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SpeciesDistributionToolkit

A collection of Julia packages forming a toolkit meant to deal with species distribution data.
https://github.com/PoisotLab/SpeciesDistributionToolkit.jl

Category: Biosphere
Sub Category: Species Distribution Modeling

Keywords

bioclim biodiversity biogeography chelsa earthenv ecology species-distribution-models

Keywords from Contributors

macroecology gbif climate-change landscape-ecology arrays ecojulia geospatial-data networks landcover geotiff

Last synced: about 12 hours ago
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Repository metadata

Work with species distributions in Julia

README.md

SpeciesDistributionToolkit

🗺️ SpeciesDistributionToolkit.jl is a collection of Julia packages forming a
toolkit meant to deal with (surprise!) species distribution data.

[!TIP]
All of the packages are installed automatically, so you can simply do
import Pkg; Pkd.add("SpeciesDistributionToolkit") and get started.

Specifically, the goal of these packages put together is to provide a consistent way to handle
occurrence data, put them on a map, and make it interact with environmental
information. The package also contains a full-featured library for species distribution models.

[!IMPORTANT]
If you use this package, please cite:

Poisot, T., Bussières-Fournel, A., Dansereau, G., and Catchen, M. D. (2025). A Julia toolkit for species distribution data. Peer Community Journal 5(e101). doi: 10.24072/pcjournal.589

Dansereau, G., and Poisot, T. (2021). SimpleSDMLayers.jl and GBIF.jl: A Framework for Species Distribution Modeling in Julia. Journal of Open Source Software 6(57), 2872, doi: 10.21105/joss.02872

The up-to-date documentation for the most recent version can be found
here. It
contains tutorials showcasing the package in action, how-to guides to serve as a
quick reference, and links to the documentation for all methods in the component
packages.

[!NOTE]
🧑‍💻 To get a sense of the next steps and help with the development, see the
issues and bugs tracker.
💬 Reach out using the
Discussions
tab on this repo!

Overview

Species Distribution Toolkit

GitHub Release

This is the top-level package, and the only one you need to install explicitely.

Species distribution modeling

GitHub Release

This package provides an explainable ML series of methods to model species distribution.

Occurrences Interface

GitHub Release

This package provides a lightweight interface for occurrence data.

Pseudo-absences generation

GitHub Release

This package generates pseudo-absences based on geospatial information about the
layers and occurrence data.

GBIF API and download wrapper

GitHub Release

This package offers a wrapper on the GBIF API, as well as download functions to
retrieve data based on their DOI.

Raster data retrieval

GitHub Release

This package offers access to standard datasets like WorldClim, EarthEnv, CHELSA, etc.

Polygon data retrieval

GitHub Release

This package offers access to standard polygon datasets like ESRI, GADM, Natural Earth, etc.

Phylopic silhouette download

GitHub Release

This package offers a way to get silhouettes from Phylopic.

Fauxcurrences creation

GitHub Release

This package offers a way to generate occurrence data with a constrained
statistical structure.

Owner metadata

GitHub Events

Total
Last Year

Committers metadata

Last synced: 5 months ago

Total Commits: 1,568
Total Committers: 13
Avg Commits per committer: 120.615
Development Distribution Score (DDS): 0.181

Commits in past year: 109
Committers in past year: 5
Avg Commits per committer in past year: 21.8
Development Distribution Score (DDS) in past year: 0.156

Name Email Commits
Timothée Poisot t****t@u****a 1284
Gabriel Dansereau g****u@u****a 175
github-actions[bot] 4****] 32
Timothée Poisot t****m@p****o 32
michael catchen m****n@g****m 18
CompatHelper Julia c****y@j****g 12
michielstock m****k@g****m 6
Michael Krabbe Borregaard m****d@s****k 4
spaette 1****e 1
rafaqz r****n@g****m 1
Jeet Sukumaran j****n 1
Daniel S. Katz d****z@i****g 1
Anshul Singhvi a****i@g****m 1

Committer domains:

Issue and Pull Request metadata

Last synced: 5 months ago

Total issues: 155
Total pull requests: 411
Average time to close issues: about 2 months
Average time to close pull requests: 7 days
Total issue authors: 6
Total pull request authors: 7
Average comments per issue: 2.75
Average comments per pull request: 1.92
Merged pull request: 274
Bot issues: 0
Bot pull requests: 120

