| r4ss-package | R tools for Stock Synthesis |
| bubble3 | Create a bubble plot. |
| DoProjectPlots | Make plots from Rebuilder program |
| getADMBHessian | Read admodel.hes file |
| make_multifig | Create multi-figure plots. |
| make_multifig_sexratio | Create multi-figure sex ratio plots. |
| mcmc.nuisance | Summarize nuisance MCMC output |
| mcmc.out | Summarize, analyze and plot key MCMC output. |
| mountains | Make shaded polygons with a mountain-like appearance |
| NegLogInt_Fn | Perform SS implementation of Laplace Approximation |
| PinerPlot | Make plot of likelihood contributions by fleet |
| plotCI | Plot points with confidence intervals. |
| r4ss | R tools for Stock Synthesis |
| r4ss_logo | Make a simple logo for r4ss organization on GitHub |
| read.admbFit | Read ADMB .par and .cor files. |
| rich.colors.short | Make a vector of colors. |
| selShapes | A Shiny app that displays various selectivity curves given parameters that would be input into SS |
| SSbiologytables | A function to create a table of biology for assessment reporting: length, weight, % mature, fecundity, and selectivity |
| SSbootstrap | Fit models to parametric bootstraps |
| SSexecutivesummary | A function to create a executive summary tables from an SS Report.sso file |
| SSgetMCMC | Read MCMC output. |
| SSgetoutput | Get output from multiple Stock Synthesis models. |
| SSmakeMmatrix | Convert a matrix of natural mortality values into inputs for Stock Synthesis |
| SSMethod.Cond.TA1.8 | Apply Francis composition weighting method TA1.8 for conditional age-at-length fits |
| SSMethod.TA1.8 | Apply Francis composition weighting method TA1.8 |
| SSmohnsrho | Calculate Mohn's Rho values for select quantities |
| SSplotAgeMatrix | Plot matrix of either length or observed age at true age |
| SSplotBiology | Plot biology related quantities. |
| SSplotCatch | Plot catch related quantities. |
| SSplotCohortCatch | Plot cumulative catch by cohort. |
| SSplotComparisons | plot model comparisons |
| SSplotComps | Plot composition data and fits. |
| SSplotData | Timeline of presence/absence of data by type, year, and fleet. |
| SSplotDiscard | Plot fit to discard fraction. |
| SSplotIndices | Plot indices of abundance and associated quantities. |
| SSplotMCMC_ExtraSelex | Plot uncertainty around chosen selectivity ogive from MCMC. |
| SSplotMnwt | Plot mean weight data and fits. |
| SSplotMovementMap | Show movement rates on a map. |
| SSplotMovementRates | Plot movement rates from model output |
| SSplotNumbers | Plot numbers-at-age related data and fits. |
| SSplotPars | Plot distributions of priors, posteriors, and estimates. |
| SSplotProfile | Plot likelihood profile results |
| SSplotRecdevs | Plot recruitment deviations |
| SSplotRecdist | Plot of recruitment distribution among areas and seasons |
| SSplotRetroRecruits | Make squid plot of retrospectives of recruitment deviations. |
| SSplotSelex | Plot selectivity |
| SSplotSexRatio | Plot sex-ratio data and fits for two sex models |
| SSplotSpawnrecruit | Plot spawner-recruit curve. |
| SSplotSPR | Plot SPR quantities. |
| SSplotSummaryF | Plot the summary F (or harvest rate). |
| SSplotTags | Plot tagging data and fits |
| SSplotTimeseries | Plot timeseries data |
| SSplotYield | Plot yield and surplus production. |
| SSsummarize | Summarize the output from multiple Stock Synthesis models. |
| SStableComparisons | make table comparing quantities across models |
| SStimeseries | A function to create a time-series table from an SS Report.sso file |
| SSunavailableSpawningOutput | Plot unavailable spawning output |
| SS_changepars | Change parameters, bounds, or phases in the control file. |
| SS_doRetro | Run retrospective analyses |
| SS_fitbiasramp | Estimate bias adjustment for recruitment deviates |
| SS_ForeCatch | Create table of fixed forecast catches |
| SS_html | Create HTML files to view figures in browser. |
| SS_makedatlist | make a list for SS data |
| SS_makeHTMLdiagnostictable | Make html diagnostic tables |
| SS_output | A function to create a list object for the output from Stock Synthesis |
| SS_parlines | Get parameter lines from Stock Synthesis control file |
| SS_plots | plot many quantities related to output from Stock Synthesis |
| SS_profile | Run a likelihood profile in Stock Synthesis. |
| SS_readctl | read control file from SS |
| SS_readctl_3.24 | read control file from SS version 3.24 |
| SS_readctl_3.30 | read control file from SS version 3.30 |
| SS_readdat | read Stock Synthesis data file |
| SS_readdat_2.00 | read data file from SS version 2.00 |
| SS_readdat_3.00 | read data file from SS version 3.00 |
| SS_readdat_3.24 | read data file from SS version 3.24 |
| SS_readdat_3.30 | read data file from SS version 3.30 |
| SS_readforecast | read forecast file |
| SS_readstarter | read starter file |
| SS_readwtatage | Read weight-at-age data file |
| SS_read_summary | read ss_summary file |
| SS_recdevs | Insert a vector of recruitment deviations into the control file. |
| SS_RunJitter | Iteratively apply the jitter option in SS |
| SS_splitdat | Split apart bootstrap data to make input file. |
| SS_tune_comps | Calculate new tunings for length and age compositions |
| SS_varadjust | Modify variance and sample size adjustments in the control file |
| SS_writectl | Srite Stock Synthesis control file |
| SS_writectl_3.24 | write control file |
| SS_writectl_3.30 | write control file for SS version 3.30 |
| SS_writedat | write Stock Synthesis data file |
| SS_writedat_3.24 | write data file for SS version 3.24 |
| SS_writedat_3.30 | write data file for SS version 3.30 |
| SS_writeforecast | write forecast file |
| SS_writestarter | write starter file |
| SS_writewtatage | Write weight-at-age file |
| stackpoly | modified from "stackpoly" by Jim Lemon from "plotrix" package |
| TSCplot | Create a plot for the TSC report |