val as val
              from
                dfrpp2 s, dfrpp1 p
              where 
                s."case"=p."case" and
                s.fleet=p.fleet and
                s.y=p.y and
                s.x=p.x and
                s.type="input";';
        dfrppp1<-sqldf::sqldf(qry);
        #--GTF fits proportions extended over sex
        fsh<-c('GTF');
        dfrpp1<-dfrp1[dfrp1$fleet %in% fsh,];
        dfrpp2<-dfrp2[dfrp2$fleet %in% fsh,];
        qry<-'select
                p."case", "Pearsons Residuals" as type, p.fleet,
                p.y, p.x, p.m, p.s, p.z, sqrt(s.val)*p.val as val
              from
                dfrpp2 s, dfrpp1 p
              where 
                s."case"=p."case" and
                s.fleet=p.fleet and
                s.y=p.y and
                s.type="input";'
        dfrppp2<-sqldf::sqldf(qry);
        dfrp<-rbind(dfrppp1,dfrppp2);
        
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfrp);
        dfrp$process<-'fishery';
        dfrp$category<-'total catch size comps';
        return(dfrp);
    }

    #----------------------------------
    # Pearson's residuals for retained catch size comps from fisheries
    #----------------------------------
    if (type[1]=="PRs.ret"){
        dfrp1<-getMDFR.FisheryQuantities(obj,type="prNatZ.ret")
        dfrp1<-reshape2::dcast(dfrp1,formula="case+fleet+y+x+m+s+z~type",fun.aggregate=sum,value.var='val')
        dfrp1$val<-(dfrp1$observed-dfrp1$predicted)/sqrt((dfrp1$predicted+1.0e-5)*(1-dfrp1$predicted));
        dfrp2<-getMDFR.FisheryQuantities(obj,type="effSS.ret");
        qry<-'select
                p."case","Pearsons Residuals" as type,p.fleet,
                p.y, p.x, p.m, p.s, p.z, sqrt(s.val)*p.val as val
              from
                dfrp2 s, dfrp1 p
              where 
                s."case"=p."case" and
                s.fleet=p.fleet and
                s.y=p.y and
                s.x=p.x and
                s.type="input";'
        dfrp<-sqldf::sqldf(qry);
        
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfrp);
        dfrp$process<-'fishery';
        dfrp$category<-'retained catch size comps';
        return(dfrp);
    }

    #----------------------------------
    #selectivity/retention functions by time period
    #----------------------------------
    if (type[1]=="sel_cxz"){
        dfr<-NULL;
        cols.out<-c("case","type","fleet","pc","x","m","s","z","val");
        for (fsh in c('TCF','SCF','RKF','GTF')){
            nm<-gsub("&&fsh",fsh,"fsh.mod.sel.&&fsh",fixed=TRUE);
            for (case in cases){
                if (fsh!='TCF'){
                    #females
                    sel_cz<-(lst[[case]]$rep)[[paste0(nm,".F")]];
                    dimnames(sel_cz)<-list(pc=c('1','2','3'),
                                           z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(sel_cz,value.name='val');
                    dfrp<-cbind(case=case,type='selectivity',fleet=fsh,
                                     x='female',m='all',s='all',dfrp);
                    dfr<-rbind(dfr,dfrp[,cols.out]);
                    #males
                    sel_cz<-(lst[[case]]$rep)[[paste0(nm,".M")]];
                    dimnames(sel_cz)<-list(pc=c('1','2','3'),
                                           z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(sel_cz,value.name='val');
                    dfrp<-cbind(case=case,type='selectivity',fleet=fsh,
                                     x='male',m='all',s='all',dfrp);
                    dfr<-rbind(dfr,dfrp[,cols.out]);
                } else { 
                    #TCF
                    #--female selectivity
                    sel_cz<-(lst[[case]]$rep)[[paste0(nm,".F")]];
                    sel_cz<-array(sel_cz,dim=c(1,length(sel_cz)));
                    dimnames(sel_cz)<-list(pc=c('1'),
                                           z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(sel_cz,value.name='val');
                    dfrp<-cbind(case=case,type='selectivity',fleet=fsh,
                                     x='female',m='all',s='all',dfrp);
                    dfr<-rbind(dfr,dfrp[,cols.out]);
                    #--male selectivity
                    sel_cz<-(lst[[case]]$rep)[[paste0(nm,".M")]];
                    dimnames(sel_cz)<-list(pc=as.character(years.m1[[case]]),
                                           z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(sel_cz,value.name='val');
                    dfrp<-cbind(case=case,type='selectivity',fleet=fsh,
                                     x='male',m='all',s='all',dfrp);
                    dfr<-rbind(dfr,dfrp[,cols.out]);
                    #--retained selectivity (male only)
                    sel_cz<-(lst[[case]]$rep)[["fsh.mod.selr.TCF.M"]];
                    dimnames(sel_cz)<-list(pc=as.character(years.m1[[case]]),
                                           z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(sel_cz,value.name='val');
                    dfrp<-cbind(case=case,type='ret-sel',fleet=fsh,
                                     x='male',m='all',s='all',dfrp);
                    dfr<-rbind(dfr,dfrp[,cols.out]);
                    #--retention functions
                        ret_cz<-(lst[[case]]$rep)[["fsh.mod.ret.TCF.M"]];
                        dimnames(ret_cz)<-list(pc=as.character(years.m1[[case]]),
                                               z=as.character(lst[[case]]$rep$mod.zBs));
                        dfrp<-reshape2::melt(ret_cz,value.name='val');
                        dfrp<-cbind(case=case,type='retention',fleet='TCF',
                                         x='male',m='all',s='all',dfrp);
                        dfr<-rbind(dfr,dfrp[,cols.out]);
                }
            }#--case
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'selectivity functions';
        return(dfrp);
    }
    
