| appendString | Append a string to another, using a separator, without... |
| calcLogPrior | Calculate log-prior distribution based on input pdfType list |
| checkHandlingMortalityConsistency | Check handling mortality/fishing equations consistency. |
| compareModels | Compare model output from TCSAM2015 and/or rsimTCSAM model... |
| compareModels.FisheryCatches | Compare fishery catches (abundance) from TCSAM2015 and... |
| compareModels.FisheryResults | Compare fisheries-related quantities from TCSAM2015 and... |
| compareModels.FisherySelFcns | Compare fishery selectivity functions from TCSAM2015 and... |
| compareModels.FisheryYields | Compare fishery yields (biomass) from TCSAM2015 and rsimTCSAM... |
| compareModels.FishingRates | Compare fishing rates from TCSAM2015 and rsimTCSAM model... |
| compareModels.Fits.AggCatchData | Compare fits to aggregated catch data (abundance or biomass)... |
| compareModels.Fits.NatZData | Compare fits to size compositions from catch data for... |
| compareModels.GrowthTransitionMatrices | Compare growth transition matrices for TCSAM2015 model runs |
| compareModels.ObjFunValues | Plot all objective function values. |
| compareModels.ParamEsts | Function to compare parameter values from different TCSAM2015... |
| compareModels.PopProcesses | Compare population process-related quantities from TCSAM2015... |
| compareModels.PopQuants | Compare population quantities from TCSAM2015 and rsimTCSAM... |
| compareModels.SelFcns.ByPC | Compare selectivity functions from TCSAM2015 and rsimTCSAM... |
| compareModels.SurveyAbundance | Compare estimated survey abundances from TCSAM2015 and... |
| compareModels.SurveyBiomass | Compare estimated survey biomass from TCSAM2015 and rsimTCSAM... |
| compareModels.SurveyQs | Compare survey Qs from TCSAM2015 and rsimTCSAM model runs. |
| compareModels.SurveyResults | Compare surveys-related quantities from TCSAM2015 and... |
| compareModels.SurveySelFcns | Compare selectivity functions from TCSAM2015 and rsimTCSAM... |
| compareModels.ZScores.AggCatchData | Compare zscores for fits to aggregated catch data (abundance... |
| compareModels.ZScores.NatZData | Compare z-scores from fits to size compositions from catch... |
| compileMCMCResults | Compiles MCMC results from a TCSAM2015 model run |
| extractModelResults.Params | Function to extract parameter values from different TCSAM2015... |
| extractModelResults.ParamsPlusStdDevs | Function to extract parameter estimates and standard... |
| extractModelResults.RepObjs | Extract (and optionally write to csv) model results from... |
| extractModelResults.StdDevs | Function to extract parameter uncertainty (std) info from... |
| getInputDataTimeframes | Get a dataframe describing the input data time frames |
| getIntervalLimits | Get interval limits from a vector of midpoints. @description... |
| getMCMCFile | Get a TCSAM2015 MCMC results file |
| getMCMCResults | Read a TCSAM2015 MCMC (.R) file |
| getMDFR | Get model arrays as a melted dataframe from TCSAM2015 and... |
| getMDFR.FitsForABData | Get fits to abundance or biomass data as a dataframe |
| getMDFR.FitsForFleets | Get model fits to abundance, biomass or size frequencies for... |
| getMDFR.FitsForSizeComps | Get fits for size comps as a dataframe |
| getMDFR.GrowthTransitionMatrices | Get growth transition matrices from model results from... |
| getMDFR.MeanGrowthIncrements | Get mean growth increments from model results from TCSAM2015... |
| getMDFR.NatMort | Get natural mortality rates from model results from TCSAM2015... |
| getMDFR.prM2M | Get molt-to-maturity ogives from model results from TCSAM2015... |
| getMDFR.RecSizeDistribution | Get recruitment size distribution from model results from... |
| getMDFR.SexRatio | Get recruitment sex ratio from model results from TCSAM2015... |
| getMDFR.ZScoresForABData | Get z-scores for abundance, biomass data from fits to data as... |
| getMDFR.ZScoresForCatchData | Get fits to catch data (abundance, biomass) as z-scores in a... |
| getMDFR.ZScoresForFleets | Get model fits to abundance, biomass or size frequencies as... |
