Man pages for wStockhausen/rTCSAM2013
Functions to run and plot output from TCSAM2013 models.

calcABCFunction to calculate ABC and OFL from projection model...
calcCIsCompute confidence intervals from cvs
compareModelResults.FisheryMeanZCsCompare estimated/predicted fishery mean size comps and...
compareModelResults.FisheryPRsCompare Pearson's residuals from fishery size comps among...
compareModelResults.FisheryQuantitiesCompare estimated/predicted fishery quantities among several...
compareModelResults.FisheryRatesCompare estimated/predicted fishery capture/mortality rates...
compareModelResults.FisheryRetFcnsCompare estimated/predicted fishery retention functions among...
compareModelResults.FisherySelFcnsCompare estimated/predicted fishery selectivity functions...
compareModelResults.FisheryTCFMaleSelFcnsCompare estimated/predicted TCF male selectivity functions...
compareModelResults.FisheryZCsCompare estimated/predicted fishery size comps among several...
compareModelResults.GrowthMatricesCompare growth matrices among several model runs
compareModelResults.MeanGrowthCompare mean post-molt growth among several model runs
compareModelResults.NatMortFunction to plot natural mortality rates by year using...
compareModelResults.ObjFunComponentsCompare changes in objective function components from a base...
compareModelResults.ParamsFunction to compare parameter values from different models
compareModelResults.PopProcessesCompare predicted population processes among several model...
compareModelResults.PopQuantitiesCompare population time series among several model runs
compareModelResults.PrM2MCompare probability of molt-to-maturity among several model...
compareModelResults.SurveyMeanZCsCompare estimated/predicted mean survey size comps and...
compareModelResults.SurveyPRsCompare Pearson's residuals from survey size comps among...
compareModelResults.SurveyQuantitiesCompare estimated/predicted survey quantities among several...
compareModelResults.SurveySelFcnsCompare estimated/predicted survey selectivity functions...
compareModelResults.SurveyZCsCompare estimated/predicted survey size comps among several...
convertToListOfResultsConvert object to a list of tcsam2013.resLst objects
exportModelComparisons.TimeSeriesExport time series from a set of model runs to csv for...
extractJitterInfoFunction to extract results from a set of previous jittered...
getMDFR.Fisheries.CatchAbundanceGet fishery catch abundance time series from model results...
getMDFR.Fisheries.CatchBiomassGet fishery catch biomass time series from model results from...
getMDFR.FisheryQuantitiesGet estimated/predicted fishery-related quantities from...
getMDFR.ObjFunComponentsGet changes to objective function components relative to a...
getMDFR.ParamsPlusStdDevsFunction to extract parameter estimates and standard...
getMDFR.Pop.AbundanceGet population abundance time series from model results from...
getMDFR.Pop.BiomassGet population biomass time series from model results from...
getMDFR.Pop.GrowthMatricesGet predicted growth matrices from several model runs
getMDFR.Pop.MatureBiomassGet predicted mature biomass (time series) from several model...
getMDFR.Pop.MeanGrowthGet predicted mean growth from several model runs
getMDFR.Pop.NaturalMortalityGet predicted natural mortality (time series) from several...
getMDFR.Pop.PrM2MGet predicted pr(M2M) from several model runs
getMDFR.Pop.ProcessesGet predicted population processes from several model runs
getMDFR.Pop.QuantitiesGet predicted population quantities (time series) from...
getMDFR.Pop.RecruitmentGet predicted recruitment (time series) from several model...
getMDFR.Pop.RecSizeDistributionGet recruitment size distributions from several model runs
getMDFR.SurveyQuantitiesGet estimated/predicted survey-related quantities from...
getMDFR.Surveys.AbundanceGet survey abundance time series from model results from...
getMDFR.Surveys.BiomassGet survey biomass time series from model results from...
getMDFR.XZGet XZ model output from several model runs
getOFCCreate a tcsam2013.ofc object from a...
getParCreate a dataframe from an ADMB par file
getPrsGet a TCSAM2013 prs object by reading initial and final...
getRepCreate a TCSAM2013 rep object from a TCSAM_OLDSTYLE R file
getResLstCreate a tcsam2013.resLst object from a model run
getRunCommandsGenerate run commands for a tcsam2013 model run
getStdCreate a dataframe (an std object) from an ADMB std file
getSubPathsExtract subpaths from a vector of file paths
getTimeInfoGet time information for a number of model runs
getWTSCreate a TCSAM2013 wts object from a TCSAM_WTS R file
plot2.ModelComparisonsGG.TimeSeriesPlot comparisons of time series from a set of model runs,...
plotABCFunction to plot ABC and OFL calculations from calcABC(...)
plotBubblesCompare size comps using bubble plots for Pearson residuals
plotDataFunction to plot TCSAM2013 input data from a .R file
plotData.Fishery.Discarded.NatZFunction to plot numbers-at-size from fishery discard data.
plotData.Fishery.Retained.NatZFunction to plot numbers-at-size from retained fishery data.
plotData.Survey.NatZFunction to plot numbers-at-size from survey data.
plotMeanSizeCompsFunction to plot comparisons of mean size comps.
plotModelComparisonsGG.TimeSeriesPlot comparisons of time series from a set of model runs
plotModelComparisonsGG.ZScoresPlot comparisons of z-scores from a set of model runs
plotModelComparisons.TimeSeriesPlot time series from a set of model runs to csv for...
plotMulti.GGPlot multiple ggplot graphs on the same page.
plotNatMortFunction to plot natural mortality rates by year
plotQuadPlotPlot a quad plot from a TCSAM report object
plotSizeCompsComparisonsFunction to plot size comps comparisons by year
plotTCSAM2013Plot TCSAM2013 model results.
plotTCSAM2013IPlot TCSAM2013 model results.
plotTCSAM2013I.GGPlot TCSAM2013 model results.
plotTCSAM_WTSPlot TCSAM_WTS...R output from a TCSAM2013 model run
plotTCSAM_WTS.ZScoresPlot z-scores from a TCSAM2013 model run
plotZScoresPlot z-scores from a set of model runs
removeImmOSRemove rows marked as immature, old shell from a dataframe
renderReportsRender reports
renderRetroReportsRender reports
runJitterFunction to run TCSAM2013 multiple times using jittered...
runProfilesFunction to run profiles on a TCSAM2013 model.
runSequenceFunction to run a sequence of TCSAM2013 models.
runTCSAM2013Function to run TCSAM2013.
wStockhausen/rTCSAM2013 documentation built on July 19, 2017, 5 a.m.