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ecostate

State-space extension of EcoPath-with-EcoSim

https://github.com/james-thorson-noaa/ecostate

Science Score: 39.0%

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    CITATION.cff file
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    DOI references
    Found 10 DOI reference(s) in README
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    Scientific vocabulary similarity
    Low similarity (11.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

State-space extension of EcoPath-with-EcoSim

Basic Info
Statistics
  • Stars: 13
  • Watchers: 13
  • Forks: 2
  • Open Issues: 3
  • Releases: 2
Created about 2 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog

README.md

EcoState

Documentation Codecov test coverage

Package ecostate fits a state-space mass-balance model EcoState intended for aquatic ecosystems, using mass-balance equations matching those from Ecopath and dynamical equations matching Ecosim. Unlike the Ecopath-with-Ecosim (EwE) package, ecostate fits both biological parameters (e.g., equilibrium biomass and predator-prey vulnerability) and measurement parameters (e.g., catchability coefficients) via fit to time-series data. ecostate also estimates additional process errors representing nonstationarity in growth efficiency, ecotrophic efficient, migration, or other unmodeled processes. These process errors allow biomass patterns to closely match available data, so that resulting consumption (and associated productivity and mortality rates) can accurately be conditioned upon any residual patterns.

Installation

ecostate can be installed from GitHub using:

r library(remotes) install_github( "James-Thorson-NOAA/ecostate" )

Or to access vignettes from your R session, please instead use:

r remotes::install_github( "James-Thorson-NOAA/ecostate", build_vignettes = TRUE ) browseVignettes("ecostate")

More details

For more background, please read:

For state-space mass-balance equilibrium and biomass-dynamic modelling

Thorson, J. Kristensen, K., Aydin, K., Gaichas, S., Kimmel, D.G., McHuron, E.A., Nielsen, J.N., Townsend, H., Whitehouse, G.A. (2025) The Benefits of Hierarchical Ecosystem Models: Demonstration Using EcoState, a New State-Space Mass-Balance Mode. Fish and Fisheries, 26(2): 203-218. https://doi.org/10.1111/faf.12874

For age-structured dynamics and bottom-up linkages to animal growth:

Thorson, J. T., Aydin, K. H., Cheng, M., Dias, B. S., Kimmel, D. G., & Kristensen, K. (2025). Bottom-up interactions in age-structured stock assessment and state-space mass-balance modelling. http://doi.org/10.1111/faf.70016

For original development of ecopath for mass-balance equilibria:

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

For development of ecosim for deterministic biomass and age-structured dynamics:

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

NOAA Enterprise GitHub 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.

Owner

  • Name: Jim Thorson
  • Login: James-Thorson-NOAA
  • Kind: user
  • Location: Seattle

GitHub Events

Total
  • Issues event: 2
  • Watch event: 4
  • Delete event: 6
  • Member event: 1
  • Issue comment event: 2
  • Push event: 47
  • Pull request event: 18
  • Fork event: 4
  • Create event: 4
Last Year
  • Issues event: 2
  • Watch event: 4
  • Delete event: 6
  • Member event: 1
  • Issue comment event: 2
  • Push event: 47
  • Pull request event: 18
  • Fork event: 4
  • Create event: 4

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 3
  • Total pull requests: 22
  • Average time to close issues: about 18 hours
  • Average time to close pull requests: 2 days
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 5.0
  • Average comments per pull request: 0.05
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 17
  • Average time to close issues: 1 day
  • Average time to close pull requests: 3 days
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.06
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • James-Thorson-NOAA (1)
  • sgaichas (1)
Pull Request Authors
  • James-Thorson-NOAA (14)
  • mcgoodman (9)
  • dendroica (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 177 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
cran.r-project.org: ecostate

State-Space Mass-Balance Model for Marine Ecosystems

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 177 Last month
Rankings
Dependent packages count: 27.7%
Dependent repos count: 34.1%
Average: 49.6%
Downloads: 87.0%
Maintainers (1)
James.Thorson@noaa.gov
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.1.0 depends
  • JABBA * enhances
  • Rpath * enhances
  • spict * enhances
  • MASS * imports
  • RTMB >= 1.5.0 imports
  • TMB * imports
  • checkmate * imports
  • ggnetwork * imports
  • ggplot2 * imports
  • intergraph * imports
  • RTMBode * suggests
  • knitr * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite