DoProjectPlots          Make plots from Rebuilder program
IOTCmove                Make a map of movement for a 5-area Indian
                        Ocean model
NegLogInt_Fn            Perform SS implementation of Laplace
                        Approximation
PinerPlot               Make plot of likelihood contributions by fleet
SSFishGraph             A function for converting Stock Synthesis
                        output to the format used by FishGraph
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_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_readctl              read control file
SS_readdat              read data file
SS_readforecast         read forecast file
SS_readstarter          read starter file
SS_recdevs              Insert a vector of recruitment deviations into
                        the control file.
SS_splitdat             Split apart bootstrap data to make input file.
SS_varadjust            Modify variance and sample size adjustments in
                        the control file
SS_write_length.fit     Write length.fit file to be used by the MFCL
                        length-comp viewer.
SS_writectl             write control file
SS_writedat             write data file
SS_writeforecast        write forecast file
SS_writestarter         write starter file
SSbootstrap             Fit models to parametric bootstraps
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
SSplotBiology           Plot biology related quantities.
SSplotCatch             Plot catch related quantities.
SSplotCohorts           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
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
TSCplot                 Create a plot for the TSC report
addSSsummarize          Add a model to the list of models to compare
bubble3                 Create a bubble plot.
getADMBHessian          Read admodel.hes file
make_multifig           Create multi-figure 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
movepars                Explore movement parameterizations in a GUI
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.
sel.line                a function for drawing selecitivity curves
selfit                  A function to visual parameterization of double
                        normal and double logistic selectivity in Stock
                        Synthesis
selfit_spline           visualize parameterization of cubic spline
                        selectivity in SS
stackpoly               modified from "stackpoly" by Jim Lemon from
                        "plotrix" package
update_r4ss_files       Old function to updates r4ss files, deprecated
                        in favor of devtools method
