ecosistem.jl

Julia package for ecosystem simulation

https://github.com/ecojulia/ecosistem.jl

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
✓
Academic publication links
Links to: arxiv.org, zenodo.org
✓
Committers with academic emails
4 of 7 committers (57.1%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (15.3%) to scientific vocabulary

Keywords

biodiversity ecology ecosystem-simulation epidemiology julia simulation

Keywords from Contributors

pde neural-operators pinn interpretability meshing fluxes standardization

Last synced: 4 months ago · JSON representation

Repository

Julia package for ecosystem simulation

Basic Info

Host: GitHub
Owner: EcoJulia
License: other
Language: Julia
Default Branch: main
Homepage:
Size: 30.6 MB

Statistics

Stars: 46
Watchers: 6
Forks: 8
Open Issues: 6
Releases: 13

Topics

biodiversity ecology ecosystem-simulation epidemiology julia simulation

Created almost 6 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Contributing License Codemeta Zenodo

EcoSISTEM

| Documentation | Build Status | DOI | |:-----------------:|:----------------:|:-------:| | | | | | | | |

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):

``julia (EcoSISTEM) pkg> activate --temp Activating new project at/var/folders/fv/1rqrvwq14ssggmgcx4v1cw0000gq/T/jl_IFxVXO`

(jlIFxVXO) pkg> dev . Resolving package versions... Updating `/private/var/folders/fv/1rqrvwq14ssggmgcx4v1cw0000gq/T/jlIFxVXO/Project.toml[ed2dc23b] + EcoSISTEM Updating/private/var/folders/fv/1rqrvwq14ssggmgcx4v1cw0000gq/T/jl_IFxVXO/Manifest.toml`

(jlIFxVXO) pkg> add Pluto Resolving package versions... Updating `/private/var/folders/fv/1rqrvwq14ssggmgcx4v1cw0000gq/T/jlIFxVXO/Project.toml[c3e4b0f8] + Pluto No Changes to/private/var/folders/fv/1rqrvwq14ssggmgcx4v1cw0000gq/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:

julia begin using Pkg Pkg.update() end

Owner

Name: EcoJulia
Login: EcoJulia
Kind: organization

Website: https://ecojulia.org/
Repositories: 16
Profile: https://github.com/EcoJulia

CodeMeta (codemeta.json)

{
  "@context": "https://w3id.org/codemeta/3.0",
  "type": "SoftwareSourceCode",
  "applicationCategory": "ecology",
  "codeRepository": "https://github.com/EcoJulia/EcoSISTEM.jl",
  "dateCreated": "2016-11-29",
  "dateModified": "2025-04-02",
  "datePublished": "2021-04-20",
  "description": "Package for running dynamic ecosystem simulations in Julia",
  "downloadUrl": "https://github.com/EcoJulia/EcoSISTEM.jl/archive/refs/tags/v0.2.6.tar.gz",
  "keywords": [
    "EcoJulia",
    "biodiversity",
    "ecology",
    "julia",
    "simulation"
  ],
  "license": "https://spdx.org/licenses/LGPL-3.0-or-later",
  "name": "EcoSISTEM.jl",
  "operatingSystem": [
    "Linux",
    "Windows",
    "macOS"
  ],
  "programmingLanguage": "julia",
  "version": "v0.2.6",
  "codemeta:contIntegration": {
    "id": "https://github.com/EcoJulia/EcoSISTEM.jl/actions/workflows/testing.yaml"
  },
  "continuousIntegration": "https://github.com/EcoJulia/EcoSISTEM.jl/actions/workflows/testing.yaml",
  "developmentStatus": "active",
  "issueTracker": "https://github.com/EcoJulia/EcoSISTEM.jl/issues",
  "identifier": "10.5281/zenodo.4705053",
  "referencePublication": "https://arxiv.org/abs/1911.12257",
  "readme": "https://github.com/EcoJulia/EcoSISTEM.jl/blob/main/README.md",
  "buildInstructions": "https://github.com/EcoJulia/EcoSISTEM.jl/blob/main/README.md",
  "author": [
    {
      "type": "Person",
      "givenName": "Claire",
      "familyName": "Harris",
      "id": "https://orcid.org/0000-0003-0852-2340",
      "affiliation": [
        {
          "type": "Organization",
          "name": "Biomathematics and Statistics Scotland",
          "identifier": "https://ror.org/03jwrz939"
        }
      ]
    },
    {
      "type": "Person",
      "givenName": "Richard",
      "familyName": "Reeve",
      "email": "richard.reeve@glasgow.ac.uk",
      "id": "https://orcid.org/0000-0003-2589-8091",
      "affiliation": [
        {
          "type": "Organization",
          "name": "University of Glasgow",
          "identifier": "https://ror.org/00vtgdb53"
        }
      ]
    }
  ]
}

