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r4ss (version 1.08)

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

1.08

License

MIT License

Maintainer

Ian Taylor

Last Published

August 11th, 2010

Functions in r4ss (1.08)

Plot fit to discard fraction.

Run a collection of simulations for Stock Synthesis.

rich.colors.short

Make a vector of colors.

a function for drawing selecitivity curves

Make plots from Rebuilder program

Summarize the output from multiple Stock Synthesis models.

Make shaded polygons with a mountain-like appearance

Plot numbers-at-age related data and fits.

Run a likelihood profile in Stock Synthesis.

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

Plot mean weight data and fits.

Insert a vector of recruitment deviations into the control file.

SSplotTimeseries

Plot timeseries data

Get output from multiple Stock Synthesis models.

Plot biology related quantities.

Plot tagging data and fits

update_r4ss_files

Updates r4ss files to newest versions on web.

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

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

Change parameters in the control file.

Make files and set up folders for simulations

Get parameter lines from Stock Synthesis control file

Plot SPR quantities.

function to plot many quantities related to output from Stock Synthesis

Plot yield and surplus production.

Plot distributions of priors, posteriors, and estimates.

Plot catch related quantities.

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

Plot indices of abundance and associated quantities.

Create a bubble plot.

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

plot many quantities related to output from Stock Synthesis

SSplotSpawnrecruit

Plot spawner-recruit curve.

Estimate bias adjustment for recruitment deviates

R tools for Stock Synthesis

Create multi-figure plots.

Plot points with confidence intervals.

Plot composition data and fits.

A function to visual parameterization of movement in Stock Synthesis

Plot recruitment deviations

Split apart bootstrap data to make input file.

Plot selectivity