r4ss: R code for Stock Synthesis

Functions for reading output, plotting, exploring and manipulating input files for Richard Methot's Stock Synthesis fisheries stock assessment modeling platform.

Author
Ian Taylor, Ian Stewart, Allan Hicks, Tommy Garrison, Andre Punt, John Wallace, Chantel Wetzel, and other contributors
Date of publication
2013-05-16 17:36:06
Maintainer
Ian Taylor <Ian.Taylor@noaa.gov>
License
GPL-3
Version
1.20
URLs

View on R-Forge

Man pages

addSSsummarize
Add a model to the list of models to compare
bubble3
Create a bubble plot.
hist2d
Compute and Plot a 2-Dimensional Histogram
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
plotCI
Plot points with confidence intervals.
r4ss-package
R tools for Stock Synthesis
RebuildPlot
Make plots from Rebuilder program
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 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
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
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
Show movement rates on a map.
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
SSplotRetroDevs
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_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_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
function "stackpoly" by Jim Lemon from "plotrix" package
TSCplot
Create a plot for the TSC report
update_r4ss_files
Updates r4ss files to newest versions on web.

Files in this package

r4ss/DESCRIPTION
r4ss/NAMESPACE
r4ss/R
r4ss/R/IOTCmove.R
r4ss/R/PinerPlot.R
r4ss/R/RebuildPlot.R
r4ss/R/SSFishGraph.R
r4ss/R/SS_changepars.R
r4ss/R/SS_doRetro.R
r4ss/R/SS_fitbiasramp.R
r4ss/R/SS_html.R
r4ss/R/SS_makedatlist.R
r4ss/R/SS_output.R
r4ss/R/SS_parlines.R
r4ss/R/SS_plots.R
r4ss/R/SS_profile.R
r4ss/R/SS_readctl.R
r4ss/R/SS_readdat.R
r4ss/R/SS_readforecast.R
r4ss/R/SS_readstarter.R
r4ss/R/SS_recdevs.R
r4ss/R/SS_splitdat.R
r4ss/R/SS_write_length.fit.R
r4ss/R/SS_writectl.R
r4ss/R/SS_writedat.R
r4ss/R/SS_writeforecast.R
r4ss/R/SS_writestarter.R
r4ss/R/SSbootstrap.R
r4ss/R/SSgetMCMC.R
r4ss/R/SSgetoutput.R
r4ss/R/SSplotBiology.R
r4ss/R/SSplotCatch.R
r4ss/R/SSplotCohorts.R
r4ss/R/SSplotComparisons.R
r4ss/R/SSplotComps.R
r4ss/R/SSplotData.R
r4ss/R/SSplotDiscard.R
r4ss/R/SSplotIndices.R
r4ss/R/SSplotMCMC_ExtraSelex.R
r4ss/R/SSplotMnwt.R
r4ss/R/SSplotMovementMap.R
r4ss/R/SSplotMovementRates.R
r4ss/R/SSplotNumbers.R
r4ss/R/SSplotPars.R
r4ss/R/SSplotProfile.R
r4ss/R/SSplotRecdevs.R
r4ss/R/SSplotRecdist.R
r4ss/R/SSplotRetroDevs.R
r4ss/R/SSplotRetroRecruits.R
r4ss/R/SSplotSPR.R
r4ss/R/SSplotSelex.R
r4ss/R/SSplotSpawnrecruit.R
r4ss/R/SSplotSummaryF.R
r4ss/R/SSplotTags.R
r4ss/R/SSplotTimeseries.R
r4ss/R/SSplotYield.R
r4ss/R/SSsummarize.R
r4ss/R/SStableComparisons.R
r4ss/R/TSCplot.R
r4ss/R/addSSsummarize.R
r4ss/R/bubble3.R
r4ss/R/hist2d.R
r4ss/R/make_multifig.R
r4ss/R/mcmc.nuisance.R
r4ss/R/mcmc.out.R
r4ss/R/mountains.R
r4ss/R/movepars.R
r4ss/R/plotCI.R
r4ss/R/rich.colors.short.R
r4ss/R/sel.line.R
r4ss/R/selfit.R
r4ss/R/selfit_spline.R
r4ss/R/stackpoly.R
r4ss/R/update_r4ss_files.R
r4ss/man
r4ss/man/IOTCmove.Rd
r4ss/man/RebuildPlot.Rd
r4ss/man/SSFishGraph.Rd
r4ss/man/SS_changepars.Rd
r4ss/man/SS_doRetro.Rd
r4ss/man/SS_fitbiasramp.Rd
r4ss/man/SS_html.Rd
r4ss/man/SS_makedatlist.Rd
r4ss/man/SS_output.Rd
r4ss/man/SS_parlines.Rd
r4ss/man/SS_plots.Rd
r4ss/man/SS_profile.Rd
r4ss/man/SS_readctl.Rd
r4ss/man/SS_readdat.Rd
r4ss/man/SS_readforecast.Rd
r4ss/man/SS_readstarter.Rd
r4ss/man/SS_recdevs.Rd
r4ss/man/SS_splitdat.Rd
r4ss/man/SS_write_length.fit.Rd
r4ss/man/SS_writectl.Rd
r4ss/man/SS_writedat.Rd
r4ss/man/SS_writeforecast.Rd
r4ss/man/SS_writestarter.Rd
r4ss/man/SSbootstrap.Rd
r4ss/man/SSgetMCMC.Rd
r4ss/man/SSgetoutput.Rd
r4ss/man/SSplotBiology.Rd
r4ss/man/SSplotCatch.Rd
r4ss/man/SSplotCohorts.Rd
r4ss/man/SSplotComparisons.Rd
r4ss/man/SSplotComps.Rd
r4ss/man/SSplotData.Rd
r4ss/man/SSplotDiscard.Rd
r4ss/man/SSplotIndices.Rd
r4ss/man/SSplotMCMC_ExtraSelex.Rd
r4ss/man/SSplotMnwt.Rd
r4ss/man/SSplotMovementMap.Rd
r4ss/man/SSplotMovementRates.Rd
r4ss/man/SSplotNumbers.Rd
r4ss/man/SSplotPars.Rd
r4ss/man/SSplotProfile.Rd
r4ss/man/SSplotRecdevs.Rd
r4ss/man/SSplotRecdist.Rd
r4ss/man/SSplotRetroDevs.Rd
r4ss/man/SSplotSPR.Rd
r4ss/man/SSplotSelex.Rd
r4ss/man/SSplotSpawnrecruit.Rd
r4ss/man/SSplotSummaryF.Rd
r4ss/man/SSplotTags.Rd
r4ss/man/SSplotTimeseries.Rd
r4ss/man/SSplotYield.Rd
r4ss/man/SSsummarize.Rd
r4ss/man/SStableComparisons.Rd
r4ss/man/TSCplot.Rd
r4ss/man/addSSsummarize.Rd
r4ss/man/bubble3.Rd
r4ss/man/hist2d.Rd
r4ss/man/make_multifig.Rd
r4ss/man/mcmc.nuisance.Rd
r4ss/man/mcmc.out.Rd
r4ss/man/mountains.Rd
r4ss/man/movepars.Rd
r4ss/man/plotCI.Rd
r4ss/man/r4ss-package.Rd
r4ss/man/rich.colors.short.Rd
r4ss/man/sel.line.Rd
r4ss/man/selfit.Rd
r4ss/man/selfit_spline.Rd
r4ss/man/stackpoly.Rd
r4ss/man/update_r4ss_files.Rd