R Code for Stock Synthesis

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Documentation for package ‘r4ss’ version 1.44.0

Help Pages

A B C D F G I M N P R S T W

-- A --

add_legend Add legend to plots

-- B --

bubble3 Create a bubble plot.

-- C --

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

-- D --

DoProjectPlots Make plots from Rebuilder program

-- F --

file_increment Rename Stock Synthesis files by adding integer value

-- G --

getADMBHessian Read admodel.hes file
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_SIS_info Gather information for the NOAA Species Information System (SIS)
get_tuning_table Get the tuning table
get_tv_parlabs Get time varying parameter labels

-- I --

is.wholenumber Utility function to test if x is "numerically" integer wrt machine epsilon taken from example section of help of is.integer

-- M --

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

-- N --

NegLogInt_Fn Perform SS implementation of Laplace Approximation

-- P --

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

-- R --

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

-- S --

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 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
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
sspar Allow Multi-Plots Set the par() to options suitable for ss3diags multi plots.
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.
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.
SSsummarize Summarize the output from multiple Stock Synthesis models.
SStableComparisons make table comparing quantities across models
SSunavailableSpawningOutput Plot unavailable spawning output
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_ForeCatch Create table of fixed forecast catches
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_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_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_Sensi_plot Create relative sensitivity plots as described in Cope and Gertseva (2020)
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
stackpoly modified from "stackpoly" by Jim Lemon from "plotrix" package

-- T --

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

-- W --

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