Man pages for wStockhausen/rCompTCMs
Package to compare TCSAM02, rsimTCSAM, and TCSAM2013 model runs
| compareData.EffortTimeSeries | Compare effort time series data by fleet among several model... |
| compareData.FleetTimeSeriesABs | Compare time series of abundance or biommass data by fleet... |
| compareData.GrowthData | Compare growth data among several model scenarios |
| compareDiffs | Function to compare differences of a quantity among several... |
| compareFits.AbundanceData | Compare fits to abundance time series by fleet among several... |
| compareFits.BiomassData | Compare fits to biomass time series by fleet among several... |
| compareFits.EffectiveNs | Function to compare effective Ns from size compositions by... |
| compareFits.EffortData | Compare fits to effort data among several model runs |
| compareFits.GrowthData | Compare fits to growth data among several model runs |
| compareFits.MaturityOgiveData | Compare fits to maturity ogive data among several model runs |
| compareFits.MeanSizeComps | Compare fits to mean size comps by fleet among several model... |
| compareFits.SingleYearSizeComps | Compare fits to single-year size comps by fleet among several... |
| compareFits.SizeComps | Compare fits to size comps by fleet among several model runs |
| compareFits.ZScores.Abundance | Compare z-scores from fitting abundance time series by fleet... |
| compareFits.ZScores.Biomass | Compare z-scores from fitting biomass time series by fleet... |
| compareFits.ZScores.PrNatZ | Compare Pearson's residuals or nll residuals from size comps... |
| compareResults.Fisheries.Catchability | Function to plot fishery catchabilities by year using ggplot2 |
| compareResults.Fisheries.CatchAbundance | Function to compare estimated fishery catch abundance by year... |
| compareResults.Fisheries.CatchBiomass | Function to compare estimated fishery catch biomass by year... |
| compareResults.Fisheries.RetFcns | Function to compare fishery retention functions by year among... |
| compareResults.Fisheries.SelFcns | Function to compare fishery selectivity functions by year... |
| compareResults.ManagementQuantities | Compare management quantities among model scenarios |
| compareResults.ParameterValues | Function to compare parameter values among several models... |
| compareResults.Pop.Abundance | Function to compare estimated population abundance by year... |
| compareResults.Pop.Abundance1 | Function to compare population abundance estimates by year... |
| compareResults.Pop.Biomass | Function to compare estimated population biomass by year... |
| compareResults.Pop.Biomass1 | Function to compare population biomass estimates by year... |
| compareResults.Pop.CohortProgression | Function to compare cohort progression by year among several... |
| compareResults.Pop.GrowthMatrices | Compare growth matrices among several model runs using bubble... |
| compareResults.Pop.GrowthMatrices.LinePlots | Compare growth matrices among several model runs using line... |
| compareResults.Pop.IF.NatZ | Function to compare initial/final population abundance... |
| compareResults.Pop.MatureBiomass | Function to compare mature biomass-at-mating estimates by... |
| compareResults.Pop.MaturityOgives | Compare predicted maturity ogives among several model runs |
| compareResults.Pop.MeanGrowth | Compare mean post-molt size among several model runs |
| compareResults.Pop.MeanGrowthPlusProbs | Compare mean and probability of post-molt size among several... |
| compareResults.Pop.NaturalMortality | Function to plot natural mortality rates by year using... |
| compareResults.Pop.NaturalMortality.BarPlot | Function to compare natural mortality rates as bars |
| compareResults.Pop.NatZ.LinePlots | Function to compare population numbers-at-size estimates by... |
| compareResults.Pop.PrM2M | Compare probability of molt-to-maturity among several model... |
| compareResults.Pop.Processes | Compare population processes from TCSAM2013 and TCSAM02 model... |
| compareResults.Pop.Quantities | Compare population quantities from TCSAM2013, TCSAM02, and... |
| compareResults.Pop.Recruitment | Function to compare recruitment estimates by year among... |
| compareResults.Pop.RecSizeDistribution | Compare recruitment size distributions among several model... |
