Man pages for wStockhausen/rTCSAM02
A set of tools to set up input for, and interact with output from, TCSAM02 model runs.

calcTCSAM02ParamsCalculate parameter values from a TCSAM2013 model for TCSAM02
calcTCSAM02Params.FisheryCsCalculate fishery catchability parameters for TCSAM02 based...
calcTCSAM02Params.NaturalMortalityCalculate natural mortality parameters for TCSAM02 based on...
calcTCSAM02Params.SelFcnsCalculate selectivity function parameters for TCSAM02 based...
calcTCSAM02Params.SurveyQsCalculate survey Q parameters for TCSAM02 based on values...
compareModels.PopQuantsCompare population quantities from TCSAM2015 and rsimTCSAM...
createRepCreate a tcsam02.rep object from components
createResLstCreate a tcsam02.rep object from components
getCorrFind substantially-correlated model parameters, based on the...
getMDFRGet model arrays as a melted dataframe from TCSAM02 model...
getMDFR.Data.EffortDataGet model fits to biomass for fleet data components
getMDFR.Data.FleetTimeSeriesGet fleet data components by model scenario
getMDFR.Data.GrowthDataGet growth data
getMDFR.EffectiveNsForSizeCompsGet effective Ns for size comps as a dataframe
getMDFR.Fisheries.CatchabilityGet annual fishery catchabilities from model results from...
getMDFR.Fisheries.CatchAbundanceGet fishery catch abundance time series from model results...
getMDFR.Fisheries.CatchBiomassGet fishery catch biomass time series from model results from...
getMDFR.Fisheries.RetFcnsGet fishery retention functions from model results from...
getMDFR.Fisheries.SelFcnsGet fishery selectivity functions from model results from...
getMDFR.Fits.EffectiveNsGet effective N's for fleet size compositions
getMDFR.Fits.EffortDataGet model fits to effort data
getMDFR.Fits.FleetDataGet model fits to biomass for fleet data components
getMDFR.FitsForABDataGet fits to abundance or biomass data as a dataframe
getMDFR.FitsForSizeCompsGet fits for size comps as a dataframe
getMDFR.Fits.GrowthDataGet model fits to growth data as a dataframe
getMDFR.Fits.MaturityDataGet model fits to maturity data
getMDFR.OFCs.DataComponentsGet data-related components from the objective function for a...
getMDFR.OFCs.EffortDataGet objective function components for effort data from a...
getMDFR.OFCs.FDevPenaltiesGet F-devs penalties from the objective function for a...
getMDFR.OFCs.FleetDataGet objective function components for growth data from a...
getMDFR.OFCs.GrowthDataGet objective function components for growth data from a...
getMDFR.OFCs.MaturityDataGet objective function components for maturity data from a...
getMDFR.OFCs.NonDataComponentsGet non-data components from the objective function for a...
getMDFR.OFLResultsGet OFL results as a datframe
getMDFR.ParametersAtBoundsGet parameters at one of their bounds from a set of TCSAM02...
getMDFR.ParameterValuesGet parameter values from a set of TCSAM02 model runs as a...
getMDFR.Pop.AbundanceGet population abundance time series from model results from...
getMDFR.Pop.BiomassGet population biomass time series from model results from...
getMDFR.Pop.CohortProgressionGet cohort progression time series from model results from...
getMDFR.Pop.GrowthMatricesGet growth transition matrices from model results from...
getMDFR.Pop.MaturityOgivesGet population maturity ogives by year from model results...
getMDFR.Pop.MeanGrowthGet mean growth increments from model results from TCSAM2015...
getMDFR.Pop.NaturalMortalityGet natural mortality rates from model results from TCSAM02...
getMDFR.Pop.PrM2MGet molt-to-maturity ogives from model results from TCSAM02...
getMDFR.Pop.QuantitiesExtract population quantities from TCSAM02 model runs as a...
getMDFR.Pop.RecSizeDistributionGet recruitment size distribution from model results from...
getMDFR.Pop.SexRatioGet recruitment sex ratio from model results from TCSAM02...
getMDFR.Surveys.AbundanceGet survey abundance time series from model results from...
getMDFR.Surveys.BiomassGet survey biomass time series from model results from...
getMDFR.Surveys.CaptureProbsGet survey capture probability (Q_vyxmsz) functions from...
getMDFR.Surveys.CatchabilityGet annual survey catchabilities from model results from...
getMDFR.Surveys.MaturityOgivesGet survey maturity ogives by year from model results from...
getMDFR.Surveys.SelFcnsGet survey selectivity functions from model results from...
getMDFR.ZScores.AbundanceGet model fits to abundance time series as z-scores for fleet...
getMDFR.ZScores.BiomassGet model fits to biomass time series as z-scores for fleet...
getMDFR.ZScoresForABDataGet z-scores for abundance, biomass data from fits to data as...
getMDFR.ZScores.PrNatZGet model fits to size frequencies as z-scores for fleet data...
getMDFR.ZScores.PrNatZ1Get residuals from size frequency fits as dataframe
getObjGet an object from a list object using the specified path...
getOFCsGet model components in the objective function as a...
getPrsGet a TCSAM02 prs object by reading initial and final...
getRepGet a TCSAM02 report object (by reading a TCSAM02 model...
getResLstCreate a tcsam02.resLst object from a model run
getResLstsCreate a list of tcsam02.resLst objects, from a set of model...
getRunCommandsGenerate run commands for a tcsam02 model run
getStdGet a TCSAM02 std object by reading a .std file
mcmc.CalcABCFunction to calculate ABC and OFL from an MCMC dataframe
mcmc.ExtractOFLResultsExtract OFL results from an mcmc run to a dataframe
mcmc.ExtractVarExtract a variable from an MCMC results list
mcmc.ExtractVarsExtract all variables from an MCMC results list
mcmc.InvertArrayElementInvert a list of mcmc results for a numeric array element to...
mcmc.InvertListElementInvert an element of a sublist list
mcmc.InvertMCMCListInvert an mcmc list
mcmc.InvertNumberElementInvert a list of mcmc results for a numeric element to a...
mcmc.InvertVectorElementInvert a list of mcmc results for a numeric vector element to...
mcmc.ReadMCMCParse TCSAM02 MCMC.R file
plotABCFunction to plot ABC and OFL calculations from calcABC(...)
plotDynamicB0Plot dyanmic B0 results
readCorFileRead the model cor (correlation) file
readParamsCSVRead a TCSAM02 model parameters csv file and return a...
readParFileCreate a TCSAM2015 par object from a par file.
reformatTimeBlocksReformat rsim, tcsam notation for time blocks to a standard...
removeImmOSRemove rows marked as immature, old shell from a dataframe
runJitterFunction to run TCSAM02 multiple times using jittered initial...
runMSEFunction to run the TCSAM02 MSE for one harvest strategy
runTCSAM02Function to run TCSAM02.
wStockhausen/rTCSAM02 documentation built on Jan. 11, 2019, 5:33 p.m.