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 fits to size compositions, by year

Fits to the size composition data available to the model(s) are presented in this section as line plots by year. Not all of the fits presented are necessarily included in the parameter optimization for each model; some fits to datasets for a particular model may be included for comparison purposes with other models which include those data in their optimization. The reader should consult the main assessment document to determine which fits are included in the optimization for any particular model.

Survey size compositions

  plts<-rCompTCMs::compareFits.SizeComps(Models,
                                         fleet.type="survey",
                                         catch.type="index",
                                         plot1stObs=plot1stObs,
                                         showPlot=FALSE,
                                         verbose=params$verbose);
  captions<-wtsUtilities::getCaptionsFromGGPlotList(plts);
  for (plt in plts) {print(plt); cat("\n\n"); fig<-fig+1;}
  rm(plt,plts);

\FloatBarrier

\clearpage

Fishery retained catch size compositions

  plts<-rCompTCMs::compareFits.SizeComps(Models,
                                         fleet.type="fishery",
                                         catch.type="retained",
                                         plot1stObs=plot1stObs,
                                         showPlot=FALSE,
                                         verbose=params$verbose);
  captions<-wtsUtilities::getCaptionsFromGGPlotList(plts);
  for (plt in plts) {print(plt); cat("\n\n"); fig<-fig+1;}
  rm(plt,plts);
  #res<-wtsUtilities::printGGList(plots=plts,figno=fig,show=TRUE);
  #fig<-res$figno;
  #rm(plts,res);

\FloatBarrier

\clearpage

Fishery total catch size compositions

  plts<-rCompTCMs::compareFits.SizeComps(Models,
                                         fleet.type="fishery",
                                         catch.type="total",
                                         plot1stObs=plot1stObs,
                                         showPlot=FALSE,
                                         verbose=params$verbose);
  captions<-wtsUtilities::getCaptionsFromGGPlotList(plts);
  for (plt in plts) {print(plt); cat("\n\n"); fig<-fig+1;}
  rm(plt,plts);

\FloatBarrier

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