| getMDFR.ZScoresForSizeComps | Get residuals from size frequency fits as dataframe |
| getObj | Get an object from a list object using the specified path... |
| getObjFunValues.AggregateCatch | Get aggregate catch components in the objective function as a... |
| getObjFunValues.CatchData | Get catch data components in the objective function as a... |
| getObjFunValues.Components | Get model components in the objective function as a melted... |
| getObjFunValues.Data | Get data components in the objective function as a melted... |
| getObjFunValues.Fleets | Get fleet data components in the objective function as a... |
| getObjFunValues.NatZ | Get size comps components in the objective function as a... |
| getObjFunValues.Penalties | Get model penalties in the objective function as a melted... |
| getObjFunValues.Priors | Get model priors in the objective function as a melted... |
| getPlotSymbology | Get symbology info for plotting purposes |
| getPrs | Get a TCSAM2015 prs object by reading initial and final... |
| getRep | Get a TCSAM2015 report object (by reading a TCSAM2015 model... |
| getRunCommands | Generate run commands for a tcsam2015 model run |
| getStd | Get a TCSAM2015 std object by reading a .std file |
| plotAggregateCatchData | Plot aggregate catch data |
| plotAggregateCatchDataGG | Plot aggregate catch data |
| plotBars | Create or add a bar plot. |
| plotCatchData | Plot catch data |
| plotCompsAsCircles | Create or add to a circle plot of age or size comp.s. |
| plotCompsAsCirclesGG | Create or add to a circle plot of age or size comp.s. |
| plotDataModelComparisons | Plot model-estimated and observed data for comparison. |
| plotEffNsForSizeFreqs | Plot ISSs and ESSs from size frequency fits as time series |
| plotEffNsGG | Plot input and estimated sample sizes from size frequency... |
| plotEffortRegressions | Plot regressions of capture rate on effort to assess effort... |
| plotErrorBars.H | Add horizontal error bars to current plot |
| plotErrorBars.V | Add vertical error bars to current plot |
| plotExploitationRatesGG | Plot time series of exploitation rates based on abundance... |
| plotFisheriesResults | Plot model results for fisheries. |
| plotFisheryCatchesGG | Plot time series of the fishery catch (numbers: captured,... |
| plotFisheryYieldsGG | Plot time series of the fishery yield (biomass: captured,... |
| plotFishingRatesGG | Plot time series of the fully-selected fishery capture rates. |
| plotFitsGG.MeanSizeComps | Plot mean size comps fits |
| plotFitsGG.SizeComps | Plot fits to size comps |
| plotInputDataTimeframes | Plot an input data timeframe dataframe |
| plotMatrix | Plot a matrix as a color map. |
| plotMCMCDensity | Calculate and plot a posterior density based on an MCMC data... |
| plotMCMCResults | Plot compiled MCMC results. |
| plotMCMCResults.forArray3D | Calculate and plot a posterior density based on a 3d MCMC... |
| plotMCMCResults.forMatrix | Calculate and plot a posterior density based on a MCMC data... |
| plotMCMCResults.forVector | Calculate and plot a posterior density based on a MCMC data... |
| plotMDFR.BarLine | Plot melted dataframe using a barchart/line-plot format. |
| plotMDFR.Bars | Plot melted dataframe using a barchart format. |
| plotMDFR.Bubbles | Create or add to a circle plot of age or size comp.s. |
| plotMDFR.XY | Plot melted dataframe using an xy-plot format. |
| plotMeanSizeComps | Plot comparison of observed and model size comps averaged... |
| plotMeanSizeCompsGG | Plot comparisons of mean model and data size compositions by... |
| plotModelResults.ScalarParams | Function to plot parameter values and associated uncertainty... |
| plotMulti.gg | Plot multiple ggplot graphs on the same page. |
| plotNatZ | Plot numbers-at-size as circles |
| plotNM.ByPC | Plot natural mortality estimates by parameter combination. |
| plotObjFunValues.Data | Plot data values (surveys and fisheries) used in the... |
| plotObjFunValues.Penalties | Plot penalties used in the objective function, grouped by... |
