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A curated list of R packages for ecological niche modelling

Author

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  • Sillero, Neftalí
  • Campos, João Carlos
  • Arenas-Castro, Salvador
  • Barbosa, A.Márcia

Abstract

The R language provides most applications (packages) currently available for ecological niche modelling. In the last few years, these packages have increased substantially. There are now numerous packages for computing ecological niche models (ENMs) with different algorithms, comparing species niches and niche models, creating virtual species, getting and preparing species and related environmental data, filtering species records, and evaluating models, amongst other tasks. This profusion of package options may be daunting for both beginners and more experienced R users. Here we provide an organised and annotated list of available packages for each task. We present a concise history of the creation of these packages, we briefly describe what each package does, and we discuss whether the current set of R packages covers all the necessities for modelling species’ ecological niches. This list will be accessible and updated over time on a dedicated website.

Suggested Citation

  • Sillero, Neftalí & Campos, João Carlos & Arenas-Castro, Salvador & Barbosa, A.Márcia, 2023. "A curated list of R packages for ecological niche modelling," Ecological Modelling, Elsevier, vol. 476(C).
    • Handle: RePEc:eee:ecomod:v:476:y:2023:i:c:s0304380022003404
    DOI: 10.1016/j.ecolmodel.2022.110242
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    References listed on IDEAS

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    1. Sillero, Neftalí & Arenas-Castro, Salvador & Enriquez‐Urzelai, Urtzi & Vale, Cândida Gomes & Sousa-Guedes, Diana & Martínez-Freiría, Fernando & Real, Raimundo & Barbosa, A.Márcia, 2021. "Want to model a species niche? A step-by-step guideline on correlative ecological niche modelling," Ecological Modelling, Elsevier, vol. 456(C).
    2. Toni Lyn Morelli & Adam B. Smith & Amanda N. Mancini & Elizabeth A. Balko & Cortni Borgerson & Rainer Dolch & Zachary Farris & Sarah Federman & Christopher D. Golden & Sheila M. Holmes & Mitchell Irwi, 2020. "The fate of Madagascar’s rainforest habitat," Nature Climate Change, Nature, vol. 10(1), pages 89-96, January.
    3. Freeman, Elizabeth A. & Moisen, Gretchen, 2008. "PresenceAbsence: An R Package for Presence Absence Analysis," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 23(i11).
    4. Rotllan-Puig, Xavier & Traveset, Anna, 2021. "Determining the minimal background area for species distribution models: MinBAR package," Ecological Modelling, Elsevier, vol. 439(C).
    5. Sillero, Neftalí, 2011. "What does ecological modelling model? A proposed classification of ecological niche models based on their underlying methods," Ecological Modelling, Elsevier, vol. 222(8), pages 1343-1346.
    6. Baddeley, Adrian & Turner, Rolf, 2005. "spatstat: An R Package for Analyzing Spatial Point Patterns," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 12(i06).
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    1. Rodrigues, Lucas dos Santos & Daudt, Nicholas Winterle & Cardoso, Luis Gustavo & Kinas, Paul Gerhard & Conesa, David & Pennino, Maria Grazia, 2023. "Species distribution modelling in the Southwestern Atlantic Ocean: A systematic review and trends," Ecological Modelling, Elsevier, vol. 486(C).
    2. Bondo, Kristin J. & Rosenberry, Christopher S. & Stainbrook, David & Walter, W. David, 2024. "Comparing risk of chronic wasting disease occurrence using Bayesian hierarchical spatial models and different surveillance types," Ecological Modelling, Elsevier, vol. 493(C).

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