    #----------------------------------
    #selectivity functions by year
    #----------------------------------
    if (type[1]=="sel_yxz"){
        dfr<-NULL;
        cols.out<-c("case","type","fleet","y","x","m","s","z","val");
        for (fsh in c('TCF','SCF','RKF','GTF')){
            nm<-gsub("&&fsh",fsh,"fsh.mod.sel.&&fsh",fixed=TRUE);
            for (case in cases){
                if (fsh!='TCF'){
                    #females
                    sel_cz<-(lst[[case]]$rep)[[paste0(nm,".FEMALE")]];
                    dimnames(sel_cz)<-list(y=years.m1[[case]],
                                           z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(sel_cz,value.name='val');
                    dfrp<-cbind(case=case,type='selectivity',fleet=fsh,
                                     x='female',m='all',s='all',dfrp);
                    dfr<-rbind(dfr,dfrp[,cols.out]);
                    #males
                    sel_cz<-(lst[[case]]$rep)[[paste0(nm,".MALE")]];
                    dimnames(sel_cz)<-list(y=years.m1[[case]],
                                           z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(sel_cz,value.name='val');
                    dfrp<-cbind(case=case,type='selectivity',fleet=fsh,
                                     x='male',m='all',s='all',dfrp);
                    dfr<-rbind(dfr,dfrp[,cols.out]);
                } else { 
                    #TCF
                    #--female selectivity
                    sel_cz<-(lst[[case]]$rep)[[paste0(nm,".FEMALE")]];
                    dimnames(sel_cz)<-list(y=years.m1[[case]],
                                           z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(sel_cz,value.name='val');
                    dfrp<-cbind(case=case,type='selectivity',fleet=fsh,
                                     x='female',m='all',s='all',dfrp);
                    dfr<-rbind(dfr,dfrp[,cols.out]);
                    #--male selectivity
                    sel_cz<-(lst[[case]]$rep)[[paste0(nm,".MALE")]];
                    dimnames(sel_cz)<-list(y=years.m1[[case]],
                                           z=as.character(lst[[case]]$rep$mod.zBs));
                    dfrp<-reshape2::melt(sel_cz,value.name='val');
                    dfrp<-cbind(case=case,type='selectivity',fleet=fsh,
                                     x='male',m='all',s='all',dfrp);
                    dfr<-rbind(dfr,dfrp[,cols.out]);
                }
            }#--case
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'selectivity functions';
        return(dfrp);
    }
    
    #----------------------------------
    #retention functions by year
    #----------------------------------
    if (type[1]=="ret_yxz"){
        dfr<-NULL;
        cols.out<-c("case","type","fleet","y","x","m","s","z","val");
        for (fsh in c('TCF')){
            nm<-gsub("&&fsh",fsh,"fsh.mod.sel.&&fsh",fixed=TRUE);
            for (case in cases){
                #--retention functions
                ret_cz<-(lst[[case]]$rep)[["fsh.mod.ret.TCF.MALE"]];
                dimnames(ret_cz)<-list(y=years.m1[[case]],
                                       z=as.character(lst[[case]]$rep$mod.zBs));
                dfrp<-reshape2::melt(ret_cz,value.name='val');
                dfrp<-cbind(case=case,type='retention',fleet='TCF',
                                 x='male',m='all',s='all',dfrp);
                dfr<-rbind(dfr,dfrp[,cols.out]);
            }#--case
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'retention functions';
        return(dfrp);
    }
    
