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r4ss (version 1.15)

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.

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Version

Install

install.packages('r4ss')

Monthly Downloads

342

Version

1.15

License

MIT License

Maintainer

Ian Taylor

Last Published

April 15th, 2011

Functions in r4ss (1.15)

SS_output

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

Get output from multiple Stock Synthesis models.
IOTCmove

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

Split apart bootstrap data to make input file.
SS_recdevs

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

Plot selectivity
SS_writectl

write control file
SSplotCatch

Plot catch related quantities.
SS_readforecast

read forecast file
SS_readstarter

read starter file
r4ss-package

R tools for Stock Synthesis
SSplotTimeseries

Plot timeseries data
SSplotMCMC_ExtraSelex

Plot uncertainty around chosen selectivity ogive from MCMC.
SSplotDiscard

Plot fit to discard fraction.
SSsummarize

Summarize the output from multiple Stock Synthesis models.
plotCI

Plot points with confidence intervals.
SSplotBiology

Plot biology related quantities.
SSv3_output

Old output reader
SS_makedatlist

make a list for SS data
SSmakesims

Make files and set up folders for simulations
mcmc.nuisance

Summarize nuisance MCMC output
SS_writeforecast

write forecast file
SSplotYield

Plot yield and surplus production.
SS_readctl

read control file
SS_fitbiasramp

Estimate bias adjustment for recruitment deviates
SSplotMnwt

Plot mean weight data and fits.
SS_readdat

read data file
SSgetMCMC

Read MCMC output.
make_multifig

Create multi-figure plots.
mountains

Make shaded polygons with a mountain-like appearance
mcmc.out

Summarize, analyze and plot key MCMC output.
SSv3_plots

old plot funciton
SSplotSPR

Plot SPR quantities.
SSplotTags

Plot tagging data and fits
SS_changepars

Change parameters in the control file.
rich.colors.short

Make a vector of colors.
stackpoly

function "stackpoly" by Jim Lemon from "plotrix" package
bubble3

Create a bubble plot.
addSSsummarize

Add a model to the list of models to compare
update_r4ss_files

Updates r4ss files to newest versions on web.
SSFishGraph

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

Plot distributions of priors, posteriors, and estimates.
DoProjectPlots

Make plots from Rebuilder program
SSplotData

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

Plot composition data and fits.
SS_writestarter

write starter file
SSplotMovementRates

Show movement rates on a map.
SS_profile

Run a likelihood profile in Stock Synthesis.
SS_parlines

Get parameter lines from Stock Synthesis control file
selfit

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

plot model comparisons
SSrunsims

Run a collection of simulations for Stock Synthesis.
SSplotNumbers

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

write data file
SS_plots

plot many quantities related to output from Stock Synthesis
SSplotRecdevs

Plot recruitment deviations
SSplotIndices

Plot indices of abundance and associated quantities.
movepars

explore movement parameterizations
SSplotRecdist

Plot of recruitment distribution among areas and seasons
sel.line

a function for drawing selecitivity curves
SSplotMovementMap

Show movement rates on a map.
SSplotSpawnrecruit

Plot spawner-recruit curve.
SStableComparisons

make table comparing quantities across models