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Open Sustainable Technology

FIMS

A software system designed and architected to support next-generation fisheries stock assessment, ecosystem, and socioeconomic modeling.
https://github.com/noaa-fims/fims

Category: Biosphere
Sub Category: Marine Life and Fishery

Keywords

noaa-nsap r-package stock-assessment

Keywords from Contributors

fisheries fisheries-stock-assessment stock-synthesis transform optimizers measurements composibility latex interpreter report

Last synced: about 19 hours ago
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Repository metadata

The repository for development of FIMS

README.md

FIMS status badge
R-CMD-check badge
Codecov test coverage
Lifecycle: experimental

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. Our software is currently operational for estimation purposes and we plan for it to be operational for management in late 2025.

Installing FIMS

A precompiled version of the latest release of FIMS is available from R universe by running the following code within R:

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

Users can also compile it themselves, like any other TMB package by running devtools::install_github("NOAA-FIMS/FIMS"). This workflow allows for the specification of a particular branch or tag using the ref argument.

Developers who are interested in building FIMS can clone this repository, e.g., git clone https://github.com/NOAA-FIMS/FIMS.git and build it with devtools::install(), which builds the package from the cloned files and installs the R library. Installing with devtools::load_all() is not recommended because it uses shim files for things like system.file(), which can cause FIMS to not function as expected. For example, if you try to optimize the same model twice, you will more than likely not get estimates of uncertainty from the second model run. Additionally, devtools::load_all() adds the debugger flag -O0 -g which leads to Windows users seeing Fatal error: can't write <xxx> bytes to section .text of FIMS.o: 'file too big. Thus, Windows users need to run withr::local_options(pkg.build_extra_flags = FALSE) at the beginning of every R session before calling devtools::load_all(). If you want to compile FIMS with the debugger turned on you will need to run the {withr} function in addition to manually modifying the call to PKG_CXXFLAGS in the Makevars.win file in src to PKG_CXXFLAGS = -DTMB_MODEL -DTMB_EIGEN_DISABLE_WARNINGS -O1 -g. For a list of development tools needed to build, test, and document FIMS see the on- and off-boarding repository for NOAA Fisheries Office of Science & Technology.

Getting Help

If you encounter a clear 🐛, please file an Issue with a minimal reproducible example on GitHub. If you are uncertain if you have actually encountered a 🐛, are looking for more information, or want to talk about some new ideas please use the Discussion Board to post your thoughts. Users, developers, lurkers, and anyone else interested in our project are welcome to join the discussions, this 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. Also, feel free to introduce yourself 👋 on the FIMS Discussion Board.

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

Issue Authors

Issue Contributors

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.

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

Owner metadata

GitHub Events

Total
Last Year

Committers metadata

Last synced: 4 days ago

Total Commits: 1,372
Total Committers: 27
Avg Commits per committer: 50.815
Development Distribution Score (DDS): 0.71

Commits in past year: 127
Committers in past year: 16
Avg Commits per committer in past year: 7.938
Development Distribution Score (DDS) in past year: 0.48

Name Email Commits
Christine Stawitz - NOAA 4****A 398
Bai Li b****i@n****v 217
Andrea-Havron-NOAA a****n@n****v 215
Matthew-Supernaw-NOAA m****w@n****v 155
Kathryn Doering k****g@n****v 114
kellijohnson-NOAA k****n@n****v 95
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
Abhinav Kumar a****3@g****m 2
KyleShertzer-NOAA 8****A 2
alexjensen-NOAA 1****A 2
dependabot[bot] 4****] 2
timjmiller t****r@n****v 2
Eric Ward 5****a 1
Mark C m****n@u****u 1
Ricardo Yin y****6@g****m 1
Srajal Dwivedi 9****d 1
Srajal Dwivedi s****3@g****m 1
Kelli.Johnson 1****2@m****l 1
Bai.Li B****i@n****l 1
e-perl-NOAA e****i@n****v 1

Committer domains:

