Package to compare TCSAM2013, TCSAM02, and rsimTCSAM model runs

compareData.EffortTimeSeries | Compare effort time series data by fleet among several model... |

compareData.FleetTimeSeries | Compare time series data by fleet among several model... |

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.MaturityData | Compare fits to maturity data among several model runs |

compareFits.MeanSizeComps | Compare fits to mean size comps by fleet among several model... |

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.ParameterValues | Function to compare cohort progression by year among several... |

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.NaturalMortality | Function to plot natural mortality rates by year using... |

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.Surveys.Abundance | Function to compare estimated survey abundance by year among... |

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 diiferences between model cases |

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.PrNatZ | Extract Pearson's or nll residuals from size comps 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.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.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.Biomass | Function to compare estimated survey biomass by year among... |

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.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.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... |

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. |

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 |

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