Man pages for cmlegault/ASAPplots
Creates Standard Plots and PDFs for ASAP3
| CalcFreqMeanSE | Calculates mean and standard error of frequency data |
| ConvertSurveyToAtAge | Converts surveys to age matrices |
| createDefaultdocxASAPcontrolfile | createDefaultdocxASAPcontrolfile |
| CreateParamList | CreateParamList |
| docxASAP | docxASAP |
| GetFixedParams | GetFixedParams |
| get_Sinclair_Z | Get Sinclair Z |
| GrabAuxFiles | Grab Auxilliary Files |
| GrabDatFileIndexSelOptions | Grab Dat File Index Selectivity Options |
| GrabNames | Grab Names |
| JitterASAP | JitterASAP Changes .pin file to use random restarts from... |
| MakeSelectivityDecoder | Make selectivity decoder |
| PlotAllBiomassTypes | Plot all biomass types |
| PlotAnnualMSY | Plot annual MSY |
| PlotAnnualSPRtargets | Plot annual SPR targets |
| PlotASAP | Plot ASAP |
| PlotCatch4Panel | Catch 4 panel plots by fleet |
| PlotCatchability | Plot survey catchability |
| PlotCatchAgeComp | Plot age composition by fleet |
| PlotCatchAgeCompBubbles | Bubble plots of catch age comps |
| PlotCatchAgeCompResids | Bubble plots of catch age comp resids |
| PlotCatchAtAgeConsistency | Plot catch at age consistency |
| PlotCatchByFleet | Plot catch by fleet |
| PlotCatchCurvesForCatch | Plot catch curves for catch |
| PlotCatchCurvesForIndices | Plot catch curves for indices |
| PlotCoh | Lattice style plot of cohorts by age |
| PlotCV | Plot CV for F, SSB, and Recruitment |
| PlotDiscard4Panel | Discard 4 panel plots by fleet |
| PlotExpSpawn | Plot expected spawnings |
| PlotFleetFmult | Plot fleet F multipliers |
| PlotFleetNeff | Plot effective sample size (Neff) |
| PlotFleetSelBlocks | Plot fleet selectivities |
| PlotFrancisFleet | Francis effective sample size plots by fleet |
| PlotFrancisIndex | Francis effective sample size plots by index |
| PlotFrontPage | Plot front page |
| PlotHighCorr | Plot high correlations among parameters |
| PlotHighCVs | Plot parameters with unusually high or low CVs |
| PlotIndexAgeCompBubbles | Bubble plots of index age comps |
| PlotIndexAgeCompResids | Bubble plots of index age comp resids |
| PlotIndexAtAgeConsistency | Plot index at age consistency |
| PlotIndexInput | Plot index input |
| PlotIndexNeff | Plot effective sample size (Neff) by index |
| PlotIndexSelectivities | Plot index selectivities |
| PlotIndices4Panel | Indices 4 panel plots |
| PlotJitter | PlotJitter |
| PlotM | Plot natural mortality rate |
| PlotMainLikelihoods | Plot main likelihoods by component |
| PlotMaturity | Plot maturity |
| PlotMCMC | Plot MCMC |
| PlotNAA | Plot numbers at age |
| PlotRecrSSByr | Scatterplot of SSB, R with 2-digit year |
| PlotRecruitmentDevs | Plot recruitment deviations |
| PlotRetroWrapper | Plot retrospectives |
| PlotRMSE95CI | Plot of RMSE values with 95 percent CI cone |
| PlotRMSEtable | Plot of RMSE table |
| PlotSARCrecSSB | SARC style plot of recruitment and SSB |
| PlotSPRtable | Plot SPR table |
| PlotSRpredLine | Standard SR plot with Beverton-Holt curve |
| PlotSSBatAge | Plot SSB at age |
| PlotSSBFtrend | Plot SSB and F time series |
| PlotWAAmatrices | Plot weight at age matrices |
| PlotYieldCurves | Plot yield curves |
| ReadASAP3DatFile | ReadASAP3DatFile |
| ReadASAP3PinFile | ReadASAP3PinFile |
| RunJitter | RunJitter |
| SummarizeASAP | Summarize ASAP |
| WriteASAP3DatFile | WriteASAP3DatFile |
| WriteASAP3PinFile | WriteASAP3PinFile |
