Learn R Programming

⚠️There's a newer version (1.44.0) of this package.Take me there.

r4ss (version 1.07)

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.

Copy Link

Version

Install

install.packages('r4ss')

Monthly Downloads

611

Version

1.07

License

MIT License

Maintainer

Ian Taylor

Last Published

July 24th, 2010

Functions in r4ss (1.07)

Change parameters in the control file.

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

Estimate bias adjustment for recruitment deviates

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

Plot biology related quantities.

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

Plot points with confidence intervals.

Plot composition data and fits.

update_r4ss_files

Updates r4ss files to newest versions on web.

Plot SPR quantities.

A function to visual parameterization of movement in Stock Synthesis

Plot catch related quantities.

Plot selectivity

Plot yield and surplus production.

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

plot many quantities related to output from Stock Synthesis

Split apart bootstrap data to make input file.

function to plot many quantities related to output from Stock Synthesis

Insert a vector of recruitment deviations into the control file.

SSplotSpawnrecruit

Plot spawner-recruit curve.

Create multi-figure plots.

Run a collection of simulations for Stock Synthesis.

Plot tagging data and fits

Plot distributions of priors, posteriors, and estimates.

R tools for Stock Synthesis

Summarize the output from multiple Stock Synthesis models.

SSplotTimeseries

Plot timeseries data

Make plots from Rebuilder program

Plot numbers-at-age related data and fits.

Run a likelihood profile in Stock Synthesis.

Get output from multiple Stock Synthesis models.

Plot recruitment deviations

Get parameter lines from Stock Synthesis control file

Plot indices of abundance and associated quantities.

Plot fit to discard fraction.

rich.colors.short

Make a vector of colors.

Create a bubble plot.

Make shaded polygons with a mountain-like appearance

Make files and set up folders for simulations

a function for drawing selecitivity curves

Plot mean weight data and fits.

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