    #----------------------------------
    # z-scores for total catch biomass
    #----------------------------------
    if (type[1]=="zscores.tot"){
        if (verbose) cat("Getting total catch biomass z-scores.\n")
        dfr<-NULL;
        for (fsh in c('TCF','SCF','RKF','GTF')){
            nmv<-gsub("&&fsh",fsh,"fsh.bio.zscr.&&fsh",fixed=TRUE);
            nmy<-gsub("&&fsh",fsh,"fsh.obs.totm.bio.yrs.&&fsh",fixed=TRUE);
            for (case in cases){
                if (fsh!='GTF'){
                    idx<-years[[case]] %in% (lst[[case]]$rep)[[nmy]];#select only years with observations
                    #females
                    val <-(lst[[case]]$rep)[[paste0(nmv,".F")]][idx];
                    dfrf<-data.frame(case=case,category='total',fleet=fsh,
                                      y=years[[case]][idx],x='female',m='all',s='all',val=val,stringsAsFactors=FALSE);
                    #males
                    val <-(lst[[case]]$rep)[[paste0(nmv,".M")]][idx];
                    dfrm<-data.frame(case=case,category='total',fleet=fsh,
                                      y=years[[case]][idx],x='male',m='all',s='all',val=val,stringsAsFactors=FALSE);
                    dfr<-rbind(dfr,dfrf,dfrm);
                } else {
                    idx<-years[[case]] %in% (lst[[case]]$rep)[[nmy]];#select only years with observations
                    val <-(lst[[case]]$rep)[[nmv]][idx];
                    dfrp<-data.frame(case=case,category='total',fleet=fsh,
                                      y=years[[case]][idx],x='all',m='all',s='all',val=val,stringsAsFactors=FALSE);
                    dfr<-rbind(dfr,dfrp);
                }
            }#--case
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$type<-'z-score';
        
        return(dfrp);
    }
        
    #----------------------------------
    # z-scores for retained catch biomass
    #----------------------------------
    if (type[1]=="zscores.ret"){
        if (verbose) cat("Getting retained catch biomass z-scores.\n")
        dfr<-NULL;
        for (case in cases){
            idx<-years[[case]] %in% as.numeric((lst[[case]]$rep)[["fsh.obs.ret.bio.yrs.TCF"]]);#select only years with observations
            val <-(lst[[case]]$rep)[["fsh.ret.zscr.TCF"]][idx];
            dfrp<-data.frame(case=case,category='retained',fleet='TCF',
                              y=years[[case]][idx],x='male',m='all',s='all',val=val,stringsAsFactors=FALSE);
            dfr<-rbind(dfr,dfrp);
        }#--case
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$type<-'z-score';
        
        return(dfrp);
    }    

    #----------------------------------
    # total catch sample sizes
    #----------------------------------
    if (type[1]=="effSS.tot"){
        dfr<-NULL;
        for (fsh in c('TCF','SCF','RKF','GTF')){
            nmi<-gsub("&&fsh",fsh,"fsh.inpSS.tot.&&fsh",fixed=TRUE);
            nme<-gsub("&&fsh",fsh,"fsh.effSS.McI.tot.&&fsh",fixed=TRUE);
            nmy<-gsub("&&fsh",fsh,"fsh.obs.tot.PrNatZ.yrs.&&fsh",fixed=TRUE);
            for (case in cases){
                if (fsh!='GTF'){
                    #input sample sizes 
                    #--females
                    val <-(lst[[case]]$rep)[[paste0(nmi,".F")]];
                    dfrp<-data.frame(case=case,type='input',fleet=fsh,
                                      y=(lst[[case]]$rep)[[nmy]],x='female',m='all',s='all',val=val);
                    dfr<-rbind(dfr,dfrp);
                    #--males
                    val <-(lst[[case]]$rep)[[paste0(nmi,".M")]];
                    dfrp<-data.frame(case=case,type='input',fleet=fsh,
                                      y=(lst[[case]]$rep)[[nmy]],x='male',m='all',s='all',val=val);
                    dfr<-rbind(dfr,dfrp);
                    #effective sample sizes (McAllister-Ianelli)
                    idx<-years[[case]] %in% (lst[[case]]$rep)[[nmy]];#select only years with observations
                    #--females
                    val <-(lst[[case]]$rep)[[paste0(nme,".F")]][idx];
                    dfrp<-data.frame(case=case,type='McAllister-Ianelli',fleet=fsh,
                                      y=(lst[[case]]$rep)[[nmy]],x='female',m='all',s='all',val=val);
                    dfr<-rbind(dfr,dfrp);
                    #--males
                    val <-(lst[[case]]$rep)[[paste0(nme,".M")]][idx];
                    dfrp<-data.frame(case=case,type='McAllister-Ianelli',fleet=fsh,
                                      y=(lst[[case]]$rep)[[nmy]],x='male',m='all',s='all',val=val);
                    dfr<-rbind(dfr,dfrp);
                } else {
                    #input sample sizes 
                    val <-(lst[[case]]$rep)[[nmi]];
                    dfrp<-data.frame(case=case,type='input',fleet=fsh,
                                      y=(lst[[case]]$rep)[[nmy]],x='all',m='all',s='all',val=val);
                    dfr<-rbind(dfr,dfrp);
                    #effective sample sizes (McAllister-Ianelli)
                    idx<-years[[case]] %in% (lst[[case]]$rep)[[nmy]];#select only years with observations
                    val <-(lst[[case]]$rep)[[nme]][idx];
                    dfrp<-data.frame(case=case,type='McAllister-Ianelli',fleet=fsh,
                                      y=(lst[[case]]$rep)[[nmy]],x='all',m='all',s='all',val=val);
                    dfr<-rbind(dfr,dfrp);
                }
            }#--case
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'total catch sample sizes';
        return(dfrp);
    }    

