R code for Stock Synthesis

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Documentation for package ‘r4ss’ version 1.11

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r4ss-package R tools for Stock Synthesis
bubble3 Create a bubble plot.
DoProjectPlots Make plots from Rebuilder program
make_multifig Create multi-figure plots.
mountains Make shaded polygons with a mountain-like appearance
movepars A function to visual parameterization of movement in Stock Synthesis
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
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.
SSplotComps Plot composition data and fits.
SSplotDiscard Plot fit to discard fraction.
SSplotIndices Plot indices of abundance and associated quantities.
SSplotMnwt Plot mean weight data and fits.
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.
SSv3_output A function to create a list object for the output from Stock Synthesis
SSv3_plots function to plot many quantities related to output from Stock Synthesis
SS_changepars Change parameters in the control file.
SS_fitbiasramp Estimate bias adjustment for recruitment deviates
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_recdevs Insert a vector of recruitment deviations into the control file.
SS_splitdat Split apart bootstrap data to make input file.
stackpoly function "stackpoly" by Jim Lemon from "plotrix" package
update_r4ss_files Updates r4ss files to newest versions on web.