r4ss: R Code for Stock Synthesis
Version 1.24.0

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.

Browse man pages Browse package API and functions Browse package files

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
URL https://github.com/r4ss
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("r4ss")

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

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

Files

NAMESPACE
NEWS.md
R
R/RebuildPlot.R
R/addSSsummarize.R
R/SStableComparisons.R
R/sel.line.R
R/SS_varadjust.R
R/SSplotSelex.R
R/SS_ForeCatch.R
R/mcmc.out.R
R/SS_writectl.R
R/SSMethod.TA1.8.R
R/movepars.R
R/SS_readforecast.R
R/SSplotIndices.R
R/SS_recdevs.R
R/stackpoly.R
R/make_multifig.R
R/SSbootstrap.R
R/SSplotCohorts.R
R/SSplotDiscard.R
R/mountains.R
R/SSgetoutput.R
R/SS_writedat.R
R/SSplotCatch.R
R/SS_writestarter.R
R/SS_splitdat.R
R/SS_readdat.R
R/IOTCmove.R
R/update_r4ss_files.R
R/SS_fitbiasramp.R
R/SSFishGraph.R
R/SS_doRetro.R
R/SSplotComps.R
R/SSplotProfile.R
R/bubble3.R
R/SS_RunJitter.R
R/mcmc.nuisance.R
R/r4ss_logo.R
R/SS_readstarter.R
R/SSplotMnwt.R
R/SSplotSPR.R
R/SS_profile.R
R/SS_html.R
R/selfit.R
R/SSplotYield.R
R/SSplotSummaryF.R
R/getADMBHessian.R
R/SSplotMovementMap.R
R/read.admbFit.R
R/SS_writeforecast.R
R/r4ss-package.R
R/SSmakeMmatrix.R
R/SSplotMovementRates.R
R/rich.colors.short.R
R/PinerPlot.R
R/SS_write_length.fit.R
R/SS_readctl.R
R/NegLogInt_Fn.R
R/SS_parlines.R
R/SSsummarize.R
R/SSgetMCMC.R
R/SSplotComparisons.R
R/SSplotNumbers.R
R/SS_makedatlist.R
R/SSplotTimeseries.R
R/SSplotRetroDevs.R
R/SSplotTags.R
R/SS_decision_table_stuff.R
R/SSplotRecdist.R
R/SSplotRetroRecruits.R
R/TSCplot.R
R/SSplotBiology.R
R/SSplotPars.R
R/SSplotMCMC_ExtraSelex.R
R/SSchangeYears.R
R/SSplotRecdevs.R
R/SSplotData.R
R/SS_output.R
R/plotCI.R
R/SSMethod.Cond.TA1.8.R
R/selfit_spline.R
R/SSplotSpawnrecruit.R
R/SS_changepars.R
R/SS_plots.R
README.md
MD5
DESCRIPTION
man
man/SSplotSPR.Rd
man/stackpoly.Rd
man/SSMethod.TA1.8.Rd
man/SSplotPars.Rd
man/SStableComparisons.Rd
man/rich.colors.short.Rd
man/SS_writeforecast.Rd
man/SSplotCatch.Rd
man/SSmakeMmatrix.Rd
man/SS_makedatlist.Rd
man/SSplotComps.Rd
man/IOTCmove.Rd
man/SS_readforecast.Rd
man/getADMBHessian.Rd
man/mcmc.out.Rd
man/SSplotTags.Rd
man/SSplotYield.Rd
man/SSplotBiology.Rd
man/SSplotIndices.Rd
man/SS_recdevs.Rd
man/SS_varadjust.Rd
man/SS_writedat.Rd
man/read.admbFit.Rd
man/SS_readstarter.Rd
man/SS_doRetro.Rd
man/addSSsummarize.Rd
man/make_multifig.Rd
man/SSplotMovementMap.Rd
man/plotCI.Rd
man/SSplotTimeseries.Rd
man/SSplotRetroRecruits.Rd
man/selfit_spline.Rd
man/SSplotNumbers.Rd
man/SSplotSpawnrecruit.Rd
man/SSgetoutput.Rd
man/SSplotDiscard.Rd
man/SSbootstrap.Rd
man/SS_profile.Rd
man/SSplotRecdevs.Rd
man/SS_writectl.Rd
man/SSplotSummaryF.Rd
man/NegLogInt_Fn.Rd
man/SSgetMCMC.Rd
man/SSplotComparisons.Rd
man/movepars.Rd
man/SSMethod.Cond.TA1.8.Rd
man/SSplotData.Rd
man/bubble3.Rd
man/sel.line.Rd
man/PinerPlot.Rd
man/SSplotProfile.Rd
man/SS_readdat.Rd
man/SSFishGraph.Rd
man/SS_changepars.Rd
man/r4ss-package.Rd
man/SS_plots.Rd
man/SSplotMovementRates.Rd
man/SS_RunJitter.Rd
man/mcmc.nuisance.Rd
man/SSplotMCMC_ExtraSelex.Rd
man/SS_writestarter.Rd
man/SSplotMnwt.Rd
man/SS_ForeCatch.Rd
man/SSsummarize.Rd
man/SSplotRecdist.Rd
man/SS_readctl.Rd
man/SSplotSelex.Rd
man/SS_output.Rd
man/SS_fitbiasramp.Rd
man/r4ss_logo.Rd
man/SS_html.Rd
man/DoProjectPlots.Rd
man/TSCplot.Rd
man/update_r4ss_files.Rd
man/mountains.Rd
man/SS_parlines.Rd
man/SSplotCohorts.Rd
man/selfit.Rd
man/SS_write_length.fit.Rd
man/SS_splitdat.Rd
r4ss documentation built on May 19, 2017, 11:46 a.m.