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 |

getCorr | Find substantially-correlated model parameters, based on the... |

getMDFR | Get model arrays as a melted dataframe from TCSAM02 model... |

getMDFR.Data.EffortData | Get model fits to biomass for fleet data components |

getMDFR.Data.FleetTimeSeries | Get fleet data components by model scenario |

getMDFR.Data.GrowthData | Get growth data |

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.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.MaturityData | Get model fits to maturity data |

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.MaturityData | Get objective function components for maturity data from a... |

getMDFR.OFCs.NonDataComponents | Get non-data components from the objective function for a... |

getMDFR.OFLResults | Get OFL results as a datframe |

getMDFR.ParametersAtBounds | Get parameters at one of their bounds from a set of TCSAM02... |

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.Surveys.Abundance | Get survey abundance time series 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.Biomass | Get model fits to biomass time series as z-scores for fleet... |

getMDFR.ZScoresForABData | Get z-scores for abundance, biomass data from fits to data as... |

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.ReadMCMC | Parse TCSAM02 MCMC.R file |

plotABC | Function to plot ABC and OFL calculations from calcABC(...) |

plotDynamicB0 | Plot dyanmic B0 results |

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 |

runTCSAM02 | Function to run TCSAM02. |

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