r4ss: R code for Stock Synthesis

Stock Synthesis is a fisheries stock assessment model written in ADMB by Rick Methot. The Stock Synthesis software and many other associated materials are available in the Stock Synthesis GitHub repository and other repositories under the nmfs-ost organization. The r4ss package is a collection of R functions for interacting with Stock Synthesis. It is based on the original work of Ian Stewart begun around 2005 and released as an open source R package in 2009. The package has a long list of authors and has benefited from a large community of users making suggestions and reporting issues.

This code 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

There is a CRAN version of r4ss but it is out of date (last updated in May 2022). Installing directly from github via either the {pak} package or {remotes} will get the most recent main branch which should always work with the latest version of Stock Synthesis (as well as many older versions). Sometimes one or the other of these installations doesn't work, in that case find where your R packages are stored using .libPaths(), navigate there and manually delete the previously downloaded {r4ss} package. Then, restart R and use the other installation method to download {r4ss}. This manual deletion approach may also for dependent packages if updating them is causing errors in the installation of r4ss.

# option 1: install via {pak}
install.packages("pak")
pak::pkg_install("r4ss/r4ss")

# option 2: install via {remotes}
install.packages("remotes")
remotes::install_github("r4ss/r4ss")

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 or follow issues and discussions in the Stock Synthesis GitHub repository. Additionally, you can follow messages on the forums on Stock Synthesis VLab, however, most communications about Stock Synthesis are distributed via GitHub rather than VLab. Note that to subscribe to the Stock Synthesis VLab forums, an account is required, but those without an account may still view and post forum messages.

The r4ss website https://r4ss.github.io/r4ss includes a vignette explaining the use of common functions and example r4ss plots from a 2019 Big Skate stock assessment for the U.S. West Coast (which used SS version 3.30.13.02 and r4ss version 1.39.0).

Citing r4ss

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 stock assessments, Fisheries Research, 239:105924. https://doi.org/10.1016/j.fishres.2021.105924.

Changes

See NEWS.md for a (not very complete) log of changes to r4ss, starting with r4ss v1.24.0 from 2014. The list of commits at https://github.com/r4ss/r4ss/commits/main provides a much more detailed list.

Contributing to r4ss

Interested in contributing to r4ss? We recognize contributions come in many forms, including but not limited to code, reporting issues, creating examples and/or documentation.

We strive to follow the NMFS Fisheries Toolbox Contribution Guide. We also have included r4ss-specific code contribution information in the Git workflow page of the r4ss wiki. Note that these are guidelines, not rules, and we are 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 this repository or by emailing the maintainer (call maintainer("r4ss") in R to view the current maintainer's name and email address).

Note that by contributing, you are expect to uphold the code of conduct.

Reporting problems

Please report any issues with this package by posting a new github issue at https://github.com/r4ss/r4ss/issues. You can also write to [email protected].

Code of conduct

This project and everyone participating in it is governed by the NMFS Fisheries Toolbox Code of Conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to [email protected]. Note that the maintainers of r4ss do not have access to this email account, so unacceptable behavior of maintainers can also be reported here.

The NMFS Fisheries Toolbox Code of Conduct is adapted from the Contributor Covenant, version 1.4, available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html

For answers to common questions about this code of conduct, see https://www.contributor-covenant.org/faq