DoProjectPlots          Make plots from Rebuilder program
NegLogInt_Fn            Perform SS implementation of Laplace
                        Approximation
PinerPlot               Make plot of likelihood contributions by fleet
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
SS_ForeCatch            Create table of fixed forecast catches
SS_RunJitter            Iteratively apply the jitter option in SS
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_html                 Create HTML files to view figures in browser.
SS_makeHTMLdiagnostictable
                        Make html diagnostic tables
SS_makedatlist          make a list for SS data
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_read_summary         read ss_summary file
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_recdevs              Insert a vector of recruitment deviations into
                        the control file.
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
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
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.
SSplotSPR               Plot SPR quantities.
SSplotSelex             Plot selectivity
SSplotSexRatio          Plot sex-ratio data and fits for two sex models
SSplotSpawnrecruit      Plot spawner-recruit curve.
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
TSCplot                 Create a plot for the TSC report
bubble3                 Create a bubble plot.
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
plotCI                  Plot points with confidence intervals.
r4ss-package            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
stackpoly               modified from "stackpoly" by Jim Lemon from
                        "plotrix" package
