Manual

SpeciesDistributionToolkit.jl is a collection of packages for species distribution modeling and biodiversity research, for the Julia programming language. It is built and maintained by the Laboratoire d'Écologie Prédictive et Interprétable pour la Crise de la Biodiversité (ÉPIC Biodiversity).

Not just for research!

This package is now used in pipelines in BON in a Box, GEOBON's project to automate the calculation and representation of the post-2020 GBF indicators. See the BON in a Box tool page.

Installation

The package is published in the Julia general repository, and can be installed with:

import Pkg
Pkg.add("SpeciesDistributionToolkit") 

This will automatically install all the sub-packages.

Upgrades

To help with dependency management, we suggest that the compat entry in the Project.toml file of your project should be:

[compat]
SpeciesDistributionToolkit = "1"

This will ensure that all releases of the v1.x.x. series will be compatible with your project. Because the modules all internally rely on this same compatibility rule, you can get the latest releases of everything with:

import Pkg
Pkg.update() 

All version of the package that share a major version number (1 for now) will always be fully interoperable, and maintain backwards compatibility.

Contents of the manual

This section of the manual presents short capsules about getting you to achieve a simple, well-defined task. Although there is some discussion of design elements for the various packages, this is not the documentation; instead, you can think of this section as a collection of snippets to re-use to build your own analysis. The vignettes also introduce, when relevant, some variations around how to perform a given task. The documentation (and complete list of functions) for each component package is accessible through the Ecosystem tab in the navigation bar.

Most manual pages end with a list of the documentation of the most important functions used. The first two sections of the manual (use cases) are more fleshed out tutorials, that are meant to illustrate how the package works. It is not a terrible idea to read them first, and then to take a deeper dive into the more detailed explanations.

If you have a question about how to achieve a specific task, feel free to share it in the Discussion page, so we can add it to the manual.

Citation

If you use the 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

as well as

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