r4ss: R Code for Stock Synthesis

A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks.

AuthorIan G. Taylor, Ian J. Stewart, Allan C. Hicks, Tommy M. Garrison, Andre E. Punt, John R. Wallace, Chantel R. Wetzel, James T. Thorson, Yukio Takeuchi, Kotaro Ono, Cole C. Monnahan, Christine C. Stawitz, Z. Teresa A'mar, Athol R. Whitten, Kelli F. Johnson, Robbie L. Emmet, Sean C. Anderson, and other contributors.
Date of publication2015-12-23 23:28:33
MaintainerIan Taylor <Ian.Taylor@noaa.gov>
LicenseGPL-3
Version1.24.0
https://github.com/r4ss

View on CRAN

Man pages

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_logo: Make a simple logo for r4ss organization on GitHub

r4ss-package: R tools for Stock Synthesis

read.admbFit: Read ADMB .par and .cor files.

rich.colors.short: Make a vector of colors.

selfit: A function to visual parameterization of double normal and...

selfit_spline: visualize parameterization of cubic spline selectivity in SS

sel.line: a function for drawing selecitivity curves

SSbootstrap: Fit models to parametric bootstraps

SS_changepars: Change parameters, bounds, or phases in the control file.

SS_doRetro: Run retrospective analyses

SSFishGraph: A function for converting Stock Synthesis output to the...

SS_fitbiasramp: Estimate bias adjustment for recruitment deviates

SS_ForeCatch: Create table of fixed forecast catches

SSgetMCMC: Read MCMC output.

SSgetoutput: Get output from multiple Stock Synthesis models.

SS_html: Create HTML files to view figures in browser.

SS_makedatlist: make a list for SS data

SSmakeMmatrix: Convert a matrix of natural mortality values into inputs for...

SSMethod.Cond.TA1.8: Apply Francis composition weighting method TA1.8 for...

SSMethod.TA1.8: Apply Francis composition weighting method TA1.8

SS_output: A function to create a list object for the output from Stock...

SS_parlines: Get parameter lines from Stock Synthesis control file

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...

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.

SS_plots: plot many quantities related to output from Stock Synthesis

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.

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...

SS_RunJitter: Iteratively apply the jitter option in SS

SS_splitdat: Split apart bootstrap data to make input file.

SSsummarize: Summarize the output from multiple Stock Synthesis models.

SStableComparisons: make table comparing quantities across models

SS_varadjust: Modify variance and sample size adjustments in the control...

SS_writectl: write control file

SS_writedat: write data file

SS_writeforecast: write forecast file

SS_write_length.fit: Write length.fit file to be used by the MFCL length-comp...

SS_writestarter: write starter file

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...

Functions

addSSsummarize Man page
bubble3 Man page
DoProjectPlots Man page
getADMBHessian Man page
IOTCmove Man page
make_multifig Man page
mcmc.nuisance Man page
mcmc.out Man page
mountains Man page
movepars Man page
NegLogInt_Fn Man page
PinerPlot Man page
plotCI Man page
r4ss Man page
r4ss_logo Man page
r4ss-package Man page
read.admbFit Man page
rich.colors.short Man page
selfit Man page
selfit_spline Man page
sel.line Man page
SSbootstrap Man page
SS_changepars Man page
SS_doRetro Man page
SSFishGraph Man page
SS_fitbiasramp Man page
SS_ForeCatch Man page
SSgetMCMC Man page
SSgetoutput Man page
SS_html Man page
SS_makedatlist Man page
SSmakeMmatrix Man page
SSMethod.Cond.TA1.8 Man page
SSMethod.TA1.8 Man page
SS_output Man page
SS_parlines Man page
SSplotBiology Man page
SSplotCatch Man page
SSplotCohorts Man page
SSplotComparisons Man page
SSplotComps Man page
SSplotData Man page
SSplotDiscard Man page
SSplotIndices Man page
SSplotMCMC_ExtraSelex Man page
SSplotMnwt Man page
SSplotMovementMap Man page
SSplotMovementRates Man page
SSplotNumbers Man page
SSplotPars Man page
SSplotProfile Man page
SSplotRecdevs Man page
SSplotRecdist Man page
SSplotRetroRecruits Man page
SS_plots Man page
SSplotSelex Man page
SSplotSpawnrecruit Man page
SSplotSPR Man page
SSplotSummaryF Man page
SSplotTags Man page
SSplotTimeseries Man page
SSplotYield Man page
SS_profile Man page
SS_readctl Man page
SS_readdat Man page
SS_readforecast Man page
SS_readstarter Man page
SS_recdevs Man page
SS_RunJitter Man page
SS_splitdat Man page
SSsummarize Man page
SStableComparisons Man page
SS_varadjust Man page
SS_writectl Man page
SS_writedat Man page
SS_writeforecast Man page
SS_write_length.fit Man page
SS_writestarter Man page
stackpoly Man page
TSCplot Man page
update_r4ss_files Man page

Files

r4ss
r4ss/NAMESPACE
r4ss/NEWS.md
r4ss/R
r4ss/R/RebuildPlot.R r4ss/R/addSSsummarize.R r4ss/R/SStableComparisons.R r4ss/R/sel.line.R r4ss/R/SS_varadjust.R r4ss/R/SSplotSelex.R r4ss/R/SS_ForeCatch.R r4ss/R/mcmc.out.R r4ss/R/SS_writectl.R r4ss/R/SSMethod.TA1.8.R r4ss/R/movepars.R r4ss/R/SS_readforecast.R r4ss/R/SSplotIndices.R r4ss/R/SS_recdevs.R r4ss/R/stackpoly.R r4ss/R/make_multifig.R r4ss/R/SSbootstrap.R r4ss/R/SSplotCohorts.R r4ss/R/SSplotDiscard.R r4ss/R/mountains.R r4ss/R/SSgetoutput.R r4ss/R/SS_writedat.R r4ss/R/SSplotCatch.R r4ss/R/SS_writestarter.R r4ss/R/SS_splitdat.R r4ss/R/SS_readdat.R r4ss/R/IOTCmove.R r4ss/R/update_r4ss_files.R r4ss/R/SS_fitbiasramp.R r4ss/R/SSFishGraph.R r4ss/R/SS_doRetro.R r4ss/R/SSplotComps.R r4ss/R/SSplotProfile.R r4ss/R/bubble3.R r4ss/R/SS_RunJitter.R r4ss/R/mcmc.nuisance.R r4ss/R/r4ss_logo.R r4ss/R/SS_readstarter.R r4ss/R/SSplotMnwt.R r4ss/R/SSplotSPR.R r4ss/R/SS_profile.R r4ss/R/SS_html.R r4ss/R/selfit.R r4ss/R/SSplotYield.R r4ss/R/SSplotSummaryF.R r4ss/R/getADMBHessian.R r4ss/R/SSplotMovementMap.R r4ss/R/read.admbFit.R r4ss/R/SS_writeforecast.R r4ss/R/r4ss-package.R r4ss/R/SSmakeMmatrix.R r4ss/R/SSplotMovementRates.R r4ss/R/rich.colors.short.R r4ss/R/PinerPlot.R r4ss/R/SS_write_length.fit.R r4ss/R/SS_readctl.R r4ss/R/NegLogInt_Fn.R r4ss/R/SS_parlines.R r4ss/R/SSsummarize.R r4ss/R/SSgetMCMC.R r4ss/R/SSplotComparisons.R r4ss/R/SSplotNumbers.R r4ss/R/SS_makedatlist.R r4ss/R/SSplotTimeseries.R r4ss/R/SSplotRetroDevs.R r4ss/R/SSplotTags.R r4ss/R/SS_decision_table_stuff.R r4ss/R/SSplotRecdist.R r4ss/R/SSplotRetroRecruits.R r4ss/R/TSCplot.R r4ss/R/SSplotBiology.R r4ss/R/SSplotPars.R r4ss/R/SSplotMCMC_ExtraSelex.R r4ss/R/SSchangeYears.R r4ss/R/SSplotRecdevs.R r4ss/R/SSplotData.R r4ss/R/SS_output.R r4ss/R/plotCI.R r4ss/R/SSMethod.Cond.TA1.8.R r4ss/R/selfit_spline.R r4ss/R/SSplotSpawnrecruit.R r4ss/R/SS_changepars.R r4ss/R/SS_plots.R
r4ss/README.md
r4ss/MD5
r4ss/DESCRIPTION
r4ss/man
