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r4ss (version 1.17)

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

611

Version

1.17

License

GPL-3

Maintainer

Ian Taylor

Last Published

June 15th, 2012

Functions in r4ss (1.17)

SS_output

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

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

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

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

Estimate bias adjustment for recruitment deviates
SS_splitdat

Split apart bootstrap data to make input file.
SS_readctl

read control file
selfit_spline

visualize parameterization of cubic spline selectivity in SS
SSsummarize

Summarize the output from multiple Stock Synthesis models.
SSplotDiscard

Plot fit to discard fraction.
DoProjectPlots

Make plots from Rebuilder program
SSplotComps

Plot composition data and fits.
SS_html

Create HTML files to view figures in browser.
plotCI

Plot points with confidence intervals.
SSplotTags

Plot tagging data and fits
SS_writestarter

write starter file
SS_writedat

write data file
SS_writectl

write control file
update_r4ss_files

Updates r4ss files to newest versions on web.
r4ss-package

R tools for Stock Synthesis
mcmc.nuisance

Summarize nuisance MCMC output
SS_plots_test

plot many quantities related to output from Stock Synthesis
SS_recdevs

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

Plot uncertainty around chosen selectivity ogive from MCMC.
SS_makedatlist

make a list for SS data
SStableComparisons

make table comparing quantities across models
bubble3

Create a bubble plot.
SSplotMovementMap

Show movement rates on a map.
SS_writeforecast

write forecast file
SSplotComparisons

plot model comparisons
SS_plots

plot many quantities related to output from Stock Synthesis
stackpoly

function "stackpoly" by Jim Lemon from "plotrix" package
hist2d

Compute and Plot a 2-Dimensional Histogram
SSplotMovementRates

Show movement rates on a map.
SSgetoutput

Get output from multiple Stock Synthesis models.
mcmc.out

Summarize, analyze and plot key MCMC output.
selfit

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

explore movement parameterizations
sel.line

a function for drawing selecitivity curves
SSplotIndices

Plot indices of abundance and associated quantities.
SSplotPars

Plot distributions of priors, posteriors, and estimates.
make_multifig

Create multi-figure plots.
SS_changepars

Change parameters in the control file.
SS_parlines

Get parameter lines from Stock Synthesis control file
SS_profile

Run a likelihood profile in Stock Synthesis.
SS_readforecast

read forecast file
rich.colors.short

Make a vector of colors.
SSplotRecdevs

Plot recruitment deviations
SSplotBiology

Plot biology related quantities.
SSplotSPR

Plot SPR quantities.
SSplotTimeseries

Plot timeseries data
mountains

Make shaded polygons with a mountain-like appearance
SSplotRecdist

Plot of recruitment distribution among areas and seasons
SSplotMnwt

Plot mean weight data and fits.
SS_readstarter

read starter file
TSCplot

Create a plot for the TSC report
SSplotNumbers

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

Plot catch related quantities.
SSplotYield

Plot yield and surplus production.
SSplotSelex

Plot selectivity
addSSsummarize

Add a model to the list of models to compare
SSgetMCMC

Read MCMC output.
SS_readdat

read data file
SSplotSpawnrecruit

Plot spawner-recruit curve.