Man pages for wStockhausen/rsimTCSAM
Simulation model for testing TCSAM2013 and TCSAM02 models.
| addError | Add error to "observations |
| asclogistic | Calculate an ascending logistic function parameterized by z50... |
| asclogistic5095 | Calculate an ascending logistic function parameterized by z50... |
| asclogistic50D95 | Calculate an ascending logistic function parameterized by z50... |
| calcEquilibriumSizeComp.TM | Calculate the equilibrium size composition for one sex of a... |
| calcFishingMortalities | Calculate size-specific fishery capture and retention rates |
| calcInitSizeComps | Calculate initial size compositions |
| calcModelProcesses | Calculate model processes |
| calcNaturalMortality | Calculate natural mortality |
| calcNatZ | Project population numbers at size forward through the model... |
| calcNatZ.Fisheries | Calculate fishery catches, mortality at size through the... |
| calcNatZ.Surveys | Calculate survey numbers at size through the model time... |
| calcPrM2M | Calculate probability-at-size (pre-molt) for immature crab... |
| calcPrMolt | Calculate probability at size of molting for immature crab by... |
| calcRatZ | Calculate proportions recruiting-at-size for one set of... |
| calcRatZ.All | Calculate proportions recruiting-at-size over all time blocks |
| calcRecruitment | Calculate recruitment-at-size (in millions) by year, sex |
| calcSelectivity | Calculate values for a selectivity curve |
| calcSelFcns | Calculate selectivity/retention functions. |
| calcStateTransitionMatrices | Calculate the state transition matrices for a single sex. |
| calcSurveyCatchabilities | Calculate size-specific survey catchabilities. |
| calcWatZ | Calculate weight-at-size by year, sex, maturity state and... |
| calcZTM | Calculate size transition matrices by year, sex, shell... |
| checkKeyword | Check string against keyword and stop if unequal. |
| compareModels.PopQuants | Compare population quantities from TCSAM2015 and rsimTCSAM... |
| compareSizeCompsGG | Compare multiple size comps. |
| dbllogistic | Calculate a double logistic function parameterized by z50 and... |
| dbllogistic5095 | Calculate a double logistic function parameterized by z50 and... |
| dimArray | Get an array |
| getMDFR | Get model arrays as a melted dataframe from rsimTCSAM models |
| 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.SelFcns | Get fishery selectivity functions from model results from... |
| 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.GrowthMatrices | Get growth transition matrices from model results from... |
| getMDFR.Pop.MeanGrowth | Get mean growth increments from model results from TCSAM2015... |
| getMDFR.Pop.NaturalMortality | Get natural mortality rates from model results from rsimTCSAM... |
| getMDFR.Pop.PrM2M | Get molt-to-maturity ogives from model results from rsimTCSAM... |
| getMDFR.Pop.Quantities | Extract population quantities from rsimTCSAM 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 rsimTCSAM... |
| 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.SelFcns | Get survey selectivity functions from model results from... |
| getObj | Get an object from a list object using the specified path... |
| getResLst | Create a rsimTCSAM.resLst object from a model run |
| midpoints | Calculate the midpoints of a vector. |
| parseMC.Dims | Parse model dimensions information from a character string... |
| parseMC.Fisheries | Parse fisheries section of a model configuration file. |
| parseMC.Growth | Parse growth section of a model configuration file. |
| parseMC.NaturalMortality | Parse natural mortality section of a model configuration... |
| parseMC.OILine | Parse output info for a fishery/survey data type from a model... |
| parseMC.OutputInfo | Parse output info for a fishery catch type or survey from a... |
| parseMC.PrM2M | Parse molt-to-maturity section of a model configuration file. |
| parseMC.Recruitment | Parse recruitment section of a model configuration file. |
| parseMC.SelFcns | Parse selectivity section of a model configuration file. |
| parseMC.Surveys | Parse surveys section of a model configuration file. |
| parseMC.WatZ | Parse weight-at-size section of a model configuration file. |
| plogis | Calculate the logistic function |
| readModelConfiguration.TCSAM | Select and read a model configuration file for a TCSAM model. |
| reformatTimeBlocks | Reformat rsim, tcsam notation for time blocks to a standard... |
| removeImmOS | Remove rows marked as immature, old shell from a dataframe |
| runModel | Run the simulation model |
| runOneYear.TM | Project one sex of the population one time step forward. |
| runSim.TCSAM | Run the TCSAM simulation model to produce a TCSAM2015 input... |
| throwModelTypeError | Throw an unrecognized model type error. |
| writeSim.TCSAM02 | Write simulation results to TCSAM02 input file2. |
| writeSim.TCSAM02.Fisheries | Write rsim fisheries results to TCSAM02 input file. |
| writeSim.TCSAM02.Surveys | Write model survey results to TCSAM02 input file. |
| writeSim.TCSAM2013 | Write simulation results to TCSAM2013 input file. |
| writeSim.TCSAM2013.Fisheries | Write rsim fisheries results to TCSAM2013 input file. |
| writeSim.TCSAM2013.Surveys | Write model survey results to TCSAM2013 input file. |
