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

  ##input model list
  Models<-params$Models;
  doc_type<-params$doc_type;

  ##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
  fig<-1;#figures
  tbl<-0;#tables

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

  if (params$includeInputData){
    cat("\n\\newpage\n")
    path = system.file("rmd/modelComparisons.InputData.Rmd",package="rCompTCMs");
    fn   = basename(path);
    message("child rmd file:",fn)
    cat(
      knitr::knit_child(fn,envir=environment(),quiet=TRUE)
    )
  } else {
    message("Skipping modelComparisons_InputData")
  }

  if (params$includeManagementQuantities){
    cat("\n\\newpage\n")
    path = system.file("rmd/modelComparisons.ManagementQuantities.Rmd",package="rCompTCMs");
    fn   = basename(path);
    message("child rmd file:",fn)
    cat(
      knitr::knit_child(fn,envir=environment(),quiet=TRUE)
    )
  } else {
    message("Skipping modelComparisons_ManagementQuantities")
  }

  if (params$includePopProcesses){
    cat("\n\\newpage\n")
    path = system.file("rmd/modelComparisons.PopProcesses.Rmd",package="rCompTCMs");
    fn   = basename(path);
    message("child rmd file:",fn)
    cat(
      knitr::knit_child(fn,envir=environment(),quiet=TRUE)
    )
  } else {
    message("Skipping modelComparisons_PopProcesses")
  }

  if (params$includePopQuantities){
    cat("\n\\newpage\n")
    path = system.file("rmd/modelComparisons.PopQuantities.Rmd",package="rCompTCMs");
    fn   = basename(path);
    message("child rmd file:",fn)
    cat(
      knitr::knit_child(fn,envir=environment(),quiet=TRUE)
    )
  } else {
    message("Skipping modelComparisons_PopQuantities")
  }

  if (params$includeModelFitsACD){
    cat("\n\\newpage\n")
    path = system.file("rmd/modelComparisons.ModelFits.ACD.Rmd",package="rCompTCMs");
    fn   = basename(path);
    message("child rmd file:",fn)
    cat(
      knitr::knit_child(fn,envir=environment(),quiet=TRUE)
    )
  } else {
    message("Skipping modelComparisons_ModelFitsACD")
  }

  if (params$includeModelFitsZCs){
    cat("\n\\newpage\n")
    path = system.file("rmd/modelComparisons.ModelFits.ZCs.All.Rmd",package="rCompTCMs");
    fn   = basename(path);
    message("child rmd file:",fn)
    cat(
      knitr::knit_child(fn,envir=environment(),quiet=TRUE)
    )
  } else {
    message("Skipping modelComparisons_ModelFitsZCs")
  }

  if (params$includeModelFitsToOtherData){
    cat("\n\\newpage\n")
    path = system.file("rmd/modelComparisons.ModelFits.OtherData.Rmd",package="rCompTCMs")
    fn   = basename(path);
    message("child rmd file:",fn)
    cat(
      knitr::knit_child(fn,envir=environment(),quiet=TRUE)
    )
  } else {
    message("Skipping modelComparisons_ModelFitsToOtherData")
  }

  if (params$includeCharacteristicsForSurveys){
    cat("\n\\newpage\n")
    path = system.file("rmd/modelComparisons.EstimatedCharacteristics.Surveys.Rmd",package="rCompTCMs");
    fn   = basename(path);
    message("child rmd file:",fn)
    cat(
      knitr::knit_child(fn,envir=environment(),quiet=TRUE)
    )
  } else {
    message("Skipping modelComparisons_CharacteristicsForSurveys")
  }

  if (params$includeCharacteristicsForFisheries){
    cat("\n\\newpage\n")
    path = system.file("rmd/modelComparisons.EstimatedCharacteristics.Fisheries.Rmd",package="rCompTCMs");
    fn   = basename(path);
    message("child rmd file:",fn)
    cat(
      knitr::knit_child(fn,envir=environment(),quiet=TRUE)
    )
  } else {
    message("Skipping modelComparisons_CharacteristicsForFisheries")
  }

  if (params$includeParameterTables){
    cat("\n\\newpage\n")
    path = system.file("rmd/modelComparisons.ParameterTables.Rmd",package="rCompTCMs");
    fn   = basename(path);
    message("child rmd file:",fn)
    cat(
      knitr::knit_child(fn,envir=environment(),quiet=TRUE)
    )
  } else {
    message("Skipping modelComparisons_ParameterTables")
  }

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