Files in wStockhausen/rTCSAM2015

A set of tools to set up input for, and interact with output from, a TCSAM2015 model run, as well as to compare TCSAM2015 and rsimTCSAM runs.

R/appendString.R R/calcLogPrior.R R/checkHandlingMortalityConsistency.R R/compareModels.FisheryCatches.R R/compareModels.FisheryResults.R R/compareModels.FisherySelFcns.R R/compareModels.FisheryYields.R R/compareModels.FishingRates.R R/compareModels.Fits.AggCatchData.R R/compareModels.Fits.NatZData.R R/compareModels.GrowthTransitionMatrices.R R/compareModels.ObjFunValues.R R/compareModels.ParamEsts.R R/compareModels.PopProcesses.R R/compareModels.PopQuants.R R/compareModels.R R/compareModels.SelFcns.ByPC.R R/compareModels.SurveyAbundance.R R/compareModels.SurveyBiomass.R R/compareModels.SurveyQs.R R/compareModels.SurveyResults.R R/compareModels.SurveySelFcns.R R/compareModels.ZScores.AggCatchData.R R/compareModels.ZScores.NatZData.R R/compileMCMCResults.R R/extractModelResults.Params.R R/extractModelResults.ParamsPlusStdDevs.R R/extractModelResults.RepObjs.R R/extractModelResults.StdDevs.R R/getInputDataTimeframes.R R/getIntervalLimits.R R/getMCMCFile.R R/getMCMCResults.R R/getMDFR.FitsForABData.R R/getMDFR.FitsForFleets.R R/getMDFR.FitsForSizeComps.R R/getMDFR.R R/getMDFR.Special.R R/getMDFR.ZScoresForABData.R R/getMDFR.ZScoresForCatchData.R R/getMDFR.ZScoresForFleets.R R/getMDFR.ZScoresForSizeComps.R R/getObj.R R/getObjFunValues.AggregateCatch.R R/getObjFunValues.CatchData.R R/getObjFunValues.Components.R R/getObjFunValues.Data.R R/getObjFunValues.Fleets.R R/getObjFunValues.NatZ.R R/getObjFunValues.Penalties.R R/getObjFunValues.Priors.R R/getPlotSymbology.R R/getPrs.R R/getRep.R R/getRunCommands.R R/getStd.R R/plotAggregateCatchData.R R/plotAggregateCatchDataGG.R R/plotBars.R R/plotCatchData.R R/plotCompsAsCircles.R R/plotCompsAsCirclesGG.R R/plotDataModelComparisons.R R/plotEffNsForSizeFreqs.R R/plotEffNsGG.R R/plotEffortRegressions.R R/plotErrorBars.H.r R/plotErrorBars.V.r R/plotExploitationRatesGG.R R/plotFisheriesResults.R R/plotFisheryCatchesGG.R R/plotFisheryYieldsGG.R R/plotFishingRatesGG.R R/plotFitsGG.MeanSizeComps.R R/plotFitsGG.SizeComps.R R/plotInputDataTimeframes.R R/plotMCMCDensity.R R/plotMCMCResults.R R/plotMCMCResults.forArray3D.R R/plotMCMCResults.forMatrix.R R/plotMCMCResults.forVector.R R/plotMDFR.BarLine.R R/plotMDFR.Bars.R R/plotMDFR.Bubbles.R R/plotMDFR.XY.R R/plotMatrix.R R/plotMeanSizeComps.r R/plotMeanSizeCompsGG.R R/plotModelResults.ScalarParams.R R/plotMulti.gg.R R/plotNM.byPC.R R/plotNatZ.r R/plotObjFunValues.CatchData.R R/plotObjFunValues.Data.R R/plotObjFunValues.Penalties.R R/plotObjFunValues.Priors.R R/plotPDFRects.R R/plotParameters.DevsVectorVector.R R/plotParameters.NumberVector.R R/plotParameters.R