| compareResults.sdRep.DerivedVars | Plot sd_report time series for recruitment and SSB from... |
| compareResults.sdRep.RecAndSSB | Plot sd_report time series for recruitment and SSB from... |
| compareResults.Surveys.Abundance | Function to compare estimated survey abundance by year among... |
| compareResults.Surveys.Availability | Function to plot survey availabilities by year using ggplot2 |
| compareResults.Surveys.AvlFcns | Function to compare survey availability functions by year... |
| compareResults.Surveys.Biomass | Function to compare estimated survey biomass by year among... |
| compareResults.Surveys.CaptureProbs | Function to compare survey capture probability functions... |
| compareResults.Surveys.Catchability | Function to plot survey catchabilities by year using ggplot2 |
| compareResults.Surveys.SelFcns | Function to compare survey selectivity functions by year... |
| computeDiffs | Compute differences between model cases |
| createLatexForTable.ParamValues.Numbers | Function to print a table of parameters from several models |
| createTable.ParamVals | Create a table for parameter values for a given set of... |
| createTable.PsAtBs | Create a table for parameters at bounds |
| dropAggregatedDataLevels | Drop levels of sex, maturity state, and shell condition that... |
| extractFits.AllScores.ACD | Extract all scores from fits to biomass/abundance time series... |
| extractFits.MeanSizeComps | Extract fits to mean size comps by fleet among several model... |
| extractFits.SizeComps | Extract fits to size comps by fleet from several model runs |
| extractFits.ZScores.ACD | Extract z-scores from fits to biomass/abundance time series... |
| extractFits.ZScores.PrNatZ | Extract Pearson's or nll residuals from size comps by fleet... |
| extractMDFR.Data.FleetTimeSeriesABs | Extract time series of abundance or biommass data by fleet... |
| extractMDFR.ExploitationRates | Function to extract exploitation rates by year among several... |
| extractMDFR.Fisheries.Catchability | Function to extract fishery catchabilities by year using... |
| extractMDFR.Fisheries.CatchAbundance | Function to extract estimated fishery catch abundance by year... |
| extractMDFR.Fisheries.CatchBiomass | Function to extract estimated fishery catch biomass by year... |
| extractMDFR.Fisheries.RetFcns | Function to extract fishery retention functions by year among... |
| extractMDFR.Fisheries.SelFcns | Function to compare fishery selectivity functions by year... |
| extractMDFR.Fits.AbundanceData | Extract fits to abundance time series by fleet among several... |
| extractMDFR.Fits.BiomassData | Extract fits to biomass time series by fleet among several... |
| extractMDFR.Fits.EffectiveNs | Function to extract effective Ns from size comps by year... |
| extractMDFR.Fits.GrowthData | Extract fits to growth data among several model runs as a... |
| extractMDFR.Fits.MaturityOgiveData | Extract fits to maturity ogive data among several model runs... |
| extractMDFR.Pop.Abundance | Function to extract estimated population abundance by year... |
| extractMDFR.Pop.Biomass | Function to extract estimated population biomass by year... |
| extractMDFR.Pop.CohortProgression | Function to extract cohort progression by year among several... |
| extractMDFR.Pop.GrowthMatrices | Extract growth matrices among several model runs |
| extractMDFR.Pop.MatureBiomass | Function to extract mature biomass estimates by year among... |
| extractMDFR.Pop.MeanGrowth | Extract mean post-molt size from several model runs |
| extractMDFR.Pop.NaturalMortality | Function to plot natural mortality rates by year using... |
| extractMDFR.Pop.PrM2M | Extract probability of molt-to-maturity from several model... |
| extractMDFR.Pop.Recruitment | Function to extract recruitment estimates by year among... |
| extractMDFR.Pop.RecSizeDistribution | Extract recruitment size distributions from several model... |
| extractMDFR.Results.ParametersAtBounds | Extract parameters at one of their bounds from several model... |
| extractMDFR.Results.ParameterValues | Extract parameter values (and associated std devs) from... |
| extractMDFR.Surveys.Abundance | Function to extract estimated survey abundance by year among... |
