modelComparisons: Render a document of model comparison plots

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

Render a document of model comparison plots

Description

Function to render a document of model comparison plots

Function to render a document of model comparison plots for various management quantities

Function to render a document of model comparison plots

Usage

modelComparisons(
  models,
  includeManagementQuantities = FALSE,
  ManagementQuantities = list(base = 1, verbose = FALSE),
  includeInputData = FALSE,
  InputData = list(includeSurveyData = TRUE, surveys = list(plotAbundance = TRUE,
    plotBiomass = TRUE, plotZCs = TRUE, fleets = "all", ci = 0.8, numRecent = 30),
    includeFisheryData = TRUE, fisheries = list(fleets = "all", retained =
    list(plotAbundance = TRUE, plotBiomass = TRUE, plotZCs = TRUE, ci = 0.8, numRecent =
    30), total = list(plotAbundance = TRUE, plotBiomass = TRUE, plotZCs = TRUE, ci = 0.8,
    numRecent = 30), effort = list(plot = TRUE, numRecent = 30)), includeGrowthData =
    TRUE, includeMaturityOgiveData = TRUE, 
     verbose = FALSE),
  includeParameterTables = FALSE,
  ParameterTables = list(categories = "all", processes = "all", types = "all", params =
    "all", verbose = FALSE),
  includePopProcesses = FALSE,
  PopProcesses = list(verbose = FALSE),
  includePopQuantities = FALSE,
  PopQuantities = list(verbose = FALSE),
  includeModelFitsToOtherData = FALSE,
  ModelFitsToOtherData = list(plot1stObs = TRUE, minSizeForMaturityData = 60, verbose =
    FALSE),
  includeModelFitsACD = FALSE,
  ModelFitsACD = list(plot1stObs = TRUE, numRecent = 30, verbose = FALSE),
  includeModelFitsZCs = FALSE,
  ModelFitsZCs = list(plot1stObs = TRUE, fleets = "all", verbose = FALSE),
  includeCharacteristicsForSurveys = FALSE,
  CharacteristicsForSurveys = list(plot1stObs = TRUE, fleets = "all", selyears = "all",
    avlyears = "all", capyears = "all", mxy = 5, verbose = FALSE),
  includeCharacteristicsForFisheries = FALSE,
  CharacteristicsForFisheries = list(plot1stObs = TRUE, fleets = "all", selyears = "all",
    retyears = "all", verbose = FALSE),
  output_format = c("word_document", "pdf_document"),
  output_dir = getwd(),
  rmd = system.file("rmd/modelComparisons.Rmd", package = "rCompTCMs"),
  docx_styles = system.file("rmd/StylesForRmdDocs.docx", package = "wtsUtilities"),
  pdf_styles = system.file("rmd/StylesForRmdPDFs.sty", package = "wtsUtilities"),
  clean = FALSE
)

modelComparisons(
  models,
  includeManagementQuantities = FALSE,
  ManagementQuantities = list(base = 1, verbose = FALSE),
  includeInputData = FALSE,
  InputData = list(includeSurveyData = TRUE, surveys = list(plotAbundance = TRUE,
    plotBiomass = TRUE, plotZCs = TRUE, fleets = "all", ci = 0.8, numRecent = 30),
    includeFisheryData = TRUE, fisheries = list(fleets = "all", retained =
    list(plotAbundance = TRUE, plotBiomass = TRUE, plotZCs = TRUE, ci = 0.8, numRecent =
    30), total = list(plotAbundance = TRUE, plotBiomass = TRUE, plotZCs = TRUE, ci = 0.8,
    numRecent = 30), effort = list(plot = TRUE, numRecent = 30)), includeGrowthData =
    TRUE, includeMaturityOgiveData = TRUE, 
     verbose = FALSE),
  includeParameterTables = FALSE,
  ParameterTables = list(categories = "all", processes = "all", types = "all", params =
    "all", verbose = FALSE),
  includePopProcesses = FALSE,
  PopProcesses = list(verbose = FALSE),
  includePopQuantities = FALSE,
  PopQuantities = list(verbose = FALSE),
  includeModelFitsToOtherData = FALSE,
  ModelFitsToOtherData = list(plot1stObs = TRUE, minSizeForMaturityData = 60, verbose =
    FALSE),
  includeModelFitsACD = FALSE,
  ModelFitsACD = list(plot1stObs = TRUE, numRecent = 30, verbose = FALSE),
  includeModelFitsZCs = FALSE,
  ModelFitsZCs = list(plot1stObs = TRUE, fleets = "all", verbose = FALSE),
  includeCharacteristicsForSurveys = FALSE,
  CharacteristicsForSurveys = list(plot1stObs = TRUE, fleets = "all", selyears = "all",
    avlyears = "all", capyears = "all", mxy = 5, verbose = FALSE),
  includeCharacteristicsForFisheries = FALSE,
  CharacteristicsForFisheries = list(plot1stObs = TRUE, fleets = "all", selyears = "all",
    retyears = "all", verbose = FALSE),
  output_format = c("word_document", "pdf_document"),
  output_dir = getwd(),
  rmd = system.file("rmd/modelComparisons.Rmd", package = "rCompTCMs"),
  docx_styles = system.file("rmd/StylesForRmdDocs.docx", package = "wtsUtilities"),
  pdf_styles = system.file("rmd/StylesForRmdPDFs.sty", package = "wtsUtilities"),
  clean = FALSE
)