| plotObjFunValues.Priors | Plot prior values used in the objective function, grouped by... |
| plotParameters | Plot initial & final values, limits, and priors for model... |
| plotParameters.DevsVectorVector | Plot initial and final parameter values associated with a... |
| plotParameters.NumberVector | Plot initial and final parameter values associated with a... |
| plotParameters.VectorVector | Plot initial and final parameter values associated with a... |
| plotPDFRects | Plot a pdfRects object on an existing plot. |
| plotPopComponents.Abundance | Plot population abundance components. |
| plotPopComponents.Biomass | Plot population biomass components. |
| plotPopQuants | Plot model-estimated population quantities such as natural... |
| plotPrGrowth.ByPC | Plot pr(z'|x,z) estimates by parameter combination. |
| plotPrMaturity.ByPC | Plot pr(mature|z) estimates by parameter combination. |
| plotRecruits | Plot time series of TCSAM 2015 model recruits |
| plotRecruits.SexRatio | Plot time series of TCSAM 2015 model sex ratio for recruits |
| plotSelFcns.ByYear | Compare selectivity functions from TCSAM2015 and rsimTCSAM... |
| plotSizeCompsComparisons0 | Plot comparisons of model and data size compositions. |
| plotSizeCompsComparisons1 | Plot comparisons of model and data size compositions by year. |
| plotSizeCompsComparisons2 | DEPRECATED: Plot comparisons of model and data size... |
| plotSizeCompsGG.Single | Plot size comps from a single year (possibly for multiple... |
| plotSpB | Plot time series of TCSAM 2014 model spawning biomass |
| plotTCSAM2015 | Plot TCSAM2015 model output |
| plotTCSAM2015I | Plot TCSAM2015 model output |
| plotTCSAM2015J | Plot TCSAM2015 model output |
| plot.xy | Convenience function to make an x-y plot |
| plotXY | Convenience function to make an x-y plot |
| plotZScores | Plot z-scores from fits to data |
| plotZScoresForAll | Plot z-scores for all components |
| plotZScoresForCatchData | Plot fits to catch data (abundance, biomass, size freq.s) as... |
| plotZScoresForFisheries | Plot model fits to abundance, biomass and size frequencies as... |
| plotZScoresForFleets | Plot model fits to abundance, biomass and size frequencies as... |
| plotZScoresForSizeFreqs | Plot residuals from size frequency fits |
| plotZScoresForSurveys | Plot model fits to abundance, biomass and size frequencies as... |
| plotZScoresGG | Plot z-scores from fits to data |
| plotZScoresGG1.SizeFreqs | Plot residuals from size frequency fits |
| plotZScoresGG.SizeFreqs | Plot residuals from size frequency fits |
| readParamsCSV | Read a TCSAM2015 model parameters csv file and return a... |
| readParFile | Create a TCSAM2015 par object from a par file. |
| readReportFile | Read a TCSAM2015 model report (.rep) file. |
| readStdFile | Read a TCSAM2015 model std file and return a dataframe of... |
| 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 TCSAM2015 multiple times using jittered... |
| runProfiles | Function to run profiles on a TCSAM2015 model. |
| runSequence | Function to run a sequence of TCSAM2015 models. |
| runTCSAM2015 | Function to run TCSAM2015. |
| selectReportFile | Get a TCSAM2015 model report file |
| sumByDims | Sum array by specified dimensions |
| writeModelResultsToCSV.Fisheries | Write fishery quantities from model results from TCSAM2015... |
| writeModelResultsToCSV.FisherySelFcns | Write fishery selectivity functions to csv from TCSAM2015 and... |
| writeModelResultsToCSV.ObjFunValues | Write all objective function values to csvs |
| writeModelResultsToCSV.ParamEsts | Function to write parameter values and standard deviations... |
| writeModelResultsToCSV.PopProcesses | Write population processes from model results from TCSAM2015... |
| writeModelResultsToCSV.PopQuants | Write population quantities from model results from TCSAM2015... |
| writeModelResultsToCSV.Surveys | Write survey quantities from model results from TCSAM2015 and... |
| writeModelResultsToCSV.SurveySelFcns | Write survey selectivity functions to csv from TCSAM2015 and... |
