In wStockhausen/rCompTCMs: Package to compare TCSAM02, rsimTCSAM, and TCSAM2013 model runs

    ##input model list
    Models<-params$Models;
    doc_type<-params$doc_type;
    plot1stObs<-params$plot1stObs;

    ##set appendix letter
    app="A";
    ##set knitr options for subsequent chunks
    knitr::opts_chunk$set(echo=FALSE, error=FALSE, message=FALSE, warning=FALSE, concordance=TRUE, fig.width=6.5, fig.height=3.5, dpi=300)

    ##set caption numbering
    if (!exists("fig")){
      fig<-1;#figures
      tbl<-0;#tables
    }

    cases<-names(Models);
    nCases<-length(cases);

Model Estimates

Survey abundance

  plts<-rCompTCMs::compareResults.Surveys.Abundance(Models,category='index',cast="x",facet_grid=x~.,scales="free_y",dodge=0,showPlot=FALSE,verbose=FALSE);
  res<-wtsUtilities::printGGList(plots=plts,figno=fig,show=TRUE);
  fig<-res$figno;
  rm(plts,res);

Survey biomass

  plts<-rCompTCMs::compareResults.Surveys.Biomass(  Models,category='index',cast="x",facet_grid=x~.,scales="free_y",dodge=0,showPlot=FALSE,verbose=FALSE)
  res<-wtsUtilities::printGGList(plots=plts,figno=fig,show=TRUE);
  fig<-res$figno;
  rm(plts,res);

Survey size compositions

  plts<-rCompTCMs::compareResults.Surveys.Abundance(Models,category='index',cast="x+z",facet_wrap=~y,showPlot=FALSE,verbose=FALSE);
  res<-wtsUtilities::printGGList(plots=plts,figno=fig,show=TRUE);
  fig<-res$figno;
  rm(plts,res);

Retained catch abundance

  plts<-rCompTCMs::compareResults.Fisheries.CatchAbundance(Models,category='retained',cast="x",facet_grid=x~.,scales="free_y",dodge=0,showPlot=FALSE,verbose=FALSE);
  res<-wtsUtilities::printGGList(plots=plts,figno=fig,show=TRUE);
  fig<-res$figno;
  rm(plts,res);

Retained catch biomass

  plts<-rCompTCMs::compareResults.Fisheries.CatchBiomass(  Models,category='retained',cast="x",facet_grid=x~.,scales="free_y",dodge=0,showPlot=FALSE,verbose=FALSE);
  res<-wtsUtilities::printGGList(plots=plts,figno=fig,show=TRUE);
  fig<-res$figno;
  rm(plts,res);

Total catch abundance

  plts<-rCompTCMs::compareResults.Fisheries.CatchAbundance(Models,category='captured',cast="x",facet_grid=x~.,scales="free_y",dodge=0,showPlot=FALSE,verbose=FALSE);
  res<-wtsUtilities::printGGList(plots=plts,figno=fig,show=TRUE);
  fig<-res$figno;
  rm(plts,res);

Total catch biomass

  plts<-rCompTCMs::compareResults.Fisheries.CatchBiomass(  Models,category='captured',cast="x",facet_grid=x~.,scales="free_y",dodge=0,showPlot=FALSE,verbose=FALSE)
  res<-wtsUtilities::printGGList(plots=plts,figno=fig,show=TRUE);
  fig<-res$figno;
  rm(plts,res);

Retained catch size compositions

  plts<-rCompTCMs::compareResults.Fisheries.CatchAbundance(Models,category='retained',cast="x+z",facet_wrap=~y,dodge=0,showPlot=FALSE,verbose=FALSE);
  res<-wtsUtilities::printGGList(plots=plts,figno=fig,show=TRUE);
  fig<-res$figno;
  rm(plts,res);

Total catch size compositions

  plts<-rCompTCMs::compareResults.Fisheries.CatchAbundance(Models,category='captured',cast="x+z",facet_wrap=~y,dodge=0,showPlot=FALSE,verbose=FALSE);
  res<-wtsUtilities::printGGList(plots=plts,figno=fig,show=TRUE);
  fig<-res$figno;
  rm(plts,res);