Past year issues: 75
Past year pull requests: 207
Past year average time to close issues: 5 days
Past year average time to close pull requests: 3 days
Past year issue authors: 3
Past year pull request authors: 5
Past year average comments per issue: 0.39
Past year average comments per pull request: 2.53
Past year merged pull request: 146
Past year bot issues: 0
Past year bot pull requests: 37

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

Top Issue Authors

  • tpoisot (134)
  • gottacatchenall (13)
  • gabrieldansereau (5)
  • KristofferC (1)
  • asinghvi17 (1)
  • JuliaTagBot (1)

Top Pull Request Authors

  • tpoisot (256)
  • github-actions[bot] (120)
  • gottacatchenall (28)
  • gabrieldansereau (3)
  • asinghvi17 (2)
  • jeetsukumaran (1)
  • spaette (1)

Top Issue Labels

  • effort:low (33)
  • 🏖️ low effort (25)
  • priority:high (24)
  • bug (20)
  • priority:medium (18)
  • ❇️ SimpleSDMPolygons (15)
  • 🚨 priority (15)
  • component:SimpleSDMLayers (15)
  • component:SDeMo (14)
  • domain:documentation (11)
  • effort:medium (11)
  • new feature (11)
  • priority:low (10)
  • domain:datasets (8)
  • component:SimpleSDMDatasets (8)
  • 📚 documentation (8)
  • 🧠 SDeMo (8)
  • effort:high (7)
  • triage (7)
  • good first issue (7)
  • component:Phylopic (7)
  • 📦 SDT (7)
  • 💾 SimpleSDMDatasets (6)
  • 👾 external (6)
  • 🐾 OccurrencesInterface (5)
  • 🗺️ SimpleSDMLayers (4)
  • component:GBIF (4)
  • domain:external API (4)
  • domain:plotting (3)
  • ⁉️ triage (3)

Top Pull Request Labels

  • domain:documentation (7)
  • new feature (6)
  • component:SDeMo (5)
  • bug (4)
  • priority:high (4)
  • component:SimpleSDMLayers (3)
  • effort:medium (2)
  • component:SimpleSDMDatasets (2)
  • domain:external API (2)
  • domain:datasets (2)
  • component:Phylopic (1)
  • component:GBIF (1)
  • effort:low (1)
  • domain:tests (1)
  • component:Fauxcurrences (1)
  • 📚 documentation (1)

Package metadata

proxy.golang.org: github.com/PoisotLab/SpeciesDistributionToolkit.jl

proxy.golang.org: github.com/poisotlab/speciesdistributiontoolkit.jl

juliahub.com: SDeMo

Work with species distributions in Julia

  • Homepage: https://poisotlab.github.io/SpeciesDistributionToolkit.jl/
  • Documentation: https://docs.juliahub.com/General/SDeMo/stable/
  • Licenses: MIT
  • Latest release: 1.5.2 (published 8 months ago)
  • Last Synced: 2025-10-29T20:14:08.409Z (5 months ago)
  • Versions: 25
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 17 Total
  • Rankings:
    • Dependent repos count: 3.227%
    • Downloads: 3.317%
    • Average: 7.617%
    • Dependent packages count: 16.308%
juliahub.com: OccurrencesInterface

Work with species distributions in Julia

  • Homepage: https://poisotlab.github.io/SpeciesDistributionToolkit.jl/
  • Documentation: https://docs.juliahub.com/General/OccurrencesInterface/stable/
  • Licenses: MIT
  • Latest release: 1.2.1 (published 10 months ago)
  • Last Synced: 2025-10-29T20:14:04.764Z (5 months ago)
  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 55 Total
  • Rankings:
    • Dependent repos count: 3.227%
    • Downloads: 3.669%
    • Average: 7.735%
    • Dependent packages count: 16.308%
juliahub.com: SimpleSDMLayers

Work with species distributions in Julia

  • Homepage: https://poisotlab.github.io/SpeciesDistributionToolkit.jl/
  • Documentation: https://docs.juliahub.com/General/SimpleSDMLayers/stable/
  • Licenses: MIT
  • Latest release: 1.3.2 (published 9 months ago)
  • Last Synced: 2025-10-29T20:14:14.474Z (5 months ago)
  • Versions: 50
  • Dependent Packages: 3
  • Dependent Repositories: 0
  • Downloads: 83 Total
  • Rankings:
    • Dependent repos count: 9.94%
    • Average: 13.266%
    • Dependent packages count: 16.592%
juliahub.com: GBIF

