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EcoSISTEM.jl

A Julia package that provides functionality for simulating species undergoing dynamic biological processes such as birth, death, competition and dispersal, as well as environmental changes in climate and habitat.
https://github.com/ecojulia/ecosistem.jl

Category: Biosphere
Sub Category: Ecological and Environmental Modeling

Keywords

biodiversity ecology ecosystem-simulation epidemiology julia simulation

Keywords from Contributors

control parallel simulations jacobians finite-volume unitful crop hybrid-differential-equations plant-disease symbolic-computation

Last synced: about 17 hours ago
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Repository metadata

Julia package for ecosystem simulation

README.md

EcoSISTEM

Documentation Build Status DOI
stable docs build tests JuliaNightly DOI
dev docs codecov

Package for running dynamic ecosystem simulations

Summary

EcoSISTEM (Ecosystem Simulation through Integrated Species-Trait Environment Modelling) is a Julia package that provides functionality for simulating species undergoing dynamic biological processes such as birth, death, competition and dispersal, as well as environmental changes in climate and habitat.

The package was primarily developed for global scale simulations of plant biodiversity. The underlying model for this is described in the arXiv paper arXiv:1911.12257 (q-bio.QM),
Dynamic virtual ecosystems as a tool for detecting large-scale
responses of biodiversity to environmental and land-use change.

There are substantial changes to the package introduced through the dev branch (docs), including epidemiological simulations and refactoring of the code base for further flexibility.

This package is in beta now, so please raise an issue if you find any problems. For more information on how to contribute, please read our contributing guidelines. We are supported by NERC's Landscape Decisions small and large maths grants and an EPSRC studentship.

Introduction to EcoSISTEM

You can now run through a full introduction to EcoSISTEM with Pluto.jl if you have the source of the package cloned. To get started (if you are in the root of the package):

(EcoSISTEM) pkg> activate --temp
  Activating new project at `/var/folders/fv/1rqrvwq14ssggm_gc_x4v1cw0000gq/T/jl_IFxVXO`

(jl_IFxVXO) pkg> dev .
   Resolving package versions...
    Updating `/private/var/folders/fv/1rqrvwq14ssggm_gc_x4v1cw0000gq/T/jl_IFxVXO/Project.toml`
  [ed2dc23b] + EcoSISTEM
    Updating `/private/var/folders/fv/1rqrvwq14ssggm_gc_x4v1cw0000gq/T/jl_IFxVXO/Manifest.toml`

(jl_IFxVXO) pkg> add Pluto
   Resolving package versions...
    Updating `/private/var/folders/fv/1rqrvwq14ssggm_gc_x4v1cw0000gq/T/jl_IFxVXO/Project.toml`
  [c3e4b0f8] + Pluto
  No Changes to `/private/var/folders/fv/1rqrvwq14ssggm_gc_x4v1cw0000gq/T/jl_IFxVXO/Manifest.toml`

julia> import Pluto

julia> Pluto.run()
┌ Info: 
└ Opening http://localhost:1235/?secret=xxxxxxxx in your default browser... ~ have fun!
┌ Info: 
│ Press Ctrl+C in this terminal to stop Pluto
└

This should open a Pluto window in your browser - from there you can find notebooks/Introduction.jl in the Open a notebook box. You can also test notebooks/InteractiveAfrica.jl to see an invasive species colonising Africa. Note that it may be slow on first launch as it must install packages and in the latter case download climate data from the internet. If you are using a different Julia version you may need to add a block at the start of the examples to update the manifest:

begin
    using Pkg
    Pkg.update()
end

Owner metadata

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Committers metadata

Last synced: 6 days ago

Total Commits: 1,312
Total Committers: 7
Avg Commits per committer: 187.429
Development Distribution Score (DDS): 0.311

Commits in past year: 96
Committers in past year: 3
Avg Commits per committer in past year: 32.0
Development Distribution Score (DDS) in past year: 0.031

Name Email Commits
Claire Harris c****2@r****k 904
Claire Harris c****s@b****k 223
richardreeve r****e@g****k 158
github-actions[bot] 4****] 18
CompatHelper Julia c****y@j****g 6
Adrien Morison a****n@g****m 2
nhz2 n****2@c****u 1

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Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 13
Total pull requests: 120
Average time to close issues: 8 months
Average time to close pull requests: about 2 months
Total issue authors: 4
Total pull request authors: 6
Average comments per issue: 3.62
Average comments per pull request: 1.83
Merged pull request: 86
Bot issues: 0
Bot pull requests: 49

Past year issues: 0
Past year pull requests: 7
Past year average time to close issues: N/A
Past year average time to close pull requests: 3 months
Past year issue authors: 0
Past year pull request authors: 3
Past year average comments per issue: 0
Past year average comments per pull request: 0.57
Past year merged pull request: 2
Past year bot issues: 0
Past year bot pull requests: 4

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/ecojulia/ecosistem.jl

Top Issue Authors

  • richardreeve (7)
  • claireh93 (3)
  • gottacatchenall (2)
  • JuliaTagBot (1)

Top Pull Request Authors

  • github-actions[bot] (49)
  • claireh93 (43)
  • richardreeve (25)
  • nhz2 (1)
  • amorison (1)
  • fossabot (1)

Top Issue Labels

  • bug (1)

Top Pull Request Labels

Package metadata

juliahub.com: EcoSISTEM

Julia package for ecosystem simulation

  • Homepage:
  • Documentation: https://docs.juliahub.com/General/EcoSISTEM/stable/
  • Licenses: LGPL-3.0
  • Latest release: 0.2.6 (published 24 days ago)
  • Last Synced: 2025-04-25T13:32:46.313Z (1 day ago)
  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Rankings:
    • Dependent repos count: 9.94%
    • Forks count: 19.353%
    • Stargazers count: 20.932%
    • Average: 22.285%
    • Dependent packages count: 38.915%

Dependencies

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Score: -Infinity