r4ss/man/SSplotSPR.Rd r4ss/man/stackpoly.Rd r4ss/man/SSMethod.TA1.8.Rd r4ss/man/SSplotPars.Rd r4ss/man/SStableComparisons.Rd r4ss/man/rich.colors.short.Rd r4ss/man/SS_writeforecast.Rd r4ss/man/SSplotCatch.Rd r4ss/man/SSmakeMmatrix.Rd r4ss/man/SS_makedatlist.Rd r4ss/man/SSplotComps.Rd r4ss/man/IOTCmove.Rd r4ss/man/SS_readforecast.Rd r4ss/man/getADMBHessian.Rd r4ss/man/mcmc.out.Rd r4ss/man/SSplotTags.Rd r4ss/man/SSplotYield.Rd r4ss/man/SSplotBiology.Rd r4ss/man/SSplotIndices.Rd r4ss/man/SS_recdevs.Rd r4ss/man/SS_varadjust.Rd r4ss/man/SS_writedat.Rd r4ss/man/read.admbFit.Rd r4ss/man/SS_readstarter.Rd r4ss/man/SS_doRetro.Rd r4ss/man/addSSsummarize.Rd r4ss/man/make_multifig.Rd r4ss/man/SSplotMovementMap.Rd r4ss/man/plotCI.Rd r4ss/man/SSplotTimeseries.Rd r4ss/man/SSplotRetroRecruits.Rd r4ss/man/selfit_spline.Rd r4ss/man/SSplotNumbers.Rd r4ss/man/SSplotSpawnrecruit.Rd r4ss/man/SSgetoutput.Rd r4ss/man/SSplotDiscard.Rd r4ss/man/SSbootstrap.Rd r4ss/man/SS_profile.Rd r4ss/man/SSplotRecdevs.Rd r4ss/man/SS_writectl.Rd r4ss/man/SSplotSummaryF.Rd r4ss/man/NegLogInt_Fn.Rd r4ss/man/SSgetMCMC.Rd r4ss/man/SSplotComparisons.Rd r4ss/man/movepars.Rd r4ss/man/SSMethod.Cond.TA1.8.Rd r4ss/man/SSplotData.Rd r4ss/man/bubble3.Rd r4ss/man/sel.line.Rd r4ss/man/PinerPlot.Rd r4ss/man/SSplotProfile.Rd r4ss/man/SS_readdat.Rd r4ss/man/SSFishGraph.Rd r4ss/man/SS_changepars.Rd r4ss/man/r4ss-package.Rd r4ss/man/SS_plots.Rd r4ss/man/SSplotMovementRates.Rd r4ss/man/SS_RunJitter.Rd r4ss/man/mcmc.nuisance.Rd r4ss/man/SSplotMCMC_ExtraSelex.Rd r4ss/man/SS_writestarter.Rd r4ss/man/SSplotMnwt.Rd r4ss/man/SS_ForeCatch.Rd r4ss/man/SSsummarize.Rd r4ss/man/SSplotRecdist.Rd r4ss/man/SS_readctl.Rd r4ss/man/SSplotSelex.Rd r4ss/man/SS_output.Rd r4ss/man/SS_fitbiasramp.Rd r4ss/man/r4ss_logo.Rd r4ss/man/SS_html.Rd r4ss/man/DoProjectPlots.Rd r4ss/man/TSCplot.Rd r4ss/man/update_r4ss_files.Rd r4ss/man/mountains.Rd r4ss/man/SS_parlines.Rd r4ss/man/SSplotCohorts.Rd r4ss/man/selfit.Rd r4ss/man/SS_write_length.fit.Rd r4ss/man/SS_splitdat.Rd

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