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

    ##input model list
    Models<-params$Models;
    doc_type<-params$doc_type;
    verbose = params$PopProcesses$verbose

    ##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=6.5,out.width="6.5in", dpi=300)

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

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

Population processes

Figures and tables in this section present comparisons between alternative model scenarios for estimated rates (e.g., natural mortality) or other attributes (e.g., molt increments) describing inferred Tanner crab population processes.

Natural mortality

  message("Starting plotPopProcessNM");
  plts<-rCompTCMs::compareResults.Pop.NaturalMortality(Models,dodge=0,showPlot=FALSE,verbose=verbose);
  captions<-wtsUtilities::getCaptionsFromGGPlotList(plts);
  for (plt in plts) {print(plt); cat("\n\n"); fig<-fig+1;}
  rm(plt,plts);

  message("Starting plotPopProcessNMbar");
  plts<-rCompTCMs::compareResults.Pop.NaturalMortality.BarPlot(Models,showPlot=FALSE,verbose=verbose);
  captions<-wtsUtilities::getCaptionsFromGGPlotList(plts);
  for (plt in plts) {print(plt); cat("\n\n"); fig<-fig+1;}
  rm(plt,plts);

\FloatBarrier

Probability of terminal molt

  message("Starting plotPopProcessPrM2M");
  plts<-rCompTCMs::compareResults.Pop.PrM2M(Models,dodge=0,showPlot=FALSE,verbose=verbose);
  captions<-paste("Probability of terminal molt.")
  print(plts); fig<-fig+1;
  rm(plts);

\FloatBarrier

Mean growth

  message("Starting plotPopProcessMnGr");
  plts<-rCompTCMs::compareResults.Pop.MeanGrowth(Models,dodge=0,showPlot=FALSE,verbose=verbose);
  captions<-paste("Mean growth.")
  print(plts);
  fig<-fig+1;
  cap<-paste("\n  \nFigure &&figno. Mean growth.\n  \n")

\FloatBarrier

\clearpage

Growth matrices

Growth matrices for each model case are compared as bubble plots in the following figure.

  message("Starting plotPopProcessGMs1");
  plts<-rCompTCMs::compareResults.Pop.GrowthMatrices(Models,showPlot=FALSE,verbose=verbose);
  captions<-wtsUtilities::getCaptionsFromGGPlotList(plts);
  for (plt in plts) {print(plt); cat("\n\n"); fig<-fig+1;}
  rm(plt,plts);

\clearpage

The same growth matrices are compared in the following figure(s) as line plots for each pre-molt size bin, by sex.

  message("Starting plotPopProcessGMs2");
  plts<-rCompTCMs::compareResults.Pop.GrowthMatrices.LinePlots(Models,dodge=0,showPlot=FALSE,verbose=verbose);
  captions<-wtsUtilities::getCaptionsFromGGPlotList(plts);
  for (plt in plts) {print(plt); cat("\n\n"); fig<-fig+1;}
  rm(plt,plts);

\clearpage

Size distribution for recruits

  message("Starting plotPopProcessRecZ");
  plts<-rCompTCMs::compareResults.Pop.RecSizeDistribution(Models,dodge=0,showPlot=FALSE,verbose=verbose);
  captions<-paste("Size distribution for recruits.")
  print(plts);
  fig<-fig+1;

\FloatBarrier

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