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_Sensi_plot           Create relative sensitivity plots as described
                        in Cope and Gertseva (2020)
SS_changepars           Change parameters, bounds, or phases in the
                        control file.
SS_decision_table_stuff
                        Extract total catch, spawning output, and
                        fraction unfished from forecast years
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_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                 Read all Stock Synthesis input files for a
                        model
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_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_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 and (re)run models
SS_varadjust            Modify variance and sample size adjustments in
                        the control file
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
SSbiologytables         A function to create a table of biology for
                        assessment reporting: length, weight, % mature,
                        fecundity, and selectivity
SSbootstrap             Fit models to parametric bootstraps
SSdiagsTime2Year        Convert Time-Steps
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.
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.
SSplotSPR               Plot Spawning Potential Ratio (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
SSunavailableSpawningOutput
                        Plot unavailable spawning output
TSCplot                 Create a plot for the TSC report
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 another
file_increment          Rename Stock Synthesis files by adding integer
                        value
getADMBHessian          Read admodel.hes file
get_SIS_info            Gather information for the NOAA Species
                        Information System (SIS)
get_comments            Collect comments lines starting from "#C" in
                        datfile, ctlfile, starter.ss, forecast.ss etc
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_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 machine epsilon taken from example
                        section of help of is.integer
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.
populate_multiple_folders
                        Populate multiple Stock Synthesis folders with
                        input files
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.
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
sspar                   Allow Multi-Plots Set the par() to options
                        suitable for ss3diags multi plots.
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
write_fwf4              Function to write formatted table similar to
                        table written by gdata::write.fwf from
                        data.frame or matrix This function does not
                        accept columns or logical with factor