GitHub Events

Total

Create event: 3
Commit comment event: 2
Release event: 1
Watch event: 3
Delete event: 3
Issue comment event: 3
Push event: 10
Pull request review event: 1
Pull request event: 4

Last Year

Create event: 3
Commit comment event: 2
Release event: 1
Watch event: 3
Delete event: 3
Issue comment event: 3
Push event: 10
Pull request review event: 1
Pull request event: 4

Committers

Last synced: 5 months ago

All Time

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

Past Year

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

Top Committers

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

Committer Domains (Top 20 + Academic)

cornell.edu: 1 julialang.org: 1 glasgow.ac.uk: 1 bioss.ac.uk: 1 research.gla.ac.uk: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

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 requests: 86
Bot issues: 0
Bot pull requests: 49

Past Year

Issues: 0
Pull requests: 5
Average time to close issues: N/A
Average time to close pull requests: 3 months
Issue authors: 0
Pull request authors: 3
Average comments per issue: 0
Average comments per pull request: 0.8
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 2

View more stats

Top Authors

Issue Authors

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

Pull Request Authors

github-actions[bot] (54)
claireh93 (42)
richardreeve (33)
nhz2 (2)
amorison (2)
fossabot (1)

Top Labels

Issue Labels

bug (1)

Pull Request Labels

Packages

Total packages: 3
Total downloads:
- julia 1 total

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 38

proxy.golang.org: github.com/ecojulia/ecosistem.jl

Documentation: https://pkg.go.dev/github.com/ecojulia/ecosistem.jl#section-documentation
License: other
Latest release: v0.2.6
published 9 months ago

Versions: 13
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 4 months ago

proxy.golang.org: github.com/EcoJulia/EcoSISTEM.jl

Documentation: https://pkg.go.dev/github.com/EcoJulia/EcoSISTEM.jl#section-documentation
License: other
Latest release: v0.2.6
published 9 months ago

Versions: 13
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 4 months ago

juliahub.com: EcoSISTEM

Julia package for ecosystem simulation

Documentation: https://docs.juliahub.com/General/EcoSISTEM/stable/
License: LGPL-3.0
Latest release: 0.2.6
published 9 months ago

Versions: 12
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 1 Total

Rankings

Dependent repos count: 9.9%

Forks count: 19.4%

Stargazers count: 20.9%

Average: 22.3%

Dependent packages count: 38.9%

Last synced: 4 months ago

Dependencies

.github/workflows/CompatHelper.yaml actions

julia-actions/setup-julia latest composite

.github/workflows/TagBot.yaml actions

JuliaRegistries/TagBot v1 composite

.github/workflows/docs.yaml actions

actions/checkout v2 composite
julia-actions/setup-julia v1 composite

.github/workflows/nightly.yaml actions

actions/checkout v2 composite
julia-actions/julia-buildpkg latest composite
julia-actions/julia-runtest latest composite
julia-actions/setup-julia v1 composite

.github/workflows/testing.yaml actions

actions/checkout v2 composite
codecov/codecov-action v1 composite
coverallsapp/github-action master composite
julia-actions/julia-buildpkg master composite
julia-actions/julia-processcoverage v1 composite
julia-actions/julia-runtest master composite
julia-actions/setup-julia v1 composite

.github/workflows/doc-cleanup.yaml actions

actions/checkout v4 composite