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r4ss (version 1.0)

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

1.0

License

MIT License

Maintainer

Ian Taylor

Last Published

November 10th, 2009

Functions in r4ss (1.0)

SS_fitbiasramp

Estimate bias adjustment for recruitment deviates
SSv3_output

A function to create a list object for the output from Stock Synthesis
SSv3_FishGraph

A function for converting Stock Synthesis output to the format used by FishGraph
SSv3_plots

function to plot many quantities related to output from Stock Synthesis
lines.sel

a function for drawing selecitivity curves
SS_changepars

Change parameters in the control file.
r4ss-package

R tools for Stock Synthesis
update_r4ss_files

Updates r4ss files to newest versions on web.
SSv3_plotpars

Plot distributions of priors, posteriors, and estimates.
selfit

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

Run a likelihood profile in Stock Synthesis.
sel.line

a function for drawing selecitivity curves
SS_parlines

Get parameter lines from Stock Synthesis control file
SS_recdevs

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

Split apart bootstrap data to make input file.
SSplotNumbers

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

A function to visual parameterization of movement in Stock Synthesis
SSplotSPR

Plot SPR quantities.
SSplotIndices

Plot indices of abundance and associated quantities.
DoProjectPlots

Make plots from Rebuilder program
SSplotSpawnrecruit

Plot spawner-recruit curve.
SSsummarize

Summarize the output from multiple Stock Synthesis models.
SSplotBiology

Plot biology related quantities.
SSFishGraph

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

Create multi-figure plots.
SSmakesims

Make files and set up folders for simulations
SSplotYield

Plot yield and surplus production.
SSrunsims

Run a collection of simulations for Stock Synthesis.
rich.colors.short

Make a vector of colors.
SSplotRecdevs

Plot recruitment deviations
SSplotMnwt

Plot mean weight data and fits.
SS_plots

plot many quantities related to output from Stock Synthesis
SS_output

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

Plot fit to discard fraction.
SSplotSelex

Plot selectivity
SSplotComps

Plot composition data and fits.
stackpoly

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

Make shaded polygons with a mountain-like appearance
bubble3

Create a bubble plot.
SSplotPars

Plot distributions of priors, posteriors, and estimates.
SSgetoutput

Get output from multiple Stock Synthesis models.
SSplotCatch

Plot catch related quantities.
SSplotTimeseries

Plot timeseries data
plotCI

Plot points with confidence intervals.
SSplotTags

Plot tagging data and fits