R Code for Stock Synthesis

A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks.


r4ss

Stock Synthesis is a fisheries stock assessment model written in ADMB by Dr. Rick Methot at the NOAA Northwest Fisheries Science Center. The R code in the r4ss package is based on the original work of Dr. Ian Stewart begun around 2005 and released as an open source R package on CRAN in 2009. The package has benefited from contributions, suggestions, and bug reports from many collaborators and users.

Code available on this website comes with no warranty or guarantee of accuracy. It merely represents an ongoing attempt to integrate output plotting, statistics and diagnostics. It is absolutely necessary that prior to use with a new application, the user checks the output manually to verify that there are no plotting or statistical bugs which could incorrectly represent the output files being analyzed.

Installation

The latest r4ss version on CRAN can be installed using a command like

install.packages("r4ss")

To get notifications about r4ss, you can watch this GitHub project and/or join the r4ss email list: https://groups.google.com/forum/#!forum/r4ss

Additional information about r4ss at the old Google Code page, https://code.google.com/p/r4ss/, will be migrated over to GitHub in the future.

More frequent enhancements and bug fixes are posted to this GitHub project. The latest version of r4ss can be installed directly from Github at any time via the devtools package in R with the following commands:

install.packages("devtools")
devtools::install_github("r4ss/r4ss")

Note: devtools will give this message: "WARNING: Rtools is required to build R packages, but is not currently installed." However, Rtools is NOT required for installing r4ss via devtools, so ignore the warning.

Once you have installed the r4ss package, it can be loaded in the regular manner:

library(r4ss)

Changes

See NEWS.md for log of changes, starting with v1.24.0.

On January 15th, 2015 and included in CRAN submission of v1.24.0, a variety of changes that were in a branch on this GitHub site have now been merged into the main code. If anything doesn't work for you, you can install an earlier version from GitHub using the devtools command:

devtools::install_github("r4ss/r4ss", ref="v1.22.1")

Changes include

  • new growth plots that facilitate comparison of mean growth to variability in growth and mean growth with maturity
  • new composition plots that show females, males, and unsexed fish in the same plot
  • automatic generation of data-weighting plots contributed by Chris Francis
  • a variety of other minor refinements

Some of these things surely won't work right for any particular model configuration. If so, please email Ian Taylor or post an "issue" on this GitHub site at https://github.com/r4ss/r4ss/issues

News

r4ss 1.24.0

  • First CRAN update since r4ss 1.22.1 in July 2014.

  • Variety of new defaults in plots

  • Help from various new contributors

  • See https://github.com/r4ss/r4ss for more detail on changes and new features

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("r4ss")

1.36.1 by Ian G. Taylor, a year ago


https://github.com/r4ss/r4ss


Report a bug at https://github.com/r4ss/r4ss/issues


Browse source code at https://github.com/cran/r4ss


Authors: Ian G. Taylor , Ian J. Stewart , Allan C. Hicks , Tommy M. Garrison , Andre E. Punt , John R. Wallace , Chantel R. Wetzel , James T. Thorson , Yukio Takeuchi , Kotaro Ono , Cole C. Monnahan , Christine C. Stawitz , Z. Teresa A'mar , Athol R. Whitten , Kelli F. Johnson , Robbie L. Emmet , Sean C. Anderson , Gwladys I. Lambert , Megan M. Stachura , Andrew B. Cooper , Andi Stephens , Neil L. Klaer , Carey R. McGilliard , Iago Mosqueira , Watal M. Iwasaki , Kathryn Doering , and Andrea M. Havron


Documentation:   PDF Manual  


GPL-3 license


Imports coda, corpcor, gdata, gplots, gtools, pso, truncnorm, kableExtra

Suggests maps, testthat, knitr, rmarkdown, shiny


Imported by ss3sim.

Suggested by MSEtool.


See at CRAN