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fims

The repository for development of FIMS

https://github.com/noaa-fims/fims

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    12 of 24 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.1%) to scientific vocabulary

Keywords

noaa-nsap r-package stock-assessment

Keywords from Contributors

fisheries stock-synthesis fisheries-stock-assessment interpretability standardization animal hack autograder report
Last synced: 6 months ago · JSON representation

Repository

The repository for development of FIMS

Basic Info
Statistics
  • Stars: 27
  • Watchers: 17
  • Forks: 19
  • Open Issues: 107
  • Releases: 12
Topics
noaa-nsap r-package stock-assessment
Created about 4 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License

README.md

<!-- badges: start --> FIMS status badge R-CMD-check Codecov test coverage Lifecycle: experimental <!-- badges: end -->

Overview

The NOAA Fisheries Integrated Modeling System (FIMS) is a software system designed to support next-generation fisheries stock assessment, ecosystem, and socioeconomic modeling. A team of experts within NOAA Fisheries is designing and developing the system, and we are advised by the FIMS Council, which includes academic, industry, and international partners. The roles of internal and external collaborators are outlined in the governance section of our Developer Guide. Our software is currently operational for estimation purposes and we plan for it to be operational for management in late 2025.

Users and developers are welcome to submit ideas or questions using the GitHub Discussion Board and bug reports using GitHub Issues. The Discussion Board is a place for all members of the assessment and open-source software community to ask and answer questions, share updates, have open-ended conversations, and follow along on decisions affecting FIMS. If you happen to find a bug, please report it in the appropriate repository, for example use issues in the collaborative workflow repository to make suggestions about the developer guide and issues in the FIMS repository for bugs in the software design.

Installing FIMS

Install the latest precompiled version of FIMS from R universe within R using the following code:

r install.packages("FIMS", repos = c("https://noaa-fims.r-universe.dev", "https://cloud.r-project.org"))

Or, you can follow the instructions in the Collaborative Workflow to install FIMS from GitHub or a local clone.

Getting Help

Please report bugs along with a minimal reproducible example on the FIMS GitHub Issues page.

Code of Conduct

All contributors participating and contributing to the FIMS project are expected to adhere to the FIMS Code of Conduct.

Contributors

All contributions to this project are gratefully acknowledged using the allcontributors package following the all-contributors specification. Contributions of any kind are welcome!

Code


ChristineStawitz-NOAA
Andrea-Havron-NOAA
Bai-Li-NOAA
msupernaw
k-doering-NOAA
kellijohnson-NOAA
nathanvaughan-NOAA

JaneSullivan-NOAA
JonBrodziak
MOshima-PIFSC
iantaylor-NOAA
timjmiller
jimianelli
peterkuriyama-NOAA

KyleShertzer-NOAA
mciechanumich
RicardoYin01
Srajald
alexjensen-NOAA

Issue Authors


Cole-Monnahan-NOAA
Andrea-Havron
Ovec8hkin
cmlegault
arni-magnusson
Schiano-NOAA

Issue Contributors


chantelwetzel-noaa
Rick-Methot-NOAA
Huihualee-NOAA
EJDick-NOAA
jimianelli-NOAA
Craig44
James-Thorson-NOAA

kristanblackhart-NOAA
jbigman-NOAA
N-DucharmeBarth-NOAA
rklasky
cgrandin
e-perl-NOAA

NOAA Disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an 'as is' basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.

Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. section 105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.

NOAA Fisheries

U.S. Department of Commerce | National Oceanographic and Atmospheric Administration | NOAA Fisheries

Owner

  • Name: NOAA-FIMS
  • Login: NOAA-FIMS
  • Kind: organization

GitHub Events

Total
  • Fork event: 9
  • Create event: 176
  • Commit comment event: 21
  • Release event: 7
  • Issues event: 122
  • Watch event: 9
  • Delete event: 166
  • Member event: 1
  • Issue comment event: 720
  • Push event: 959
  • Pull request event: 274
  • Pull request review comment event: 303
  • Pull request review event: 357
Last Year
  • Fork event: 9
  • Create event: 176
  • Commit comment event: 21
  • Release event: 7
  • Issues event: 122
  • Watch event: 9
  • Delete event: 166
  • Member event: 1
  • Issue comment event: 720
  • Push event: 959
  • Pull request event: 274
  • Pull request review comment event: 303
  • Pull request review event: 357

