Man pages for wStockhausen/rTCSAM02
A set of tools to set up input for, and interact with output from, TCSAM02 model runs
| calcTCSAM02Params | Calculate parameter values from a TCSAM2013 model for TCSAM02 |
| calcTCSAM02Params.FisheryCs | Calculate fishery catchability parameters for TCSAM02 based... |
| calcTCSAM02Params.NaturalMortality | Calculate natural mortality parameters for TCSAM02 based on... |
| calcTCSAM02Params.SelFcns | Calculate selectivity function parameters for TCSAM02 based... |
| calcTCSAM02Params.SurveyQs | Calculate survey Q parameters for TCSAM02 based on values... |
| compareModels.PopQuants | Compare population quantities from TCSAM2015 and rsimTCSAM... |
| createRep | Create a tcsam02.rep object from components |
| createResLst | Create a tcsam02.rep object from components |
| findOptDiffByCat | Find differences between 'optimal' fits to models |
| findOptDiffs | Find differences between 'optimal' fits to models across all... |
| getCorr | Find substantially-correlated model parameters, based on the... |
| getMDFR | Get model arrays as a melted dataframe from TCSAM02 model... |
| getMDFR.AllScores.Abundance | Get all scores related to model fits to abundance time series... |
| getMDFR.AllScores.Abundance1 | Get all scores related to model fits to abundance time series... |
| getMDFR.AllScores.Biomass | Get all scores related to model fits to biomass time series... |
| getMDFR.AllScores.Biomass1 | Get all scores related to model fits to biomass time series... |
| getMDFR.AllScoresForABData | Get z-scores and other model fits info for abundance or... |
| getMDFR.CanonicalFormat | Convert dataframe to canonical format |
| getMDFR.Data.ChelaHeightData | Get chela height data as a dataframe |
| getMDFR.Data.EffortData | Get model fits to biomass for fleet data components |
| getMDFR.Data.FleetSizeComps | Get fleet size comps by model scenario |
| getMDFR.Data.FleetTimeSeries | Get fleet data components by model scenario |
| getMDFR.Data.GrowthData | Get growth data |
| getMDFR.Data.MaturityOgiveData | Get maturity ogive data as a dataframe |
| getMDFR.Data.TimeFrames | Get time frames for model data components as a dataframe |
| getMDFR.EffectiveNsForSizeComps | Get effective Ns for size comps as a dataframe |
| getMDFR.Fisheries.Catchability | Get annual fishery catchabilities from model results from... |
| getMDFR.Fisheries.CatchAbundance | Get fishery catch abundance time series from model results... |
| getMDFR.Fisheries.CatchBiomass | Get fishery catch biomass time series from model results from... |
| getMDFR.Fisheries.RetFcns | Get fishery retention functions from model results from... |
| getMDFR.Fisheries.SelFcns | Get fishery selectivity functions from model results from... |
| getMDFR.Fits.ChelaHeightData | Get model fits to chela height data |
| getMDFR.Fits.EffectiveNs | Get effective N's for fleet size compositions |
| getMDFR.Fits.EffortData | Get model fits to effort data |
| getMDFR.Fits.FleetData | Get model fits to biomass for fleet data components |
| getMDFR.FitsForABData | Get fits to abundance or biomass data as a dataframe |
| getMDFR.FitsForSizeComps | Get fits for size comps as a dataframe |
| getMDFR.Fits.GrowthData | Get model fits to growth data as a dataframe |
| getMDFR.Fits.MaturityOgiveData | Get model fits to maturity ogive data |
| getMDFR.ManagementQuantities | Get management quantities from multiple model scenarios |
| getMDFR.OFCs.ChelaHeightData | Get objective function components for chela height data from... |
| getMDFR.OFCs.DataComponents | Get data-related components from the objective function for a... |
| getMDFR.OFCs.EffortData | Get objective function components for effort data from a... |
| getMDFR.OFCs.FDevPenalties | Get F-devs penalties from the objective function for a... |
| getMDFR.OFCs.FleetData | Get objective function components for growth data from a... |
| getMDFR.OFCs.GrowthData | Get objective function components for growth data from a... |
| getMDFR.OFCs.MaturityOgiveData | Get objective function components for maturity ogive data... |
| getMDFR.OFCs.NonDataComponents | Get non-data components from the objective function for a... |
| getMDFR.OFLResults | Get OFL results as a dataframe |
| getMDFR.ParametersAtBounds | Get active parameters estimated at one of their bounds from a... |
| getMDFR.ParameterValues | Get parameter values from a set of TCSAM02 model runs as a... |
| getMDFR.Pop.Abundance | Get population abundance time series from model results from... |
