Learn R Programming
⚠️There's a newer version (1.44.0) of this package.Take me there.

r4ss (version 1.16)

R code for Stock Synthesis

Description

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

Copy Link

Version

Install

install.packages('r4ss')

Monthly Downloads

342

Version

1.16

License

MIT License

Maintainer

Ian Taylor

Last Published

June 29th, 2011

Functions in r4ss (1.16)

IOTCmove

Make a map of movement for a 5-area Indian Ocean model
SS_profile

Run a likelihood profile in Stock Synthesis.
SSplotNumbers

Plot numbers-at-age related data and fits.
SS_readforecast

read forecast file
SS_makedatlist

make a list for SS data
SS_parlines

Get parameter lines from Stock Synthesis control file
SSplotSelex

Plot selectivity
SSplotMovementRates

Show movement rates on a map.
SSFishGraph

A function for converting Stock Synthesis output to the format used by FishGraph
SSplotDiscard

Plot fit to discard fraction.
SS_output

A function to create a list object for the output from Stock Synthesis
SSplotYield

Plot yield and surplus production.
SS_writedat

write data file
SStableComparisons

make table comparing quantities across models
SSplotData

Timeline of presence/absence of data by type, year, and fleet.
SS_writeforecast

write forecast file
SSplotMCMC_ExtraSelex

Plot uncertainty around chosen selectivity ogive from MCMC.
SSplotSPR

Plot SPR quantities.
SS_splitdat

Split apart bootstrap data to make input file.
bubble3

Create a bubble plot.
movepars

explore movement parameterizations
SS_changepars

Change parameters in the control file.
SSplotSpawnrecruit

Plot spawner-recruit curve.
SS_readdat

read data file
stackpoly

function "stackpoly" by Jim Lemon from "plotrix" package
SSrunsims

Run a collection of simulations for Stock Synthesis.
SSplotMnwt

Plot mean weight data and fits.
SSplotRecdevs

Plot recruitment deviations
SSgetoutput

Get output from multiple Stock Synthesis models.
rich.colors.short

Make a vector of colors.
mountains

Make shaded polygons with a mountain-like appearance
sel.line

a function for drawing selecitivity curves
SSplotComparisons

plot model comparisons
SSplotCatch

Plot catch related quantities.
SSplotTimeseries

Plot timeseries data
plotCI

Plot points with confidence intervals.
SSplotPars

Plot distributions of priors, posteriors, and estimates.
r4ss-package

R tools for Stock Synthesis
SS_recdevs

Insert a vector of recruitment deviations into the control file.
DoProjectPlots

Make plots from Rebuilder program
SSplotBiology

Plot biology related quantities.
update_r4ss_files

Updates r4ss files to newest versions on web.
SSmakesims

Make files and set up folders for simulations
SSgetMCMC

Read MCMC output.
mcmc.out

Summarize, analyze and plot key MCMC output.
SS_writestarter

write starter file
SS_writectl

write control file
SSplotIndices

Plot indices of abundance and associated quantities.
addSSsummarize

Add a model to the list of models to compare
SS_plots

plot many quantities related to output from Stock Synthesis
selfit

A function to visual parameterization of double normal and double logistic selectivity in Stock Synthesis
SS_readctl

read control file
make_multifig

Create multi-figure plots.
SS_fitbiasramp

Estimate bias adjustment for recruitment deviates
SSplotComps

Plot composition data and fits.
SSplotMovementMap

Show movement rates on a map.
mcmc.nuisance

Summarize nuisance MCMC output
SS_readstarter

read starter file
SSplotTags

Plot tagging data and fits
SSsummarize

Summarize the output from multiple Stock Synthesis models.
SSplotRecdist

Plot of recruitment distribution among areas and seasons