| add_legend | Add legend to plots |
| bubble3 | Create a bubble plot. |
| check_inputlist | Check input argument 'inputlist' |
| check_model | Check input argument 'model' |
| copy_SS_inputs | Copy a the Stock Synthesis input files from one directory to... |
| DoProjectPlots | Make plots from Rebuilder program |
| file_increment | Rename Stock Synthesis files by adding integer value |
| getADMBHessian | Read admodel.hes file |
| get_comments | Collect comments lines starting from "#C" in datfile,... |
| get_dat_new_name | Get the name of the data .ss_new file in a directory |
| get_last_phase | Get the highest phase used in the control file |
| get_SIS_info | Gather information for the NOAA Species Information System... |
| get_tuning_table | Get the tuning table |
| get_tv_parlabs | Get time varying parameter labels |
| is.wholenumber | Utility function to test if x is "numerically" integer wrt... |
| 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. |
| populate_multiple_folders | Populate multiple Stock Synthesis folders with input files |
| r4ss_logo | Make a simple logo for r4ss organization on GitHub |
| r4ss-package | r4ss: R Code for Stock Synthesis |
| read.admbFit | Read ADMB .par and .cor files. |
| rich.colors.short | Make a vector of colors. |
| run_SS_models | Run multiple Stock Synthesis models |
| save_png | Open png device and return info on the file being created |
| selShapes | Launch a shiny app that displays various selectivity curves |
| SSbiologytables | A function to create a table of biology for assessment... |
| SSbootstrap | Fit models to parametric bootstraps |
| SS_changepars | Change parameters, bounds, or phases in the control file. |
| SS_decision_table_stuff | Extract total catch, spawning output, and fraction unfished... |
| SSdiagsTime2Year | Convert Time-Steps |
| SS_doRetro | Run retrospective analyses |
| SSexecutivesummary | A function to create a executive summary tables from an SS... |
| SS_fitbiasramp | Estimate bias adjustment for recruitment deviates |
| SS_ForeCatch | Create table of fixed forecast catches |
| SSgetMCMC | Read MCMC output. |
| SSgetoutput | Get output from multiple Stock Synthesis models. |
| SS_html | Create HTML files to view figures in browser. |
| SS_makeHTMLdiagnostictable | Make html diagnostic tables |
| SSmakeMmatrix | Convert a matrix of natural mortality values into inputs for... |
| SSMethod.Cond.TA1.8 | Apply Francis composition weighting method TA1.8 for... |
| SSMethod.TA1.8 | Apply Francis composition weighting method TA1.8 |
| SSmohnsrho | Calculate Mohn's Rho values for select quantities |
| SS_output | A function to create a list object for the output from Stock... |
| sspar | Allow Multi-Plots Set the par() to options suitable for... |
| SS_parlines | Get parameter lines from Stock Synthesis control file |
| 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... |
| SSplotDiscard | Plot fit to discard fraction. |
| SSplotDynamicB0 | Plot Dynamic B0 |
| 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. |
| SS_plots | plot many quantities related to output from Stock Synthesis |
| SSplotSelex | Plot selectivity |
| SSplotSexRatio | Plot sex-ratio data and fits for two sex models |
| SSplotSpawnrecruit | Plot spawner-recruit curve. |
| SSplotSPR | Plot Spawning Potential Ratio (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. |
| SS_profile | Run a likelihood profile in Stock Synthesis. |
| SS_read | Read all Stock Synthesis input files for a model |
| 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_readpar_3.24 | read ss.par file from SS version 3.24 |
| SS_readpar_3.30 | read ss.par file from SS version 3.30 |
| SS_readstarter | read starter file |
| SS_read_summary | read ss_summary file |
| SS_readwtatage | Read weight-at-age data file |
| SS_recdevs | Insert a vector of recruitment deviations into the control... |
| SS_RunJitter | Iteratively apply the jitter option in SS |
| SS_Sensi_plot | Create relative sensitivity plots as described in Cope and... |
| SS_splitdat | Split apart bootstrap data to make input file. |
| SSsummarize | Summarize the output from multiple Stock Synthesis models. |
| SStableComparisons | make table comparing quantities across models |
| SS_tune_comps | Calculate new tunings for length and age compositions and... |
| SSunavailableSpawningOutput | Plot unavailable spawning output |
| SS_varadjust | Modify variance and sample size adjustments in the control... |
| SS_write | Write all Stock Synthesis input files for a model |
| SS_writectl | Write 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_writepar_3.24 | write ss.par file from SS version 3.24 |
| SS_writepar_3.30 | write ss.par file from SS version 3.30 |
| SS_writestarter | write starter file |
| SS_writewtatage | Write weight-at-age file |
| stackpoly | modified from "stackpoly" by Jim Lemon from "plotrix" package |
| translate_3.30_to_3.24_Q_setup | Use 3.30 q options to create the 3.24 q setup |
| translate_3.30_to_3.24_var_adjust | Use 3.30 variance adjustments to create the 3.24 formatting |
| TSCplot | Create a plot for the TSC report |
| write_fwf4 | Function to write formatted table similar to table written by... |