| getMDFR.Pop.Biomass | Get population biomass time series from model results from... |
| getMDFR.Pop.CohortProgression | Get cohort progression time series from model results from... |
| getMDFR.Pop.GrowthMatrices | Get growth transition matrices from model results from... |
| getMDFR.Pop.MaturityOgives | Get population maturity ogives by year from model results... |
| getMDFR.Pop.MeanGrowth | Get mean growth increments from model results from TCSAM2015... |
| getMDFR.Pop.NaturalMortality | Get natural mortality rates from model results from TCSAM02... |
| getMDFR.Pop.PrM2M | Get molt-to-maturity ogives from model results from TCSAM02... |
| getMDFR.Pop.Quantities | Extract population quantities from TCSAM02 model runs as a... |
| getMDFR.Pop.RecSizeDistribution | Get recruitment size distribution from model results from... |
| getMDFR.Pop.SexRatio | Get recruitment sex ratio from model results from TCSAM02... |
| getMDFR.SdRep.DerivedVars | Get sd_report info on derived quantities as a dataframe |
| getMDFR.SdRep.RecAndSSB | Get sd_report info on recruitment and SSB time series... |
| getMDFR.Surveys.Abundance | Get survey abundance time series from model results from... |
| getMDFR.Surveys.Availability | Get annual survey availabilities from model results from... |
| getMDFR.Surveys.AvlFcns | Get survey availability functions from model results from... |
| getMDFR.Surveys.Biomass | Get survey biomass time series from model results from... |
| getMDFR.Surveys.CaptureProbs | Get survey capture probability (Q_vyxmsz) functions from... |
| getMDFR.Surveys.Catchability | Get annual survey catchabilities from model results from... |
| getMDFR.Surveys.MaturityOgives | Get survey maturity ogives by year from model results from... |
| getMDFR.Surveys.SelFcns | Get survey selectivity functions from model results from... |
| getMDFR.ZScores.Abundance | Get model fits to abundance time series as z-scores for fleet... |
| getMDFR.ZScores.Abundance.old | Get model fits to abundance time series as z-scores for fleet... |
| getMDFR.ZScores.Biomass | Get model fits to biomass time series as z-scores for fleet... |
| getMDFR.ZScores.PrNatZ | Get model fits to size frequencies as z-scores for fleet data... |
| getMDFR.ZScores.PrNatZ1 | Get residuals from size frequency fits as dataframe |
| getObj | Get an object from a list object using the specified path... |
| getOFCs | Get model components in the objective function as a... |
| getPrs | Get a TCSAM02 prs object by reading initial and final... |
| getRep | Get a TCSAM02 report object (by reading a TCSAM02 model... |
| getResLst | Create a tcsam02.resLst object from a model run |
| getResLsts | Create a list of tcsam02.resLst objects, from a set of model... |
| getRunCommands | Generate run commands for a tcsam02 model run |
| getStd | Get a TCSAM02 std object by reading a .std file |
| mcmc.CalcABC | Function to calculate ABC and OFL from an MCMC dataframe |
| mcmc.ExtractOFLResults | Extract OFL results from an mcmc run to a dataframe |
| mcmc.ExtractVar | Extract a variable from an MCMC results list |
| mcmc.ExtractVars | Extract all variables from an MCMC results list |
| mcmc.InvertArrayElement | Invert a list of mcmc results for a numeric array element to... |
| mcmc.InvertListElement | Invert an element of a sublist list |
| mcmc.InvertMCMCList | Invert an mcmc list |
| mcmc.InvertNumberElement | Invert a list of mcmc results for a numeric element to a... |
| mcmc.InvertVectorElement | Invert a list of mcmc results for a numeric vector element to... |
| mcmc.PlotABC | Function to plot ABC and OFL calculations from... |
| mcmc.ReadMCMC | Parse TCSAM02 MCMC.R file |
| plotDynamicB0 | Plot dyanmic B0 results |
| plotMQs.QuadPlot | Make a quad plot of F vs. B over time |
| readCorFile | Read the model cor (correlation) file |
| readParamsCSV | Read a TCSAM02 model parameters csv file and return a... |
| readParFile | Create a TCSAM2015 par object from a par file. |
| reformatTimeBlocks | Reformat rsim, tcsam notation for time blocks to a standard... |
| removeImmOS | Remove rows marked as immature, old shell from a dataframe |
| runJitter | Function to run TCSAM02 multiple times using jittered initial... |
| runMSE | Function to run the TCSAM02 MSE for one harvest strategy |
| runSims | Function to run TCSAM02 multiple times using initial... |
| runTCSAM02 | Function to run TCSAM02. |
| sdRep.CalcABC | Function to calculate ABCs from sd_report output |
| sdRep.PlotABC | Plot ABC and OFL from 'sdRep.CalcABC()' output |
