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r4ss (version 1.13)

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

1.13

License

MIT License

Maintainer

Ian Taylor

Last Published

January 5th, 2011

Functions in r4ss (1.13)

Estimate bias adjustment for recruitment deviates

read starter file

plot many quantities related to output from Stock Synthesis

Change parameters in the control file.

Get parameter lines from Stock Synthesis control file

SSplotMovementMap

Show movement rates on a map.

read control file

SSplotComparisons

plot model comparisons

Plot indices of abundance and associated quantities.

SSplotMovementRates

Show movement rates on a map.

Plot tagging data and fits

explore movement parameterizations

Plot recruitment deviations

update_r4ss_files

Updates r4ss files to newest versions on web.

Get output from multiple Stock Synthesis models.

Plot composition data and fits.

SS_readforecast

read forecast file

Insert a vector of recruitment deviations into the control file.

SS_writeforecast

write forecast file

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

old plot funciton

Summarize the output from multiple Stock Synthesis models.

Split apart bootstrap data to make input file.

Plot mean weight data and fits.

Plot SPR quantities.

Plot numbers-at-age related data and fits.

make a list for SS data

SS_writestarter

write starter file

SSplotSpawnrecruit

Plot spawner-recruit curve.

Plot catch related quantities.

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

Plot selectivity

Create multi-figure plots.

write data file

Plot of recruitment distribution among areas and seasons

Create a bubble plot.

Make shaded polygons with a mountain-like appearance

Old output reader

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

Run a likelihood profile in Stock Synthesis.

Make plots from Rebuilder program

Make files and set up folders for simulations

Run a collection of simulations for Stock Synthesis.

Plot distributions of priors, posteriors, and estimates.

SSplotTimeseries

Plot timeseries data

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

R tools for Stock Synthesis

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

write control file

Plot biology related quantities.

Plot fit to discard fraction.

Plot yield and surplus production.

rich.colors.short

Make a vector of colors.

Plot points with confidence intervals.

a function for drawing selecitivity curves