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

Estimated 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);

Estimated 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);

Estimated 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);

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