    #----------------------------------
    # retained catch sample sizes
    #----------------------------------
    if (type[1]=="effSS.ret"){
        dfr<-NULL;
        for (fsh in c('TCF')){
            nmi<-gsub("&&fsh",fsh,"fsh.inpSS.ret.&&fsh",fixed=TRUE);
            nme<-gsub("&&fsh",fsh,"fsh.effSS.McI.ret.&&fsh",fixed=TRUE);
            nmy<-gsub("&&fsh",fsh,"fsh.obs.ret.PrNatZ.yrs.&&fsh",fixed=TRUE);
            for (case in cases){
                #input sample sizes 
                val <-(lst[[case]]$rep)[[nmi]];
                dfrp<-data.frame(case=case,type='input',fleet=fsh,
                                  y=(lst[[case]]$rep)[[nmy]],x='male',m='all',s='all',val=val);
                dfr<-rbind(dfr,dfrp);
                #effective sample sizes (McAllister-Ianelli)
                idx<-years[[case]] %in% (lst[[case]]$rep)[[nmy]];#select only years with observations
                val <-(lst[[case]]$rep)[[nme]][idx];
                dfrp<-data.frame(case=case,type='McAllister-Ianelli',fleet=fsh,
                                  y=(lst[[case]]$rep)[[nmy]],x='male',m='all',s='all',val=val);
                dfr<-rbind(dfr,dfrp);
            }#--case
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'retained catch sample sizes';
        return(dfrp);
    }    

    #----------------------------------
    # fishery catchabilities
    #----------------------------------
    if (type[1]=="qFsh_xy"){
        dfr<-NULL;
        for (fsh in c('TCF','SCF','RKF','GTF')){
            nmcr<-gsub("&&fsh",fsh,"fsh.mod.fcr.fully.selected.&&fsh",fixed=TRUE);
            for (case in cases){
                #fishery catchability rates
                vals<-(lst[[case]]$rep)[[nmcr]];
                if (!is.null(vals)){
                    ##males
                    dfrp<-data.frame(case=case,type="capture",fleet=fsh,
                                     y=years.m1[[case]],x="male",m="all",s="all",val=vals);
                    dfr<-rbind(dfr,dfrp);
                    ##females
                    nmpr<-gsub("&&fsh",fsh," pAvgLnF_&&fshF",fixed=TRUE);
                    pLnF_F<-(lst[[case]]$prs)$value[(lst[[case]]$prs)$name==nmpr];
                    dfrp<-data.frame(case=case,type="capture",fleet=fsh,
                                     y=years.m1[[case]],x="female",m="all",s="all",val=vals*exp(pLnF_F));
                    dfr<-rbind(dfr,dfrp);
                    rm(pLnF_F);
                }
            }#--case
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'catchability';
        return(dfrp);
    }
    
