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Rpath

An implementation of the Ecopath (mass-balance) and Ecosim (dynamic simulation) methods for the modeling of food webs.
https://github.com/noaa-edab/rpath

Category: Biosphere
Sub Category: Ecological and Environmental Modeling

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R implementation of the mass balance model Ecopath with Ecosim

README.md

Rpath

gitleaks
pkgdown
R-CMD-check

Package Rpath is an R/Rcpp implementation of the Ecopath (mass-balance) and Ecosim (dynamic simulation) methods for the modeling of food webs. The Rpath package includes sensitivity analysis tools, bioenergetics forcing, and the ability to
develop adaptive dynamic simulations with annual adjustment/feedback for use
in management strategy evaluations and similar analyses.

Installation

To install the package and build all of the vignettes locally

remotes::install_github("noaa-edab/Rpath",build_vignettes=TRUE)

If you experience issues installing the package using remotes or don't need the vignettes locally then please use this alternative

pak::pak("noaa-edab/Rpath")

More details

For more background, please see:

For Rpath description and methods:

Lucey, S. M., Gaichas, S. K., & Aydin, K. Y. (2020).
Conducting reproducible ecosystem modeling using the open source mass balance model Rpath.
Ecological Modelling 427(2020), 109057.
https://doi.org/10.1016/j.ecolmodel.2020.109057.

For use of Rpath for management strategy evaluations:

Lucey, S. M., Aydin, K. Y., Gaichas, S. K., Cadrin, S. X., Fay, G., Fogarty, M. J., & Punt, A. (2021).
Evaluating fishery management strategies using an ecosystem model as an operating model.
Fisheries Research 234(2021), 105780.
https://doi.org/10.1016/j.fishres.2020.105780.

For incorporation of bioenergetics into Rpath simulations:

Heinichen, M., McManus, M. C., Lucey, S. M., Aydin, K. Y., Humphries, A., Innes-Gold, A., & Collie, J. (2022).
Incorporating temperature-dependent fish bioenergetics into a Narragansett Bay food web model.
Ecological Modelling 466(2022), 109911.
https://doi.org/10.1016/j.ecolmodel.2022.109911.

For use of Rpath sensitivity tools:

Whitehouse, G.A., & Aydin, K.Y. (2020).
Assessing the sensitivity of three Alaska marine food webs to perturbations: an example of Ecosim simulations using Rpath.
Ecological Modelling 429(2020), 109074.
https://doi.org/10.1016/j.ecolmodel.2020.109074.

For original development of Ecopath and Ecosim:

Polovina, J. J. (1984).
Model of a coral reef ecosystem.
Coral Reefs 3(1), 1–11.
https://doi.org/10.1007/BF00306135.

Christensen, V., & Walters, C. J. (2004).
Ecopath with Ecosim: Methods, capabilities and limitations.
Ecological Modelling 172(2), 109–139.
https://doi.org/10.1016/j.ecolmodel.2003.09.003.

Walters, C., Pauly, D., Christensen, V., & Kitchell, J. F. (2000).
Representing Density Dependent Consequences of Life History Strategies in Aquatic Ecosystems: EcoSim II.
Ecosystems 3(1), 70–83.
https://doi.org/10.1007/s100210000011.

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.

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

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Last synced: 3 days ago

Total Commits: 1,156
Total Committers: 22
Avg Commits per committer: 52.545
Development Distribution Score (DDS): 0.537

Commits in past year: 42
Committers in past year: 3
Avg Commits per committer in past year: 14.0
Development Distribution Score (DDS) in past year: 0.452

Name Email Commits
Sean Lucey S****y@N****v 535
Ronald.Klasky r****y@n****v 327
kaydin k****m@u****u 91
andybeet 2****t 87
Andy Whitehouse a****e@n****v 28
kerim aydin k****m@uw 25
sgaichas s****s@n****v 22
Maxwell Grezlik m****k@n****v 8
Bia Dias b****s@n****v 7
unknown S****y@N****l 5
SarahJWeisberg s****g@n****v 4
Bhusson-imr 7****r 2
unknown K****n@A****l 2
Sean Lucey s****y@n****v 2
SarahJWeisberg s****g@s****u 2
Bia Dias b****s@u****u 2
Bia Dias -****s@g****m 2
Blublahh 5****h 1
Kelly Kearney k****y@g****m 1
Ronald.Klasky R****y@n****l 1
Andy Whitehouse A****e@n****l 1
Scott Large s****e 1

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Last synced: 5 days ago

Total issues: 78
Total pull requests: 67
Average time to close issues: over 1 year
Average time to close pull requests: 3 months
Total issue authors: 18
Total pull request authors: 12
Average comments per issue: 2.12
Average comments per pull request: 1.0
Merged pull request: 43
Bot issues: 0
Bot pull requests: 0

Past year issues: 5
Past year pull requests: 14
Past year average time to close issues: N/A
Past year average time to close pull requests: 1 day
Past year issue authors: 2
Past year pull request authors: 3
Past year average comments per issue: 0.0
Past year average comments per pull request: 0.36
Past year merged pull request: 8
Past year bot issues: 0
Past year bot pull requests: 0

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Top Pull Request Authors

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Top Issue Labels

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Dependencies

DESCRIPTION cran
  • MASS * imports
  • Rcpp >= 0.11.3 imports
  • data.table * imports
  • grDevices * imports
  • graphics * imports
  • stats * imports
  • utils * imports
  • knitr * suggests
  • rmarkdown * suggests
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  • actions/upload-artifact main composite
  • r-lib/actions/check-r-package v1 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
  • r-lib/actions/setup-r-dependencies v1 composite
.github/workflows/pkgdown.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite
.github/workflows/secretScan.yml actions
  • actions/checkout v2 composite
  • gitleaks/gitleaks-action v1.6.0 composite

Score: 6.982862751468943