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r4ss (version 1.11)

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

1.11

License

MIT License

Maintainer

Ian Taylor

Last Published

September 21st, 2010

Functions in r4ss (1.11)

Get output from multiple Stock Synthesis models.

Estimate bias adjustment for recruitment deviates

Plot numbers-at-age related data and fits.

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

plot many quantities related to output from Stock Synthesis

Plot SPR quantities.

update_r4ss_files

Updates r4ss files to newest versions on web.

Plot yield and surplus production.

Make plots from Rebuilder program

Plot fit to discard fraction.

Run a likelihood profile in Stock Synthesis.

Split apart bootstrap data to make input file.

Plot composition data and fits.

Plot tagging data and fits

Run a collection of simulations for Stock Synthesis.

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

Plot recruitment deviations

Plot biology related quantities.

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

Plot mean weight data and fits.

Plot indices of abundance and associated quantities.

R tools for Stock Synthesis

Plot distributions of priors, posteriors, and estimates.

A function to visual parameterization of movement in Stock Synthesis

Summarize the output from multiple Stock Synthesis models.

Change parameters in the control file.

Create multi-figure plots.

Make shaded polygons with a mountain-like appearance

SSplotSpawnrecruit

Plot spawner-recruit curve.

a function for drawing selecitivity curves

SSplotTimeseries

Plot timeseries data

Plot catch related quantities.

Make files and set up folders for simulations

Plot selectivity

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

Plot points with confidence intervals.

rich.colors.short

Make a vector of colors.

function to plot many quantities related to output from Stock Synthesis

Plot of recruitment distribution among areas and seasons

Get parameter lines from Stock Synthesis control file

Create a bubble plot.

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

Insert a vector of recruitment deviations into the control file.