Man pages for r4ss
R Code for Stock Synthesis

addSSsummarizeAdd a model to the list of models to compare
bubble3Create a bubble plot.
DoProjectPlotsMake plots from Rebuilder program
getADMBHessianRead admodel.hes file
IOTCmoveMake a map of movement for a 5-area Indian Ocean model
make_multifigCreate multi-figure plots.
mcmc.nuisanceSummarize nuisance MCMC output
mcmc.outSummarize, analyze and plot key MCMC output.
mountainsMake shaded polygons with a mountain-like appearance
moveparsExplore movement parameterizations in a GUI
NegLogInt_FnPerform SS implementation of Laplace Approximation
PinerPlotMake plot of likelihood contributions by fleet
plotCIPlot points with confidence intervals.
r4ss_logoMake a simple logo for r4ss organization on GitHub
r4ss-packageR tools for Stock Synthesis
read.admbFitRead ADMB .par and .cor files.
rich.colors.shortMake a vector of colors.
selfitA function to visual parameterization of double normal and...
selfit_splinevisualize parameterization of cubic spline selectivity in SS
sel.linea function for drawing selecitivity curves
SSbootstrapFit models to parametric bootstraps
SS_changeparsChange parameters, bounds, or phases in the control file.
SS_doRetroRun retrospective analyses
SSFishGraphA function for converting Stock Synthesis output to the...
SS_fitbiasrampEstimate bias adjustment for recruitment deviates
SS_ForeCatchCreate table of fixed forecast catches
SSgetMCMCRead MCMC output.
SSgetoutputGet output from multiple Stock Synthesis models.
SS_htmlCreate HTML files to view figures in browser.
SS_makedatlistmake a list for SS data
SSmakeMmatrixConvert a matrix of natural mortality values into inputs for...
SSMethod.Cond.TA1.8Apply Francis composition weighting method TA1.8 for...
SSMethod.TA1.8Apply Francis composition weighting method TA1.8
SS_outputA function to create a list object for the output from Stock...
SS_parlinesGet parameter lines from Stock Synthesis control file
SSplotBiologyPlot biology related quantities.
SSplotCatchPlot catch related quantities.
SSplotCohortsPlot cumulative catch by cohort.
SSplotComparisonsplot model comparisons
SSplotCompsPlot composition data and fits.
SSplotDataTimeline of presence/absence of data by type, year, and...
SSplotDiscardPlot fit to discard fraction.
SSplotIndicesPlot indices of abundance and associated quantities.
SSplotMCMC_ExtraSelexPlot uncertainty around chosen selectivity ogive from MCMC.
SSplotMnwtPlot mean weight data and fits.
SSplotMovementMapShow movement rates on a map.
SSplotMovementRatesPlot movement rates from model output
SSplotNumbersPlot numbers-at-age related data and fits.
SSplotParsPlot distributions of priors, posteriors, and estimates.
SSplotProfilePlot likelihood profile results
SSplotRecdevsPlot recruitment deviations
SSplotRecdistPlot of recruitment distribution among areas and seasons
SSplotRetroRecruitsMake squid plot of retrospectives of recruitment deviations.
SS_plotsplot many quantities related to output from Stock Synthesis
SSplotSelexPlot selectivity
SSplotSpawnrecruitPlot spawner-recruit curve.
SSplotSPRPlot SPR quantities.
SSplotSummaryFPlot the summary F (or harvest rate).
SSplotTagsPlot tagging data and fits
SSplotTimeseriesPlot timeseries data
SSplotYieldPlot yield and surplus production.
SS_profileRun a likelihood profile in Stock Synthesis.
SS_readctlread control file
SS_readdatread data file
SS_readforecastread forecast file
SS_readstarterread starter file
SS_recdevsInsert a vector of recruitment deviations into the control...
SS_RunJitterIteratively apply the jitter option in SS
SS_splitdatSplit apart bootstrap data to make input file.
SSsummarizeSummarize the output from multiple Stock Synthesis models.
SStableComparisonsmake table comparing quantities across models
SS_varadjustModify variance and sample size adjustments in the control...
SS_writectlwrite control file
SS_writedatwrite data file
SS_writeforecastwrite forecast file
SS_write_length.fitWrite file to be used by the MFCL length-comp...
SS_writestarterwrite starter file
stackpolymodified from "stackpoly" by Jim Lemon from "plotrix" package
TSCplotCreate a plot for the TSC report
update_r4ss_filesOld function to updates r4ss files, deprecated in favor of...
r4ss documentation built on May 29, 2017, 2:24 p.m.