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 1,333
  • Total Committers: 24
  • Avg Commits per committer: 55.542
  • Development Distribution Score (DDS): 0.701
Past Year
  • Commits: 88
  • Committers: 13
  • Avg Commits per committer: 6.769
  • Development Distribution Score (DDS): 0.489
Top Committers
Name Email Commits
Christine Stawitz - NOAA 4****A 398
Andrea-Havron-NOAA a****n@n****v 214
Bai Li b****i@n****v 206
Matthew-Supernaw-NOAA m****w@n****v 155
Kathryn Doering k****g@n****v 112
kellijohnson-NOAA k****n@n****v 74
github-actions[bot] 4****] 68
Nathan Vaughan n****n@n****v 38
Christine.Stawitz c****z 22
Jane Sullivan j****n@n****v 13
Jon Kenton Tarsus Brodziak j****k@n****v 6
MOshima-PIFSC m****a@n****v 6
Ian Taylor i****r@n****v 4
peterkuriyama-NOAA 1****A 3
timjmiller t****r@n****v 2
alexjensen-NOAA 1****A 2
KyleShertzer-NOAA 8****A 2
Abhinav Kumar a****3@g****m 2
Mark C m****n@u****u 1
Ricardo Yin y****6@g****m 1
Srajal Dwivedi s****3@g****m 1
Kelli.Johnson 1****2@m****l 1
Bai.Li B****i@n****l 1
Srajal Dwivedi 9****d 1
Committer Domains (Top 20 + Academic)
noaa.gov: 11 umich.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 328
  • Total pull requests: 419
  • Average time to close issues: 5 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 19
  • Total pull request authors: 22
  • Average comments per issue: 3.34
  • Average comments per pull request: 2.87
  • Merged pull requests: 243
  • Bot issues: 0
  • Bot pull requests: 29
Past Year
  • Issues: 81
  • Pull requests: 292
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 7 days
  • Issue authors: 12
  • Pull request authors: 21
  • Average comments per issue: 1.64
  • Average comments per pull request: 2.83
  • Merged pull requests: 142
  • Bot issues: 0
  • Bot pull requests: 29
View more stats
Top Authors
Issue Authors
  • kellijohnson-NOAA (67)
  • ChristineStawitz-NOAA (64)
  • Andrea-Havron-NOAA (60)
  • Bai-Li-NOAA (54)
  • k-doering-NOAA (34)
  • msupernaw (14)
  • JaneSullivan-NOAA (10)
  • iantaylor-NOAA (5)
  • nathanvaughan-NOAA (5)
  • Cole-Monnahan-NOAA (4)
  • KyleShertzer-NOAA (2)
  • MOshima-PIFSC (2)
  • Ovec8hkin (1)
  • peterkuriyama-NOAA (1)
  • JonBrodziak (1)
Pull Request Authors
  • kellijohnson-NOAA (97)
  • ChristineStawitz-NOAA (78)
  • Bai-Li-NOAA (62)
  • Andrea-Havron-NOAA (43)
  • k-doering-NOAA (40)
  • github-actions[bot] (17)
  • dependabot[bot] (12)
  • msupernaw (12)
  • Srajald (10)
  • nathanvaughan-NOAA (8)
  • abhinav-1305 (8)
  • MOshima-PIFSC (6)
  • iantaylor-NOAA (5)
  • JonBrodziak (4)
  • JaneSullivan-NOAA (4)
Top Labels
Issue Labels
status: triage_needed (75) kind: refactor (69) kind: bug (29) P3 (28) status: needs discussion (24) status: in progress (23) kind: documentation (22) P2 (21) theme: NLL refactor (21) attribute: low hanging 🍎 (20) theme: code cleanup (20) kind: feature (19) P1 (17) kind: question (17) kind: test case (12) low hanging 🍎 (10) theme: documentation (10) sprint 1 (9) theme: r interface (9) attribute: case study features (8) theme: more features (6) attribute: good first issue (5) theme: pilot studies (5) attribute: needs discussion (5) theme: R interface (4) status: help wanted (3) kind: vignette (3) good first issue (3) sprint 2 (3) status: wishlist (3)
Pull Request Labels
auto-update (17) dependencies (12) github_actions (12) kind: documentation (12) theme: code cleanup (11) P3 (11) kind: refactor (10) kind: bug (10) theme: documentation (6) theme: R interface (6) kind: feature (4) status: in progress (3) attribute: low hanging 🍎 (2) theme: more features (2) vignette (1)

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 20
proxy.golang.org: github.com/NOAA-FIMS/FIMS
  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/noaa-fims/fims
  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.4 depends
  • Rcpp * imports
  • TMB >= 1.8.0 imports
  • usethis * imports
  • covr * suggests
  • testthat >= 3.0.0 suggests
.github/workflows/build-deploy-doxygen.yml actions
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.github/workflows/build-doxygen.yml actions
  • actions/checkout v3 composite
.github/workflows/pr-checklist.yml actions
  • actions/checkout v3 composite
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.github/workflows/run-clang-format.yml actions
  • DoozyX/clang-format-lint-action v0.14 composite
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.github/workflows/run-clang-tidy.yml actions
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.github/workflows/run-googletest.yml actions
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.github/workflows/call-r-cmd-check.yml actions
.github/workflows/call-update-pkgdown.yml actions
.github/workflows/get-gtest-codecov.yml actions
  • actions/checkout v3 composite
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  • codecov/codecov-action v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite