A Julia toolkit for species distribution data
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Abstract
(1) Species distribution modeling requires to handle varied types of data, and benefits from an integrated approach to programming. (2) We introduce SpeciesDistributionToolkit , a Julia package aiming to facilitate the production of species distribution models. It covers various steps of the data collection and analysis process, extending to the development of interfaces for integration of additional functionalities. (3) By relying on semantic versioning and strong design choices on modularity, we expect that this package will lead to improved reproducibility and long-term maintainability. (4) We illustrate the functionalities of the package through several case studies, accompanied by reproducible code.
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Applied researchers increasingly demand efficient and user-friendly software to conduct ever more sophisticated analyses. Scientists often face challenges when using multiple software tools for a single task, especially when trying to reconcile results from different platforms not designed to work together. This is particularly true for those studying the past, present, and future distribution of species.
Species distribution models (SDMs) have become essential tools for understanding how biodiversity is changing and for identifying strategies to mitigate negative impacts. In this context, Poisot and collaborators introduce SpeciesDistributionToolkit, a Julia meta-package that broadens the range of options available to ecologists working on species distribution analyses.
This package offers a simple yet robust solution for modeling …
Applied researchers increasingly demand efficient and user-friendly software to conduct ever more sophisticated analyses. Scientists often face challenges when using multiple software tools for a single task, especially when trying to reconcile results from different platforms not designed to work together. This is particularly true for those studying the past, present, and future distribution of species.
Species distribution models (SDMs) have become essential tools for understanding how biodiversity is changing and for identifying strategies to mitigate negative impacts. In this context, Poisot and collaborators introduce SpeciesDistributionToolkit, a Julia meta-package that broadens the range of options available to ecologists working on species distribution analyses.
This package offers a simple yet robust solution for modeling species distributions, with an emphasis on high reproducibility. It includes a suite of functions that allow users to complete their entire analysis within a single platform. Notably, it provides tools to download and processing species occurrence data from GBIF. Also the package offers alternatives to download environmental layers from sources such as WorldClim and CHELSA, whereas the range of modeling algorithms is currently more limited compared to established alternatives like Biomod2 in R. Probably for some users, the absence of common algorithms like maxent, random forests or svm could be a limitation, but it is likely that support for additional methods will expand over time.
The manuscript, supplementary materials, and package vignettes are clearly written and easy to follow. The inclusion of case studies helps to clarify how to use the various functions in practical applications.
Overall, the SpeciesDistributionToolkit package in Julia is a promising and welcome addition for researchers in conservation biology and invasion ecology, where the need for robust, scalable, and reproducible modeling tools is rapidly growing.
References
Timothée Poisot, Ariane Bussières-Fournel, Gabriel Dansereau, Michael Catchen (2025) A Julia toolkit for species distribution data. A Julia toolkit for species distribution data, ver.3 peer-reviewed and recommended by PCI Ecology https://doi.org/10.32942/X2405R
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