    #----------------------------------
    # max fishery capture rates
    #----------------------------------
    if (type[1]=="qFsh_xy"){
        dfr<-NULL;
        for (fsh in c('TCF','SCF','RKF','GTF')){
            nmcr<-gsub("&&fsh",fsh,"fsh.fcr.max.&&fsh",fixed=TRUE);
            for (case in cases){
                for (x in c('male','female')){
                    #fishery capture rates
                    vals<-(lst[[case]]$rep)[[paste0(nmcr,".",toupper(substr(x,1,1)))]];
                    if (!is.null(vals)){
                        dfrp<-data.frame(case=case,type="capture",fleet=fsh,
                                         y=years.m1[[case]],x=x,m="all",s="all",val=vals);
                        dfr<-rbind(dfr,dfrp);
                    }
                }#--x
            }#--case
        }#--fsh
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'max capture rate';
        return(dfrp);
    }
    
    #----------------------------------
    # max fishing mortality rates
    #----------------------------------
    if (type[1]=="max rates"){
        dfr<-NULL;
        for (fsh in c('TCF','SCF','RKF','GTF')){
            nmmr<-gsub("&&fsh",fsh,"fsh.fmr.max.&&fsh",fixed=TRUE);
            nmcr<-gsub("&&fsh",fsh,"fsh.fcr.max.&&fsh",fixed=TRUE);
            for (case in cases){
                for (x in c('male','female')){
                    #fishing mortality rates
                    vals<-(lst[[case]]$rep)[[paste0(nmmr,".",toupper(substr(x,1,1)))]];
                    if (!is.null(vals)){
                        dfrp<-data.frame(case=case,type="total mortality",fleet=fsh,
                                         y=years.m1[[case]],x=x,m="all",s="all",val=vals);
                        dfr<-rbind(dfr,dfrp);
                    }
                    #fishery capture rates
                    vals<-(lst[[case]]$rep)[[paste0(nmcr,".",toupper(substr(x,1,1)))]];
                    if (!is.null(vals)){
                        dfrp<-data.frame(case=case,type="capture",fleet=fsh,
                                         y=years.m1[[case]],x=x,m="all",s="all",val=vals);
                        dfr<-rbind(dfr,dfrp);
                    }
                }#--x
            }#--case
        }#--fsh
        #retained mortality
        for (case in cases){
            for (x in c('male')){
                #retained mortality rates in TCF
                vals<-(lst[[case]]$rep)[["fsh.rmr.max"]];
                dfrp<-data.frame(case=case,type='retained mortality',fleet="TCF",
                                 y=years.m1[[case]],x=x,m="all",s="all",val=vals);
                dfr<-rbind(dfr,dfrp);
            }#--x
        }#--case
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'max fishing mortality rates';
        return(dfrp);
    }
    
    #----------------------------------
    # mean fishing mortality rates
    #----------------------------------
    if (type[1]=="mean rates"){
        dfr<-NULL;
        for (fsh in c('TCF','SCF','RKF','GTF')){
            nmmr<-gsub("&&fsh",fsh,"fsh.fmr.mean.&&fsh",fixed=TRUE);
            nmcr<-gsub("&&fsh",fsh,"fsh.fcr.mean.&&fsh",fixed=TRUE);
            for (case in cases){
                for (x in c('male','female')){
                    #fishing mortality rates
                    vals<-(lst[[case]]$rep)[[paste0(nmmr,".",toupper(substr(x,1,1)))]];
                    if (!is.null(vals)){
                        dfrp<-data.frame(case=case,type="total mortality",fleet=fsh,
                                         y=years.m1[[case]],x=x,m="all",s="all",val=vals);
                        dfr<-rbind(dfr,dfrp);
                    }
                    #fishery capture rates
                    vals<-(lst[[case]]$rep)[[paste0(nmcr,".",toupper(substr(x,1,1)))]];
                    if (!is.null(vals)){
                        dfrp<-data.frame(case=case,type="capture",fleet=fsh,
                                         y=years.m1[[case]],x=x,m="all",s="all",val=vals);
                        dfr<-rbind(dfr,dfrp);
                    }
                }#--x
            }#--case
        }#--fsh
        #retained mortality
        for (case in cases){
            for (x in c('male')){
                #retained mortality rates in TCF
                vals<-(lst[[case]]$rep)[["fsh.rmr.mean"]];
                dfrp<-data.frame(case=case,type='retained mortality',fleet="TCF",
                                 y=years.m1[[case]],x=x,m="all",s="all",val=vals);
                dfr<-rbind(dfr,dfrp);
            }#--x
        }#--case
        dfrp<-rCompTCMs::getMDFR.CanonicalFormat(dfr);
        dfrp$process<-'fishery';
        dfrp$category<-'mean fishing mortality rates';
        return(dfrp);
    }
    
    cat("Requested type '",type,"' not found!\n",sep="");
}