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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 latex noaa noaa-fisheries

Last synced: about 2 hours ago
JSON representation

Repository metadata

The repository for development of FIMS

README.md

FIMS status badge
R-CMD-check badge
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Lifecycle: experimental

Overview

FIMS is an R package for fitting integrated statistical population-dynamics models to fishery data. The back end is written in C++, and the use of Rcpp allows users to easily interact with the models using R. The package is unique because it includes multiple model types, e.g., surplus production and catch-at-age models. This reduces the burden of learning a new framework when exploring major changes in model structure. Stay tuned for the addition of even more model types.

If you are new to FIMS, the best place to start is the "Introducing FIMS" vignette.

Ask DeepWiki

Installation

A precompiled version of the latest release is available from the instance of R universe hosted by NOAA Fisheries Integrated Toolbox. You can install the latest version from GitHub.

# Install the pre-compiled version of the latest release
install.packages(
  "FIMS",
  repos = c(
    "https://noaa-fisheries-integrated-toolbox.r-universe.dev",
    "https://cloud.r-project.org"
  )
)

# Compile and install it yourself, where you can specify the branch
pak::pak("NOAA-FIMS/FIMS@main")

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 src/Makevars.win file to include -O1 -g.

A comprehensive list of all the tools needed to build, test, and document FIMS can be found here. Additionally, information on best practices regarding how to install each requirement can be found on the NOAA Fisheries Office of Science and Technology on- and off-boarding repository.

Cheatsheet

Usage

library(FIMS)
# Load sample data
data("data_big")
# Prepare data for FIMS model
data_4_model <- FIMSFrame(data_big)

# Create parameters
parameters <- data_4_model |>
  create_default_configurations() |>
  create_default_parameters(data = data_4_model)

# Run the  model with optimization
fit <- parameters |>
  initialize_fims(data = data_4_model) |>
  fit_fims(optimize = TRUE)
# Clear memory post-run
clear()

Troubleshooting

If you encounter a 🐛, please file an Issue with a minimal reproducible example on GitHub.

If you are uncertain that 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. Anyone interested in our project is 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. Please introduce yourself 👋 on the Introduction Discussion.

More information can be found on the NOAA-FIMS website, particularly on our blog.

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 Oceanic and Atmospheric Administration | NOAA Fisheries

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Last synced: 1 day ago

Total Commits: 1,592
Total Committers: 37
Avg Commits per committer: 43.027
Development Distribution Score (DDS): 0.75

Commits in past year: 259
Committers in past year: 22
Avg Commits per committer in past year: 11.773
Development Distribution Score (DDS) in past year: 0.587

Name Email Commits
Christine Stawitz - NOAA 4****A 398
Bai Li b****i@n****v 234
Andrea-Havron-NOAA a****n@n****v 228
kellijohnson-NOAA k****n@n****v 181
Matthew-Supernaw-NOAA m****w@n****v 163
Kathryn Doering k****g@n****v 115
github-actions[bot] 4****] 70
Nathan Vaughan n****n@n****v 43
Christine.Stawitz c****z 22
copilot-swe-agent[bot] 1****t 21
dependabot[bot] 4****] 16
Jane Sullivan j****n@n****v 13
Eshaan e****a@g****m 13
Elizabeth Perl e****i@n****v 8
Dr. Wilson 1****a 8
Szu-Yun s****n@n****m 7
Jon Kenton Tarsus Brodziak j****k@n****v 6
MOshima-PIFSC m****a@n****v 6
Ian Taylor i****r@n****v 6
Elizabeth Perl e****l@n****v 4
Rohith-1717 d****p@g****m 4
Eric Ward 5****a 3
alexjensen-NOAA 1****A 3
peterkuriyama-NOAA 1****A 3
timjmiller t****r@n****v 2
KyleShertzer-NOAA 8****A 2
Aman Raj s****0@g****m 2
Abhinav Kumar a****3@g****m 2
Lukas Novotny l****o@l****z 1
Mark C m****n@u****u 1
and 7 more...

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Issue and Pull Request metadata

Last synced: about 16 hours ago

Total issues: 366
Total pull requests: 486
Average time to close issues: 5 months
Average time to close pull requests: 8 days
Total issue authors: 26
Total pull request authors: 32
Average comments per issue: 3.55
Average comments per pull request: 2.97
Merged pull request: 269
Bot issues: 1
Bot pull requests: 42

Past year issues: 38
Past year pull requests: 74
Past year average time to close issues: about 1 month
Past year average time to close pull requests: 6 days
Past year issue authors: 11
Past year pull request authors: 17
Past year average comments per issue: 2.16
Past year average comments per pull request: 3.36
Past year merged pull request: 30
Past year bot issues: 1
Past year bot pull requests: 13

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

Top Issue Authors

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  • Andrea-Havron-NOAA (65)
  • ChristineStawitz-NOAA (64)
  • Bai-Li-NOAA (63)
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Top Pull Request Authors

  • kellijohnson-NOAA (115)
  • ChristineStawitz-NOAA (78)
  • Bai-Li-NOAA (70)
  • Andrea-Havron-NOAA (48)
  • k-doering-NOAA (40)
  • github-actions[bot] (25)
  • dependabot[bot] (17)
  • msupernaw (14)
  • Srajald (10)
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  • MOshima-PIFSC (6)
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  • e-perl-NOAA (4)
  • JaneSullivan-NOAA (4)

Top Issue Labels

  • kind: refactor (83)
  • status: triage_needed (77)
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  • status: needs discussion (27)
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  • P3 (26)
  • attribute: low hanging 🍎 (25)
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  • P1 (20)
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  • theme: more features (6)
  • good first issue (6)
  • attribute: needs discussion (5)
  • theme: pilot studies (5)
  • attribute: good first issue (5)
  • status: in dev (4)
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  • kind: vignette (3)

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  • kind: refactor (10)
  • theme: R interface (6)
  • theme: documentation (6)
  • kind: feature (4)
  • status: in progress (3)
  • theme: more features (2)
  • attribute: low hanging 🍎 (2)
  • status: needs discussion (1)
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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: v0.9.4 (published 13 days ago)
  • Last Synced: 2026-08-11T12:06:30.284Z (about 2 hours ago)
  • Versions: 19
  • 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: v0.9.4 (published 13 days ago)
  • Last Synced: 2026-08-11T12:06:30.384Z (about 2 hours ago)
  • Versions: 19
  • 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
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Score: -Infinity