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Open Sustainable Technology

A curated list of open technology projects to sustain a stable climate, energy supply, biodiversity and natural resources.

r4ss

A fisheries stock assessment model written by Rick Methot.
https://github.com/r4ss/r4ss

Category: Biosphere
Sub Category: Marine Life and Fishery

Keywords

fisheries fisheries-stock-assessment r rstats stock-synthesis

Keywords from Contributors

stock-assessment latex noaa-nsap shiny rmarkdown ecology spatial-analysis species-distribution-modelling bookdown virtual

Last synced: about 22 hours ago
JSON representation

Repository metadata

files for r4ss package

README.md

r4ss: R code for Stock Synthesis

release date
call-r-cmd-check
codecov

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There is a CRAN version of r4ss but it is out of date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

Owner metadata

GitHub Events

Total
Last Year

Committers metadata

Last synced: 6 days ago

Total Commits: 3,363
Total Committers: 60
Avg Commits per committer: 56.05
Development Distribution Score (DDS): 0.506

Commits in past year: 163
Committers in past year: 8
Avg Commits per committer in past year: 20.375
Development Distribution Score (DDS) in past year: 0.337

Name Email Commits
Ian Taylor i****r@n****v 1661
kathryn.doering k****g@n****v 421
[email protected] I****r@n****v@7****9 212
[email protected] i****r@n****v@7****9 159
e-gugliotti-NOAA e****i@n****v 135
iantaylornmfs i****s@7****9 128
kellijohnson-NOAA k****n@n****v 122
Chantel Wetzel c****l@n****v 113
[email protected] I****S@g****m@7****9 44
Nathan Vaughan n****n@n****v 42
[email protected] I****t@n****v@7****9 40
kellijohnson-NOAA k****n@n****v 40
colemonnahan m****c@u****u 23
allanhicks f****s@g****m 20
[email protected] a****S@g****m@7****9 17
[email protected] a****s@n****v@7****9 13
Sean Anderson s****n@s****a 13
James-Thorson J****q@g****m 13
MOshima-PIFSC m****a@n****v 12
Yukio Takeuchi y****i@i****m 11
github-actions[bot] 4****] 11
Jason Cope j****e@n****v 9
Chantel Wetzel c****l@n****v 8
efletcherPIFSC 3****C 6
christine.stawitz c****z@n****v 6
Watal M. Iwasaki h****l 6
Iago Mosqueira i****o@m****u 6
Allan Hicks a****s@i****t 5
[email protected] i****s@g****m@7****9 5
ahavron a****n@g****m 4
and 30 more...

Committer domains:

Issue and Pull Request metadata

Last synced: 2 days ago

Total issues: 553
Total pull requests: 472
Average time to close issues: 12 months
Average time to close pull requests: 6 days
Total issue authors: 55
Total pull request authors: 35
Average comments per issue: 2.91
Average comments per pull request: 1.41
Merged pull request: 441
Bot issues: 0
Bot pull requests: 102

Past year issues: 26
Past year pull requests: 56
Past year average time to close issues: 11 days
Past year average time to close pull requests: 7 days
Past year issue authors: 9
Past year pull request authors: 7
Past year average comments per issue: 1.96
Past year average comments per pull request: 1.59
Past year merged pull request: 49
Past year bot issues: 0
Past year bot pull requests: 5

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/r4ss/r4ss

Top Issue Authors

  • iantaylor-NOAA (288)
  • k-doering-NOAA (48)
  • kellijohnson-NOAA (45)
  • chantelwetzel-noaa (43)
  • yukio-takeuchi (14)
  • iagomosqueira (8)
  • e-perl-NOAA (8)
  • mkapur (7)
  • allanhicks (7)
  • okenk (5)
  • colemonnahan (4)
  • e-gugliotti-NOAA (4)
  • MOshima-PIFSC (4)
  • John-R-Wallace-NOAA (4)
  • shcaba (4)

Top Pull Request Authors

  • iantaylor-NOAA (127)
  • github-actions[bot] (102)
  • k-doering-NOAA (58)
  • kellijohnson-NOAA (40)
  • e-perl-NOAA (35)
  • nathanvaughan-NOAA (18)
  • e-gugliotti-NOAA (14)
  • chantelwetzel-noaa (11)
  • okenk (7)
  • iagomosqueira (6)
  • yukio-takeuchi (6)
  • heavywatal (5)
  • seananderson (5)
  • cgrandin (4)
  • colemonnahan (3)

Top Issue Labels

  • enhancement (150)
  • bug (73)
  • plots (58)
  • SS_read/SS_write (32)
  • question (30)
  • quick fix (23)
  • in progress (21)
  • output (18)
  • style/refactor (18)
  • low priority (16)
  • testing (14)
  • documentation (12)
  • epic: running models (8)
  • help wanted (7)
  • ss3_utility_functions (5)
  • open-ended (5)
  • needs testing (3)
  • duplicate (2)
  • shiny (2)
  • lots of work (2)
  • guidance (1)

Top Pull Request Labels

  • plots (15)
  • bug (12)
  • SS_read/SS_write (10)
  • enhancement (10)
  • output (9)
  • style/refactor (6)
  • documentation (5)
  • quick fix (4)
  • testing (2)
  • epic: running models (1)
  • low priority (1)
  • question (1)
  • needs testing (1)
  • workflows (1)

Package metadata

cran.r-project.org: r4ss

R Code for Stock Synthesis

  • Homepage: https://github.com/r4ss/r4ss
  • Documentation: http://cran.r-project.org/web/packages/r4ss/r4ss.pdf
  • Licenses: GPL-3
  • Latest release: 1.44.0 (published almost 3 years ago)
  • Last Synced: 2025-04-25T13:35:17.238Z (2 days ago)
  • Versions: 24
  • Dependent Packages: 3
  • Dependent Repositories: 19
  • Downloads: 370 Last month
  • Docker Downloads: 141
  • Rankings:
    • Forks count: 2.308%
    • Dependent repos count: 6.491%
    • Stargazers count: 8.677%
    • Average: 9.061%
    • Dependent packages count: 10.63%
    • Downloads: 17.197%
  • Maintainers (1)

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • coda * imports
  • corpcor * imports
  • dplyr * imports
  • forcats * imports
  • ggplot2 * imports
  • kableExtra * imports
  • lifecycle * imports
  • stringr * imports
  • tidyr * imports
  • flextable * suggests
  • ggpubr * suggests
  • gplots * suggests
  • gtools * suggests
  • knitr * suggests
  • maps * suggests
  • pso * suggests
  • reshape2 * suggests
  • rmarkdown * suggests
  • shiny * suggests
  • testthat * suggests
  • truncnorm * suggests
.devcontainer/Dockerfile docker
  • ${BASE_IMAGE} ${VARIANT} build
.github/workflows/call-calc-coverage.yml actions
.github/workflows/call-doc-and-style-r.yml actions
.github/workflows/call-r-cmd-check.yml actions
.github/workflows/call-spell-check.yml actions
.github/workflows/call-update-pkgdown.yml actions
.github/workflows/r4ss-extra-tests.yml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite

Score: 15.639301498022991