R Code for Stock Synthesis


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Documentation for package ‘r4ss’ version 1.24.0

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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
getADMBHessian Read admodel.hes file
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 in a GUI
NegLogInt_Fn Perform SS implementation of Laplace Approximation
PinerPlot Make plot of likelihood contributions by fleet
plotCI Plot points with confidence intervals.
r4ss 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
SSbootstrap Fit models to parametric bootstraps
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.
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
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.
SSplotSelex Plot selectivity
SSplotSpawnrecruit Plot spawner-recruit curve.
SSplotSPR Plot 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
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_ForeCatch Create table of fixed forecast catches
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_RunJitter Iteratively apply the jitter option in SS
SS_splitdat Split apart bootstrap data to make input file.
SS_varadjust Modify variance and sample size adjustments in the control file
SS_writectl write control file
SS_writedat write data file
SS_writeforecast write forecast file
SS_writestarter write starter file
SS_write_length.fit Write length.fit file to be used by the MFCL length-comp viewer.
stackpoly modified from "stackpoly" by Jim Lemon from "plotrix" package
TSCplot Create a plot for the TSC report
update_r4ss_files Old function to updates r4ss files, deprecated in favor of devtools method