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.
Important links
- Stock Synthesis version 3.04B is available for download at http://nft.nefsc.noaa.gov
- Anyone unfamiliar with R can learn more here: http://www.r-project.org
- The R code is now in a package which can be installed within R using
- 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
Within this site, there is documentation of the main two functions, SSv3_output and SSv3_plots, on the Documentation page. 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. You can also click the "updates" link above to see a list of past changes to the code and this website. Note that this is different from getting added as a project member on this site.
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.
Disclaimer
This website was prepared by Dr. Ian Taylor under award NA17RJ1232 from NOAA Fisheries, Department of Commerce. The statements, findings,conclusions and recommendations are those of the authors and do not necessarily reflect the views of NOAA Fisheries or the U.S. Department of Commerce.
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.