Issue and Pull Request metadata

Last synced: 4 days ago

Total issues: 345
Total pull requests: 451
Average time to close issues: 5 months
Average time to close pull requests: 8 days
Total issue authors: 21
Total pull request authors: 25
Average comments per issue: 3.52
Average comments per pull request: 2.8
Merged pull request: 260
Bot issues: 1
Bot pull requests: 33

Past year issues: 93
Past year pull requests: 307
Past year average time to close issues: about 2 months
Past year average time to close pull requests: 6 days
Past year issue authors: 13
Past year pull request authors: 23
Past year average comments per issue: 2.08
Past year average comments per pull request: 2.55
Past year merged pull request: 148
Past year bot issues: 1
Past year bot pull requests: 33

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

Top Issue Authors

  • kellijohnson-NOAA (73)
  • ChristineStawitz-NOAA (64)
  • Andrea-Havron-NOAA (61)
  • Bai-Li-NOAA (58)
  • k-doering-NOAA (34)
  • msupernaw (15)
  • JaneSullivan-NOAA (10)
  • iantaylor-NOAA (5)
  • nathanvaughan-NOAA (5)
  • Cole-Monnahan-NOAA (4)
  • awilnoaa (4)
  • KyleShertzer-NOAA (2)
  • MOshima-PIFSC (2)
  • github-actions[bot] (1)
  • Ovec8hkin (1)

Top Pull Request Authors

  • kellijohnson-NOAA (111)
  • ChristineStawitz-NOAA (78)
  • Bai-Li-NOAA (67)
  • Andrea-Havron-NOAA (46)
  • k-doering-NOAA (40)
  • github-actions[bot] (17)
  • dependabot[bot] (16)
  • msupernaw (12)
  • Srajald (10)
  • nathanvaughan-NOAA (8)
  • abhinav-1305 (8)
  • iantaylor-NOAA (6)
  • MOshima-PIFSC (6)
  • JonBrodziak (4)
  • JaneSullivan-NOAA (4)

Top Issue Labels

  • kind: refactor (80)
  • status: triage_needed (71)
  • status: in progress (31)
  • kind: documentation (28)
  • P3 (26)
  • kind: bug (26)
  • attribute: low hanging 🍎 (25)
  • status: needs discussion (25)
  • P1 (20)
  • theme: NLL refactor (20)
  • theme: code cleanup (19)
  • kind: test case (18)
  • kind: question (18)
  • P2 (18)
  • kind: feature (17)
  • low hanging 🍎 (10)
  • attribute: case study features (9)
  • sprint 1 (9)
  • theme: documentation (8)
  • theme: r interface (8)
  • theme: more features (6)
  • attribute: good first issue (5)
  • good first issue (5)
  • theme: pilot studies (5)
  • attribute: needs discussion (5)
  • github_actions (4)
  • dependencies (4)
  • status: in dev (4)
  • theme: R interface (4)
  • sprint 2 (3)

Top Pull Request Labels

  • auto-update (17)
  • dependencies (16)
  • github_actions (16)
  • 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)

Package metadata

proxy.golang.org: github.com/noaa-fims/fims

  • Homepage:
  • Documentation: https://pkg.go.dev/github.com/noaa-fims/fims#section-documentation
  • Licenses: gpl-3.0
  • Latest release: v0.6.3 (published 3 months ago)
  • Last Synced: 2025-10-29T20:17:31.406Z (4 days ago)
  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Rankings:
    • Dependent packages count: 5.395%
    • Average: 5.576%
    • Dependent repos count: 5.758%
proxy.golang.org: github.com/NOAA-FIMS/FIMS

  • Homepage:
  • Documentation: https://pkg.go.dev/github.com/NOAA-FIMS/FIMS#section-documentation
  • Licenses: gpl-3.0
  • Latest release: v0.6.3 (published 3 months ago)
  • Last Synced: 2025-10-29T20:17:31.430Z (4 days ago)
  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Rankings:
    • Dependent packages count: 5.395%
    • Average: 5.576%
    • Dependent repos count: 5.758%

Dependencies

DESCRIPTION cran
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  • Rcpp * imports
  • TMB >= 1.8.0 imports
  • usethis * imports
  • covr * suggests
  • testthat >= 3.0.0 suggests
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Score: -Infinity