R/plotParameters.VectorVector.R R/plotPopComponents.Abundance.R R/plotPopComponents.Biomass.R R/plotPopQuants.R R/plotPrGrowth.byPC.R R/plotPrMaturity.byPC.R R/plotRecruits.R R/plotRecruits.SexRatio.R R/plotSelFcns.ByYear.R R/plotSizeCompsComparisons0.R R/plotSizeCompsComparisons1.R R/plotSizeCompsComparisons2.R R/plotSizeCompsGG.Single.R R/plotSpB.R R/plotTCSAM2015.R R/plotTCSAM2015I.R R/plotTCSAM2015J.R R/plotXY.R R/plotZScores.R R/plotZScoresForAll.R R/plotZScoresForCatchData.R R/plotZScoresForFisheries.R R/plotZScoresForFleets.R R/plotZScoresForSizeFreqs.R R/plotZScoresForSurveys.R R/plotZScoresGG.R R/plotZScoresGG.SizeFreqs.R R/plotZScoresGG1.SizeFreqs.R R/readParFile.R R/readParamsCSV.R R/readReportFile.R R/readStdFile.R R/reformatTimeBlocks.R R/removeImmOS.R R/runJitter.R R/runProfiles.R R/runSequence.R R/runTCSAM2015.R R/selectReportFile.R R/sumByDims.R R/writeModelResultsToCSV.Fisheries.R R/writeModelResultsToCSV.FisherySelFcns.R R/writeModelResultsToCSV.ObjFunValues.R R/writeModelResultsToCSV.ParamEsts.R R/writeModelResultsToCSV.PopProcesses.R R/writeModelResultsToCSV.PopQuants.R R/writeModelResultsToCSV.SurveySelFcns.R R/writeModelResultsToCSV.Surveys.R README.md man/appendString.Rd man/calcLogPrior.Rd man/checkHandlingMortalityConsistency.Rd man/compareModels.FisheryCatches.Rd man/compareModels.FisheryResults.Rd man/compareModels.FisherySelFcns.Rd man/compareModels.FisheryYields.Rd man/compareModels.FishingRates.Rd man/compareModels.Fits.AggCatchData.Rd man/compareModels.Fits.NatZData.Rd man/compareModels.GrowthTransitionMatrices.Rd man/compareModels.ObjFunValues.Rd man/compareModels.ParamEsts.Rd man/compareModels.PopProcesses.Rd man/compareModels.PopQuants.Rd man/compareModels.Rd man/compareModels.SelFcns.ByPC.Rd man/compareModels.SurveyAbundance.Rd man/compareModels.SurveyBiomass.Rd man/compareModels.SurveyQs.Rd man/compareModels.SurveyResults.Rd man/compareModels.SurveySelFcns.Rd man/compareModels.ZScores.AggCatchData.Rd man/compareModels.ZScores.NatZData.Rd man/compileMCMCResults.Rd man/extractModelResults.Params.Rd man/extractModelResults.ParamsPlusStdDevs.Rd man/extractModelResults.RepObjs.Rd man/extractModelResults.StdDevs.Rd man/getInputDataTimeframes.Rd man/getIntervalLimits.Rd man/getMCMCFile.Rd man/getMCMCResults.Rd man/getMDFR.FitsForABData.Rd man/getMDFR.FitsForFleets.Rd man/getMDFR.FitsForSizeComps.Rd man/getMDFR.GrowthTransitionMatrices.Rd man/getMDFR.MeanGrowthIncrements.Rd man/getMDFR.NatMort.Rd man/getMDFR.Rd man/getMDFR.RecSizeDistribution.Rd man/getMDFR.SexRatio.Rd man/getMDFR.ZScoresForABData.Rd man/getMDFR.ZScoresForCatchData.Rd man/getMDFR.ZScoresForFleets.Rd man/getMDFR.ZScoresForSizeComps.Rd man/getMDFR.prM2M.Rd man/getObj.Rd man/getObjFunValues.AggregateCatch.Rd man/getObjFunValues.CatchData.Rd man/getObjFunValues.Components.Rd man/getObjFunValues.Data.Rd man/getObjFunValues.Fleets.Rd man/getObjFunValues.NatZ.Rd man/getObjFunValues.Penalties.Rd man/getObjFunValues.Priors.Rd man/getPlotSymbology.Rd man/getPrs.Rd man/getRep.Rd man/getRunCommands.Rd man/getStd.Rd man/plot.xy.Rd man/plotAggregateCatchData.Rd man/plotAggregateCatchDataGG.Rd man/plotBars.Rd man/plotCatchData.Rd man/plotCompsAsCircles.Rd man/plotCompsAsCirclesGG.Rd man/plotDataModelComparisons.Rd man/plotEffNsForSizeFreqs.Rd man/plotEffNsGG.Rd man/plotEffortRegressions.Rd man/plotErrorBars.H.Rd man/plotErrorBars.V.Rd man/plotExploitationRatesGG.Rd man/plotFisheriesResults.Rd man/plotFisheryCatchesGG.Rd man/plotFisheryYieldsGG.Rd man/plotFishingRatesGG.Rd man/plotFitsGG.MeanSizeComps.Rd man/plotFitsGG.SizeComps.Rd man/plotInputDataTimeframes.Rd man/plotMCMCDensity.Rd man/plotMCMCResults.Rd man/plotMCMCResults.forArray3D.Rd man/plotMCMCResults.forMatrix.Rd man/plotMCMCResults.forVector.Rd man/plotMDFR.BarLine.Rd man/plotMDFR.Bars.Rd man/plotMDFR.Bubbles.Rd man/plotMDFR.XY.Rd man/plotMatrix.Rd man/plotMeanSizeComps.Rd man/plotMeanSizeCompsGG.Rd man/plotModelResults.ScalarParams.Rd man/plotMulti.gg.Rd man/plotNM.ByPC.Rd man/plotNatZ.Rd man/plotObjFunValues.Data.Rd man/plotObjFunValues.Penalties.Rd man/plotObjFunValues.Priors.Rd man/plotPDFRects.Rd man/plotParameters.DevsVectorVector.Rd man/plotParameters.NumberVector.Rd man/plotParameters.Rd man/plotParameters.VectorVector.Rd man/plotPopComponents.Abundance.Rd man/plotPopComponents.Biomass.Rd man/plotPopQuants.Rd man/plotPrGrowth.ByPC.Rd man/plotPrMaturity.ByPC.Rd man/plotRecruits.Rd man/plotRecruits.SexRatio.Rd man/plotSelFcns.ByYear.Rd man/plotSizeCompsComparisons0.Rd man/plotSizeCompsComparisons1.Rd man/plotSizeCompsComparisons2.Rd man/plotSizeCompsGG.Single.Rd man/plotSpB.Rd man/plotTCSAM2015.Rd man/plotTCSAM2015I.Rd man/plotTCSAM2015J.Rd man/plotXY.Rd man/plotZScores.Rd man/plotZScoresForAll.Rd man/plotZScoresForCatchData.Rd man/plotZScoresForFisheries.Rd man/plotZScoresForFleets.Rd man/plotZScoresForSizeFreqs.Rd man/plotZScoresForSurveys.Rd man/plotZScoresGG.Rd man/plotZScoresGG.SizeFreqs.Rd man/plotZScoresGG1.SizeFreqs.Rd man/readParFile.Rd man/readParamsCSV.Rd man/readReportFile.Rd man/readStdFile.Rd man/reformatTimeBlocks.Rd man/removeImmOS.Rd man/runJitter.Rd man/runProfiles.Rd man/runSequence.Rd man/runTCSAM2015.Rd man/selectReportFile.Rd man/sumByDims.Rd man/writeModelResultsToCSV.Fisheries.Rd man/writeModelResultsToCSV.FisherySelFcns.Rd man/writeModelResultsToCSV.ObjFunValues.Rd man/writeModelResultsToCSV.ParamEsts.Rd man/writeModelResultsToCSV.PopProcesses.Rd man/writeModelResultsToCSV.PopQuants.Rd man/writeModelResultsToCSV.SurveySelFcns.Rd man/writeModelResultsToCSV.Surveys.Rd