r4ss: R Code for Stock Synthesis

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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.

Author
Ian 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 publication
2015-12-23 23:28:33
Maintainer
Ian Taylor <Ian.Taylor@noaa.gov>
License
GPL-3
Version
1.24.0
URLs

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...

Files in this package

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