Functions to run and plot output from TCSAM2013 models.

calcABC | Function to calculate ABC and OFL from projection model... |

calcCIs | Compute confidence intervals from cvs |

compareModelResults.FisheryMeanZCs | Compare estimated/predicted fishery mean size comps and... |

compareModelResults.FisheryPRs | Compare Pearson's residuals from fishery size comps among... |

compareModelResults.FisheryQuantities | Compare estimated/predicted fishery quantities among several... |

compareModelResults.FisheryRates | Compare estimated/predicted fishery capture/mortality rates... |

compareModelResults.FisheryRetFcns | Compare estimated/predicted fishery retention functions among... |

compareModelResults.FisherySelFcns | Compare estimated/predicted fishery selectivity functions... |

compareModelResults.FisheryTCFMaleSelFcns | Compare estimated/predicted TCF male selectivity functions... |

compareModelResults.FisheryZCs | Compare estimated/predicted fishery size comps among several... |

compareModelResults.GrowthMatrices | Compare growth matrices among several model runs |

compareModelResults.MeanGrowth | Compare mean post-molt growth among several model runs |

compareModelResults.NatMort | Function to plot natural mortality rates by year using... |

compareModelResults.ObjFunComponents | Compare changes in objective function components from a base... |

compareModelResults.Params | Function to compare parameter values from different models |

compareModelResults.PopProcesses | Compare predicted population processes among several model... |

compareModelResults.PopQuantities | Compare population time series among several model runs |

compareModelResults.PrM2M | Compare probability of molt-to-maturity among several model... |

compareModelResults.SurveyMeanZCs | Compare estimated/predicted mean survey size comps and... |

compareModelResults.SurveyPRs | Compare Pearson's residuals from survey size comps among... |

compareModelResults.SurveyQuantities | Compare estimated/predicted survey quantities among several... |

compareModelResults.SurveySelFcns | Compare estimated/predicted survey selectivity functions... |

compareModelResults.SurveyZCs | Compare estimated/predicted survey size comps among several... |

convertToListOfResults | Convert object to a list of tcsam2013.resLst objects |

exportModelComparisons.TimeSeries | Export time series from a set of model runs to csv for... |

extractJitterInfo | Function to extract results from a set of previous jittered... |

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.FisheryQuantities | Get estimated/predicted fishery-related quantities from... |

getMDFR.ObjFunComponents | Get changes to objective function components relative to a... |

getMDFR.ParamsPlusStdDevs | Function to extract parameter estimates and standard... |

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 predicted growth matrices from several model runs |

getMDFR.Pop.MatureBiomass | Get predicted mature biomass (time series) from several model... |

getMDFR.Pop.MeanGrowth | Get predicted mean growth from several model runs |

getMDFR.Pop.NaturalMortality | Get predicted natural mortality (time series) from several... |

getMDFR.Pop.PrM2M | Get predicted pr(M2M) from several model runs |

getMDFR.Pop.Processes | Get predicted population processes from several model runs |

getMDFR.Pop.Quantities | Get predicted population quantities (time series) from... |

getMDFR.Pop.Recruitment | Get predicted recruitment (time series) from several model... |

getMDFR.Pop.RecSizeDistribution | Get recruitment size distributions from several model runs |

getMDFR.SurveyQuantities | Get estimated/predicted survey-related quantities from... |

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.XZ | Get XZ model output from several model runs |

getOFC | Create a tcsam2013.ofc object from a... |

getPar | Create a dataframe from an ADMB par file |

getPrs | Get a TCSAM2013 prs object by reading initial and final... |

getRep | Create a TCSAM2013 rep object from a TCSAM_OLDSTYLE R file |

getResLst | Create a tcsam2013.resLst object from a model run |

getRunCommands | Generate run commands for a tcsam2013 model run |

getStd | Create a dataframe (an std object) from an ADMB std file |

getSubPaths | Extract subpaths from a vector of file paths |

getTimeInfo | Get time information for a number of model runs |

getWTS | Create a TCSAM2013 wts object from a TCSAM_WTS R file |

plot2.ModelComparisonsGG.TimeSeries | Plot comparisons of time series from a set of model runs,... |

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

plotBubbles | Compare size comps using bubble plots for Pearson residuals |

plotData | Function to plot TCSAM2013 input data from a .R file |

plotData.Fishery.Discarded.NatZ | Function to plot numbers-at-size from fishery discard data. |

plotData.Fishery.Retained.NatZ | Function to plot numbers-at-size from retained fishery data. |

plotData.Survey.NatZ | Function to plot numbers-at-size from survey data. |

plotMeanSizeComps | Function to plot comparisons of mean size comps. |

plotModelComparisonsGG.TimeSeries | Plot comparisons of time series from a set of model runs |

plotModelComparisonsGG.ZScores | Plot comparisons of z-scores from a set of model runs |

plotModelComparisons.TimeSeries | Plot time series from a set of model runs to csv for... |

plotMulti.GG | Plot multiple ggplot graphs on the same page. |

plotNatMort | Function to plot natural mortality rates by year |

plotQuadPlot | Plot a quad plot from a TCSAM report object |

plotSizeCompsComparisons | Function to plot size comps comparisons by year |

plotTCSAM2013 | Plot TCSAM2013 model results. |

plotTCSAM2013I | Plot TCSAM2013 model results. |

plotTCSAM2013I.GG | Plot TCSAM2013 model results. |

plotTCSAM_WTS | Plot TCSAM_WTS...R output from a TCSAM2013 model run |

plotTCSAM_WTS.ZScores | Plot z-scores from a TCSAM2013 model run |

plotZScores | Plot z-scores from a set of model runs |

removeImmOS | Remove rows marked as immature, old shell from a dataframe |

renderReports | Render reports |

renderRetroReports | Render reports |

runJitter | Function to run TCSAM2013 multiple times using jittered... |

runProfiles | Function to run profiles on a TCSAM2013 model. |

runSequence | Function to run a sequence of TCSAM2013 models. |

runTCSAM2013 | Function to run TCSAM2013. |

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