modelComparisons(
  models,
  includeManagementQuantities = FALSE,
  ManagementQuantities = list(base = 1, verbose = FALSE),
  includeInputData = FALSE,
  InputData = list(includeSurveyData = TRUE, surveys = list(plotAbundance = TRUE,
    plotBiomass = TRUE, plotZCs = TRUE, fleets = "all", ci = 0.8, numRecent = 30),
    includeFisheryData = TRUE, fisheries = list(fleets = "all", retained =
    list(plotAbundance = TRUE, plotBiomass = TRUE, plotZCs = TRUE, ci = 0.8, numRecent =
    30), total = list(plotAbundance = TRUE, plotBiomass = TRUE, plotZCs = TRUE, ci = 0.8,
    numRecent = 30), effort = list(plot = TRUE, numRecent = 30)), includeGrowthData =
    TRUE, includeMaturityOgiveData = TRUE, 
     verbose = FALSE),
  includeParameterTables = FALSE,
  ParameterTables = list(categories = "all", processes = "all", types = "all", params =
    "all", verbose = FALSE),
  includePopProcesses = FALSE,
  PopProcesses = list(verbose = FALSE),
  includePopQuantities = FALSE,
  PopQuantities = list(verbose = FALSE),
  includeModelFitsToOtherData = FALSE,
  ModelFitsToOtherData = list(plot1stObs = TRUE, minSizeForMaturityData = 60, verbose =
    FALSE),
  includeModelFitsACD = FALSE,
  ModelFitsACD = list(plot1stObs = TRUE, numRecent = 30, verbose = FALSE),
  includeModelFitsZCs = FALSE,
  ModelFitsZCs = list(plot1stObs = TRUE, fleets = "all", verbose = FALSE),
  includeCharacteristicsForSurveys = FALSE,
  CharacteristicsForSurveys = list(plot1stObs = TRUE, fleets = "all", selyears = "all",
    avlyears = "all", capyears = "all", mxy = 5, verbose = FALSE),
  includeCharacteristicsForFisheries = FALSE,
  CharacteristicsForFisheries = list(plot1stObs = TRUE, fleets = "all", selyears = "all",
    retyears = "all", verbose = FALSE),
  output_format = c("word_document", "pdf_document"),
  output_dir = getwd(),
  rmd = system.file("rmd/modelComparisons.Rmd", package = "rCompTCMs"),
  docx_styles = system.file("rmd/StylesForRmdDocs.docx", package = "wtsUtilities"),
  pdf_styles = system.file("rmd/StylesForRmdPDFs.sty", package = "wtsUtilities"),
  clean = FALSE
)

Arguments

models	named list of model results (as resLst objects) to compare
includeManagementQuantities	flag to include comparison of management quantities
ManagementQuantities	list controlling comparison of management quantities (see modelComparisons.ManagementQuantities())
includeInputData	flag (T/F) to include section
InputData	list controlling what gets plotted
includeParameterTables	flag (T/F) to include section
ParameterTables	list(verbose=FALSE) (see modelComparisons.ParameterTables())
includePopProcesses	flag (T/F) to include section
PopProcesses	list(verbose=FALSE) (see modelComparisons.PopProcesses())
includePopQuantities	flag (T/F) to include section
PopQuantities	list(verbose=FALSE) (see modelComparisons.PopQuantitiess())
includeModelFitsToOtherData	flag (T/F) to include section
ModelFitsToOtherData	list(plot1stObs=TRUE,minSizeForMaturityData=60,verbose=FALSE) (see modelComparisons.ModelFitsToOtherData())
includeModelFitsACD	flag (T/F) to include section
ModelFitsACD	list(plot1stObs=TRUE,numRecent=30,verbose=FALSE) (see modelComparisons.ModelFitsACD())
includeModelFitsZCs	flag (T/F) to include section
ModelFitsZCs	list(plot1stObs=TRUE,fleets="all",verbose=FALSE) (see modelComparisons.ModelFitsZCs())
includeCharacteristicsForSurveys	flag (T/F) to include section
CharacteristicsForSurveys	list(plot1stObs=TRUE,fleets="all",selyears="all",avlyears="all",capyears="all",mxy=5,verbose=FALSE) (see modelComparisons.CharacteristicsSurveys())
includeCharacteristicsForFisheries	flag (T/F) to include section
CharacteristicsForFisheries	list(plot1stObs=TRUE,fleets="all",selyears="all",retyears="all",verbose=FALSE) (see modelComparisons.CharacteristicsFisheries())
output_format	"word_document" or "pdf_document"
output_dir	path to folder to use for output
rmd	Rmd file to process (defalut=system.file("rmd/modelComparisons.Rmd",package="rCompTCMs"))
docx_styles	full path to Word (docx) style template for Word documents
pdf_styles	full path to style template for pdf documents
clean	T/F to delete intermediate files
plot1stObs	flag to plot observed data only from first model
rmd_dir	folder enclosing rmd file
base	name or index of base case for difference calculations
verbose	flag (T/F) to print diagnostic output

Details

Resulting document title will be of the form "ModelComparisons.mmm.ext", where "ext" is the appropriate file extension and "mmm" is a dash-separated string of model names.

Resulting document title will be of the form "ModelComparisons.ManagementQuantities.mmm.ext", where "ext" is the appropriate file extension and "mmm" is a dash-separated string of model names.

Resulting document title will be of the form "ModelComparisons.mmm.ext", where "ext" is the appropriate file extension and "mmm" is a dash-separated string of model names.

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