| extractMDFR.Surveys.Availability | Function to extract survey availabilities |
| extractMDFR.Surveys.AvlFcns | Function to extract survey availability functions by year... |
| extractMDFR.Surveys.Biomass | Function to compare estimated survey biomass by year among... |
| extractMDFR.Surveys.CaptureProbs | Function to extract survey capture probability functions by... |
| extractMDFR.Surveys.Catchability | Function to extract survey catchabilities |
| extractMDFR.Surveys.SelFcns | Function to extract survey selectivity functions by year... |
| getMDFR.CanonicalFormat | Convert dataframe to canonical format |
| getResLsts | Create a list of TCSAM2013, TCSAM02 and rsimTCSAM resLst... |
| modelComparisons | Render a document of model comparison plots |
| modelComparisons.Characteristics.Fisheries | Render a document of comparison plots of estimated fishery... |
| modelComparisons.Characteristics.Surveys | Render a document of comparison plots of estimated survey... |
| modelComparisons.ModelFits.ACD | Render a document of comparison plots for model fits to... |
| modelComparisons.ModelFits.ACD.Fisheries | Render a document of comparison plots for model fits to... |
| modelComparisons.ModelFits.ACD.Surveys | Render a document of comparison plots for model fits to... |
| modelComparisons.ModelFits.OtherData | Render a document of comparison plots for model fits to... |
| modelComparisons.ModelFits.ZCs | Render a document of comparison plots for model fits to size... |
| modelComparisons.ModelFits.ZCsByYear | Render a document of comparison plots for model fits to size... |
| modelComparisons.ModelFits.ZCsByYear.Fisheries | Render a document of comparison plots for model fits to... |
| modelComparisons.ModelFits.ZCsByYear.Surveys | Render a document of comparison plots for model fits to... |
| modelComparisons.ParameterTables | Render a document of parameter tables for model comparisons |
| modelComparisons.PopProcesses | Render a document of comparison plots of estimated population... |
| modelComparisons.PopQuantities | Render a document of comparison plots of estimated population... |
| plotLollipops.ACD | plot lollipops for fits to aggregated catch data |
| plotLollipops.GrowthData | plot lollipops for fits to growth data |
| plotLollipops.MaturityOgiveData | plot lollipops for fits to maturity ogive data |
| plotLollipops.ZCs | plot lollipops for fits to size composition 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.Fits.SizeComps | Plot fits to size comps by fleet among several model runs... |
| plotMDFR.Fits.TimeSeries | Plot comparisons of fits to time series from a set of model... |
| plotMDFR.Fits.TimeSeries1 | Plot comparisons of fits to time series from a set of model... |
| plotMDFR.XY | Plot melted dataframe using an xy-plot format. |
| plotPop.CohortProgression | Function to plot cohort progression by year among several... |
| plotPop.MeanGrowth | Plot mean post-molt size for several model runs |
| plotPop.MeanGrowthPlusProbs | Plot mean and probability of post-molt size for several model... |
| plotPop.NaturalMortality | Function to plot natural mortality rates by year using... |
| plotPop.PrM2M | Function to plot probability of molt-to-maturity for several... |
| plotPop.PrMolt | Function to plot annual molt probability for immature crab... |
| plotPop.RecSizeDistribution | Plot recruitment size distributions among several model runs |
| plotZScores | Plot z-scores from a set of model runs |
| printResults.ParametersAtBounds | Function to print a table of parameters at bounds for several... |
| printResults.ParameterValues | Function to print a table of parameters from several models |
| retroCalcMohnsRho | Calculate Mohn's rho from a dataframe of retrospective... |
| retroGetMDFR | Get a melted dataframe of model estimates from a list of... |
| retroPlotFitsAsTimeSeries | Create a plot of model fits to time series from a... |
| retroPlotOFLResults | Create plots of several OFL-related quantities from a... |
| retroPlotTimeSeries | Create a plot of time series from a retrospective analysis |
| retroPlotValuesAsBars | Create a plot of values from a retrospective analysis as bars |
| retroPlotValuesBySize | Create a plot of values across size from a retrospective... |
