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r4ss (version 1.10)

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

1.10

License

MIT License

Maintainer

Ian Taylor

Last Published

August 17th, 2010

Functions in r4ss (1.10)

plot many quantities related to output from Stock Synthesis

SSplotTimeseries

Plot timeseries data

Summarize the output from multiple Stock Synthesis models.

rich.colors.short

Make a vector of colors.

Plot biology related quantities.

R tools for Stock Synthesis

Create a bubble plot.

Split apart bootstrap data to make input file.

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

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

Plot tagging data and fits

Make files and set up folders for simulations

update_r4ss_files

Updates r4ss files to newest versions on web.

Make plots from Rebuilder program

Change parameters in the control file.

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

A function to visual parameterization of movement in Stock Synthesis

Plot selectivity

Plot catch related quantities.

Plot distributions of priors, posteriors, and estimates.

Plot yield and surplus production.

function to plot many quantities related to output from Stock Synthesis

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

Insert a vector of recruitment deviations into the control file.

Plot fit to discard fraction.

Plot numbers-at-age related data and fits.

Plot recruitment deviations

Create multi-figure plots.

Plot points with confidence intervals.

Plot mean weight data and fits.

Run a likelihood profile in Stock Synthesis.

Run a collection of simulations for Stock Synthesis.

Get output from multiple Stock Synthesis models.

a function for drawing selecitivity curves

Plot indices of abundance and associated quantities.

SSplotSpawnrecruit

Plot spawner-recruit curve.

Get parameter lines from Stock Synthesis control file

Plot composition data and fits.

Estimate bias adjustment for recruitment deviates

Make shaded polygons with a mountain-like appearance

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

Plot SPR quantities.