R code for reading and plotting output from Stock Synthesis

Stock Synthesis is a fisheries stock assessment model written in ADMB by Dr. Rick Methot at the NMFS Northwest Fisheries Science Center. The R code presented here is based on the original work of Dr. Ian Stewart, also at NWFSC, and now includes contributions from various collaborators. This code makes use of the statistical software R to analyze and plot the output from Stock Synthesis version 3. Additional developments are planned, as described in Wishlist page in the Wiki section of this website.

Installation

The R code is now in a package which can be installed within R using the commands

> install.packages("r4ss")

> library(r4ss)

After installing the package, you can use the function

> update_r4ss_files()

to have R source the latest development versions of the package files from the Source page of this website.

Note: if you have trouble installing the package, it may be that your version of R is too old. You need to update to version 2.10 (October, 2009) or later. You can check your version using the command

> version

Important links

• Stock Synthesis version 3.20 is available for download at http://nft.nefsc.noaa.gov
• Anyone unfamiliar with R can learn more here: http://www.r-project.org
• Link to CRAN r4ss site: http://cran.r-project.org/web/packages/r4ss/index.html

Documentation

A PDF file for documentation associated with the new R Package for this code is at http://cran.r-project.org/web/packages/r4ss/r4ss.pdf

The documentation on the Documentation page of this site contains some additional information, but is not up to date on function details. Additional functions are described in Documentation_part2. See the full list of informational pages using the Wiki tab above.

Keeping up to date

To sign up on an email list associated with this site, go to http://groups.google.com/group/r4ss/subscribe?hl=en. Note that this is different from becoming a project member on this site, which you are also welcome to do (see below). Click the "updates" link above to see a list of past changes to the code and this website. Once the 'r4ss' package is installed, you can source the latest files from this website (which may be newer than the package files) by running the function,

> update_r4ss_files()

Making contributions

Google Code websites require registration to make comments or add issues. To register, provide an email address and create a password at http://www.google.com/accounts/NewAccount. If you would also like to edit the documentation in the wiki or post files for download, please register first and then email Ian Taylor <Ian.Taylor -at- noaa.gov> to be added as a project member. Instructions for connecting to this code repository are in the UsingSubversion page in the wiki section of this website.

Disclaimer

This website is maintained by students and staff of the MPAM group at the School of Aquatic and Fishery Sciences, UW. Support for this project are provided by NOAA through grant NA17R1232.

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.