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$PopQuantities$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 quantities

Figures and tables in this section present comparisons between alternative model scenarios for estimated quantities (e.g., recruitment, abundance time series) describing the inferred Tanner crab population.

\blandscape

Recruitment

  message("Starting plotPopRecruitment");
  plts<-rCompTCMs::compareResults.Pop.Recruitment(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);

\FloatBarrier

\elandscape

Mature biomass

  message("Starting plotMatureBiomass");
  plts<-rCompTCMs::compareResults.Pop.MatureBiomass(Models,dodge=0,showPlot=FALSE,verbose=verbose)
  captions<-wtsUtilities::getCaptionsFromGGPlotList(plts);
  #res<-wtsUtilities::printGGList(plots=plts,figno=fig,show=TRUE);
  #fig<-res$figno;
  for (plt in plts) {print(plt); cat("\n\n"); fig<-fig+1;}
  rm(plt,plts);

\FloatBarrier

\clearpage

Population abundance

  message("Starting plotPopAbundance");
  plts<-rCompTCMs::compareResults.Pop.Abundance1(Models,dodge=0,type="N_yxm",facet_grid=x+m~.,scales="free_y",showPlot=FALSE,verbose=verbose)
  captions<-wtsUtilities::getCaptionsFromGGPlotList(plts);
  for (plt in plts) {print(plt); cat("\n\n"); fig<-fig+1;}
  rm(plt,plts);

\FloatBarrier

\clearpage

Population biomass

  message("Starting plotPopBiomass");
  plts<-rCompTCMs::compareResults.Pop.Biomass1(Models,dodge=0,type="B_yxm",facet_grid=x+m~.,scales="free_y",showPlot=FALSE,verbose=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.