Stock Synthesis is a fisheries stock assessment model written in ADMBby Rick Methot. The Stock Synthesis software and many other associatedmaterials are available on the NOAA Virtual Laboratory athttps://vlab.noaa.gov/web/stock-synthesis/home.The r4ss package is a collection of R functions for interacting withStock Synthesis. It is based on the original work of Ian Stewart begunaround 2005 and released as an open source R package in 2009. Thepackage has a long list of authors and has benefited from a largecommunity of users making suggestions and reporting issues.
This code comes with no warranty or guarantee of accuracy. Itmerely represents an ongoing attempt to integrate output plotting,statistics and diagnostics. It is absolutely necessary that prior to usewith a new application, the user checks the output manually to verifythat there are no plotting or statistical bugs which could incorrectlyrepresent the output files being analyzed.
The CRAN version of r4ss is out of date. For now, it is necessary toinstall the main branch directly from GitHub:
install.packages("remotes")remotes::install_github("r4ss/r4ss")Ongoing development of r4ss used to take place in the “development”branch, but now is in the “main” branch. Thus, you should no longer needto reference a branch when installing from github unless you are seekinga specific feature that hasn’t yet been merged into the main branch.
Once you have installed the r4ss package, it can be loaded using:
library(r4ss)To get notifications about r4ss, you can watch this GitHub project orfollow messages on theforums onStock Synthesis VLab. Note that to subscribe to the Stock SynthesisVLab forums, an account is required, but those without an account maystill view and post forum messages.
A basic vignette can be viewed athttps://r4ss.github.io/r4ss/vignettes/r4ss-intro-vignette.htmlor built locally on your computer using this command to install thepackage:
remotes::install_github("r4ss/r4ss", build_vignettes= TRUE)Please cite r4ss as:
Ian G. Taylor, Kathryn L. Doering, Kelli F. Johnson, Chantel R.Wetzel, Ian J. Stewart, 2021. Beyond visualizing catch-at-age models:Lessons learned from the r4ss package about software to support stockassessments, Fisheries Research, 239:105924.https://doi.org/10.1016/j.fishres.2021.105924.
SeeNEWS.md for a(not very complete) log of changes to r4ss, starting with r4ss v1.24.0from 2014. The list of commits athttps://github.com/r4ss/r4ss/commits/main provides amuch more detailed list.
Interested in contributing to r4ss? We recognize contributions comein many forms, including but not limited to code, reporting issues,creating examples and/or documentation.
We strive to follow theNMFSFisheries Toolbox Contribution Guide. We also have includedr4ss-specific code contribution information in theGit workflow pageof the r4ss wiki. Note that these are guidelines, not rules, and weare open to collaborations in other ways that may work better for you.Please feel free to reach out to us by opening an issue in thisrepository or by emailing the maintainer (callmaintainer("r4ss") in R to view the current maintainer’sname and email address).
Note that by contributing, you are expect to uphold thecode of conduct.
Please report any issues with this package by posting a new githubissue athttps://github.com/r4ss/r4ss/issues. You can also writeto Ian.Taylor@noaa.gov.
This project and everyone participating in it is governed by theNMFSFisheries Toolbox Code of Conduct. By participating, you areexpected to uphold this code. Please report unacceptable behavior tofisheries.toolbox@noaa.gov.Note that the maintainers of r4ss do not have access to this emailaccount, so unacceptable behavior of maintainers can also be reportedhere.
The NMFS Fisheries Toolbox Code of Conduct is adapted from theContributor Covenant,version 1.4, available athttps://www.contributor-covenant.org/version/1/4/code-of-conduct.html
For answers to common questions about this code of conduct, seehttps://www.contributor-covenant.org/faq