A Julia toolkit for species distribution data

2025 · doi:10.32942/x2405r
preprint OA: closed
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This paper presents SpeciesDistributionToolkit, a new Julia software package intended to support species distribution modeling by handling varied data types and providing an integrated programming workflow. The authors describe how the toolkit covers steps from data collection through analysis, including interfaces to add additional functionality, and they demonstrate capabilities via multiple case studies using reproducible code. A key limitation noted is not a scientific one but rather that the work is framed around software design choices (semantic versioning and modularity) rather than introducing new ecological results. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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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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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. DOI https://doi.org/10.32942/X2405R Subjects Biodiversity, Other Ecology and Evolutionary Biology

Keywords

species distribution models, biogeography, occurrence data, land use, climatic data, pseudo-absences Dates Published: 2025-02-18 11:07 Last Updated: 2025-07-18 22:11 Older Versions License CC BY Attribution 4.0 International Additional Metadata Conflict of interest statement: None Data and Code Availability Statement: All code required to reproduce the examples in the manuscript is available at https://github.com/PoisotLab/ms_sdt_software Language: English

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