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);

Introduction

Model-estimated fishery-related quantities such as time series of retained catch abundance and biomass, retained catch size compositions, total catch abundance and biomass, and total catch siae compositions are presented in this section. Note that these plots do not indicate model fit, because they only show estimated, not observed, quantitities.

Estimated 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);

Estimated 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);

Estimated 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);

Estimated 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);

Estimated 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);

Estimated 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);

wStockhausen/rCompTCMs documentation built on Sept. 12, 2023, 3:13 p.m.