R code for Stock Synthesis

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Documentation for package ‘r4ss’ version 1.14

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r4ss-package R tools for Stock Synthesis
addSSsummarize Add a model to the list of models to compare
bubble3 Create a bubble plot.
DoProjectPlots Make plots from Rebuilder program
IOTCmove Make a map of movement for a 5-area Indian Ocean model
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
plotCI Plot points with confidence intervals.
r4ss R tools for Stock Synthesis
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
SSFishGraph A function for converting Stock Synthesis output to the format used by FishGraph
SSgetMCMC Read MCMC output.
SSgetoutput Get output from multiple Stock Synthesis models.
SSmakesims Make files and set up folders for simulations
SSplotBiology Plot biology related quantities.
SSplotCatch Plot catch related quantities.
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 Show movement rates on a map.
SSplotNumbers Plot numbers-at-age related data and fits.
SSplotPars Plot distributions of priors, posteriors, and estimates.
SSplotRecdevs Plot recruitment deviations
SSplotRecdist Plot of recruitment distribution among areas and seasons
SSplotSelex Plot selectivity
SSplotSpawnrecruit Plot spawner-recruit curve.
SSplotSPR Plot SPR quantities.
SSplotTags Plot tagging data and fits
SSplotTimeseries Plot timeseries data
SSplotYield Plot yield and surplus production.
SSrunsims Run a collection of simulations for Stock Synthesis.
SSsummarize Summarize the output from multiple Stock Synthesis models.
SStableComparisons make table comparing quantities across models
SSv3_output Old output reader
SSv3_plots old plot funciton
SS_changepars Change parameters in the control file.
SS_fitbiasramp Estimate bias adjustment for recruitment deviates
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_writectl write control file
SS_writedat write data file
SS_writeforecast write forecast file
SS_writestarter write starter file
stackpoly function "stackpoly" by Jim Lemon from "plotrix" package
update_r4ss_files Updates r4ss files to newest versions on web.