Work with species distributions in Julia

  • Homepage: https://poisotlab.github.io/SpeciesDistributionToolkit.jl/
  • Documentation: https://docs.juliahub.com/General/GBIF/stable/
  • Licenses: MIT
  • Latest release: 1.1.1 (published 8 months ago)
  • Last Synced: 2025-10-29T20:14:07.580Z (5 months ago)
  • Versions: 21
  • Dependent Packages: 2
  • Dependent Repositories: 0
  • Downloads: 54 Total
  • Rankings:
    • Dependent repos count: 9.94%
    • Average: 20.093%
    • Forks count: 21.666%
    • Dependent packages count: 22.97%
    • Stargazers count: 25.797%
juliahub.com: SimpleSDMPolygons

Work with species distributions in Julia

  • Homepage: https://poisotlab.github.io/SpeciesDistributionToolkit.jl/
  • Documentation: https://docs.juliahub.com/General/SimpleSDMPolygons/stable/
  • Licenses: MIT
  • Latest release: 1.2.2 (published 8 months ago)
  • Last Synced: 2025-10-29T20:14:07.042Z (5 months ago)
  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 16 Total
  • Rankings:
    • Dependent repos count: 8.44%
    • Average: 22.436%
    • Dependent packages count: 36.433%
juliahub.com: Fauxcurrences

Work with species distributions in Julia

  • Homepage: https://poisotlab.github.io/SpeciesDistributionToolkit.jl/
  • Documentation: https://docs.juliahub.com/General/Fauxcurrences/stable/
  • Licenses: MIT
  • Latest release: 1.0.0 (published over 1 year ago)
  • Last Synced: 2025-10-29T20:14:04.453Z (5 months ago)
  • Versions: 6
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 14 Total
  • Rankings:
    • Dependent repos count: 9.94%
    • Average: 24.427%
    • Dependent packages count: 38.915%
juliahub.com: PseudoAbsences

Work with species distributions in Julia

  • Homepage: https://poisotlab.github.io/SpeciesDistributionToolkit.jl/
  • Documentation: https://docs.juliahub.com/General/PseudoAbsences/stable/
  • Licenses: MIT
  • Latest release: 1.0.1 (published 12 months ago)
  • Last Synced: 2025-10-29T20:14:04.232Z (5 months ago)
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 14 Total
  • Rankings:
    • Dependent repos count: 8.491%
    • Average: 26.637%
    • Stargazers count: 29.154%
    • Forks count: 32.282%
    • Dependent packages count: 36.62%
juliahub.com: Phylopic

Work with species distributions in Julia

  • Homepage: https://poisotlab.github.io/SpeciesDistributionToolkit.jl/
  • Documentation: https://docs.juliahub.com/General/Phylopic/stable/
  • Licenses: MIT
  • Latest release: 1.0.2 (published 9 months ago)
  • Last Synced: 2025-10-29T20:14:05.015Z (5 months ago)
  • Versions: 8
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 14 Total
  • Rankings:
    • Dependent repos count: 9.849%
    • Average: 37.636%
    • Dependent packages count: 38.707%
    • Stargazers count: 46.74%
    • Forks count: 55.246%
juliahub.com: SpeciesDistributionToolkit

Work with species distributions in Julia

  • Homepage: https://poisotlab.github.io/SpeciesDistributionToolkit.jl/
  • Documentation: https://docs.juliahub.com/General/SpeciesDistributionToolkit/stable/
  • Licenses: MIT
  • Latest release: 1.7.1 (published 9 months ago)
  • Last Synced: 2025-10-29T20:14:12.276Z (5 months ago)
  • Versions: 37
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 20 Total
  • Rankings:
    • Dependent repos count: 9.94%
    • Dependent packages count: 38.915%
    • Average: 43.896%
    • Forks count: 53.523%
    • Stargazers count: 73.205%
juliahub.com: SimpleSDMDatasets

Work with species distributions in Julia

  • Homepage: https://poisotlab.github.io/SpeciesDistributionToolkit.jl/
  • Documentation: https://docs.juliahub.com/General/SimpleSDMDatasets/stable/
  • Licenses: MIT
  • Latest release: 1.0.3 (published about 1 year ago)
  • Last Synced: 2025-10-29T20:14:05.197Z (5 months ago)
  • Versions: 11
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 17 Total
  • Rankings:
    • Dependent repos count: 9.94%
    • Dependent packages count: 38.915%
    • Average: 43.896%
    • Forks count: 53.523%
    • Stargazers count: 73.205%

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