SDT.jl

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Manual ​

SpeciesDistributionToolkit.jl is a collection of packages for species distribution modeling and biodiversity research, for the Julia programming language.

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.

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. EcoEvoRxiv. 10.32942/X2405R

Getting started ​

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

julia
import Pkg
Pkg.add("SpeciesDistributionToolkit")

This will automatically install all the sub-packages.

A note about versions (and updates)

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

toml
[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 run

julia
import Pkg
Pkg.update()

to get the latest features of each component package

Contents of the package ​

Overview of the package

The package offers a series of methods to acces data required to build species distribution models, including:

  • a wrapper around the GBIF occurrences API to access occurrence data

  • a wrapper around the Phylopic images API

  • ways to generate fake occurrences with statistical properties similar to actual occurrences

  • ways to generate pseudo-absences based on a series of heuristics

  • a simple way to represent layers as mutable objects

  • utility functions for teaching species distribution models

  • a way to collect historic and future climate and land-use data to feed into the models, pre-loaded with datasets like CHELSA, WorldClim, EarthEnv, PaleoClim, etc

  • an interface to Makie for plotting and data visualisation

  • interfaces with many different packages from the Julia ecosystem

Contents of the manual ​

This manual is split into two sections: tutorials, which are longer examples of using the full functionality of the package; and how-tos, which are shorter (and denser) summaries of how to achieve a specific task. It is a good idea to start skimming the tutorials to get a sense for what using the package feels like, and then dive into the how-to examples for specific tasks.