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

<p align="center"> <img src="https://github.com/PoisotLab/SpeciesDistributionToolkit.jl/blob/main/structure.drawio.png?raw=true" alt="Package overview"/> </p>

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

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

Species distribution modeling

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

Occurrences Interface

This package provides a lightweight interface for occurrence data.

Pseudo-absences generation

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

GBIF API and download wrapper

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

Raster data retrieval

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

Polygon data retrieval

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

Phylopic silhouette download

This package offers a way to get silhouettes from Phylopic.

Fauxcurrences creation

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