gbif.range - An R package to generate species range maps based on ecoregions and a user-friendly GBIF wrapper

Although species range may be obtained using expert maps or modeling methods, expert data is often species-limited and statistical models need more technical expertise as well as many species observations. When unavailable, such information may be extracted from the Global Biodiversity Information facility (GBIF), the largest public data repository inventorying georeferenced species observations worldwide. However, retrieving GBIF records at large scale may be tedious if users are unaware of specific tools and functions that need to be employed. Here we present gbif.range, an R library that contains automated methods to generate species range maps from scratch using in-house ecoregions shapefiles and an easy-to-use GBIF download wrapper. Finally, this library also offers a set of additional very useful parameters and functions for large GBIF datasets (generate doi, extract GBIF taxonomy, records filtering...). gbif.range R project

Funding Information:

This work was supported by:
  • ERC (link) (Grant/Award: 101003296)
  • SNF (Grant/Award: 310030L_170059)
  • ANR (link) (Grant/Award: ANR-16-CE93-004)

Related Datasets

Chamberlain, S., Oldoni, D., & Waller, J. (2022). rgbif: interface to the global biodiversity information facility API. doi: 10.5281/zenodo.6023735

Zizka, A., Silvestro, D., Andermann, T., Azevedo, J., Duarte Ritter, C., Edler, D., ... & Antonelli, A. (2019). CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases. Methods in Ecology and Evolution, 10(5), 744-751. doi: 10.1111/2041-210X.13152

Hijmans, Robert J. "terra: Spatial Data Analysis. R Package Version 1.6-7." (2022). CRAN repository

Olson, D. M., Dinerstein, E., Wikramanayake, E. D., Burgess, N. D., Powell, G. V. N., Underwood, E. C., D'Amico, J. A., Itoua, I., Strand, H. E., Morrison, J. C., Loucks, C. J., Allnutt, T. F., Ricketts, T. H., Kura, Y., Lamoreux, J. F., Wettengel, W. W., Hedao, P., Kassem, K. R. 2001. Terrestrial ecoregions of the world: a new map of life on Earth. Bioscience 51(11):933-938. doi: 10.1641/0006-3568(2001)051

Mark D. Spalding, Helen E. Fox, Gerald R. Allen, Nick Davidson, Zach A. Ferdaña, Max Finlayson, Benjamin S. Halpern, Miguel A. Jorge, Al Lombana, Sara A. Lourie, Kirsten D. Martin, Edmund McManus, Jennifer Molnar, Cheri A. Recchia, James Robertson, Marine Ecoregions of the World: A Bioregionalization of Coastal and Shelf Areas, BioScience, Volume 57, Issue 7, July 2007, Pages 573–583. doi: 10.1641/B570707

Robin Abell, Michele L. Thieme, Carmen Revenga, Mark Bryer, Maurice Kottelat, Nina Bogutskaya, Brian Coad, Nick Mandrak, Salvador Contreras Balderas, William Bussing, Melanie L. J. Stiassny, Paul Skelton, Gerald R. Allen, Peter Unmack, Alexander Naseka, Rebecca Ng, Nikolai Sindorf, James Robertson, Eric Armijo, Jonathan V. Higgins, Thomas J. Heibel, Eric Wikramanayake, David Olson, Hugo L. López, Roberto E. Reis, John G. Lundberg, Mark H. Sabaj Pérez, Paulo Petry, Freshwater Ecoregions of the World: A New Map of Biogeographic Units for Freshwater Biodiversity Conservation, BioScience, Volume 58, Issue 5, May 2008, Pages 403–414. doi: 10.1641/B580507

Related Publications

Oskar Hagen, Lisa Vaterlaus, Camille Albouy, Andrew Brown, Flurin Leugger, Renske E. Onstein, Charles Novaes de Santana, Christopher R. Scotese, Loïc Pellissier. (2019) Mountain building, climate cooling and the richness of cold-adapted plants in the Northern Hemisphere. Journal of Biogeography. doi: 10.1111/jbi.13653

Chauvier, Y., Thuiller, W., Brun, P., Lavergne, S., Descombes, P., Karger, D. N., ... & Zimmermann, N. E. (2021). Influence of climate, soil, and land cover on plant species distribution in the European Alps. Ecological monographs, 91(2), e01433. 10.1002/ecm.1433

Lyu, L., Leugger, F., Hagen, O., Fopp, F., Boschman, L. M., Strijk, J. S., ... & Pellissier, L. (2022). An integrated high‐resolution mapping shows congruent biodiversity patterns of Fagales and Pinales. New Phytologist, 235(2), 759-772 10.1111/nph.18158


Chauvier, Yohann; Hagen, Oskar; Albouy, Camille; Descombes, Patrice; Fopp, Fabian; Nobis, Michael P.; Brun, Philipp; Lyu, Lisha; Pellissier, Loïc; Csilléry, Katalin (2022). gbif.range - An R package to generate species range maps based on ecoregions and a user-friendly GBIF wrapper. EnviDat. doi:10.16904/envidat.352.

DataCite ISO 19139 GCMD DIF README.txt BibTex RIS

Data and Resources


Field Values
DOI 10.16904/envidat.352
Publication State Published
  • Email: yohann.chauvierfoo(at) ORCID: 0000-0001-9399-3192 Given Name: Yohann Family Name: Chauvier Affiliation: Swiss Federal Institute for Forest, Snow and Landscape Research WSL | Unit of Land Change Science DataCRediT: Software, Curation, Collection, Validation
  • Email: oskar.hagenfoo(at) ORCID: 0000-0002-7931-6571 Given Name: Oskar Family Name: Hagen Affiliation: WSL DataCRediT: Software, Curation, Collection, Validation
  • Email: albouycamillefoo(at) ORCID: 0000-0003-1629-2389 Given Name: Camille Family Name: Albouy Affiliation: ETH DataCRediT: Software, Validation, Curation
  • Email: patrice.descombesfoo(at) ORCID: 0000-0002-3760-9907 Given Name: Patrice Family Name: Descombes Affiliation: ETHZ | Department of Environmental Systems Science | Institute of Terrestrial Ecosystems | Landscape Ecology DataCRediT: Software, Validation
  • Email: fabian.foppfoo(at) ORCID: 0000-0003-0648-8484 Given Name: Fabian Family Name: Fopp Affiliation: WSL DataCRediT: Software
  • Email: michael.nobisfoo(at) ORCID: 0000-0003-3285-1590 Given Name: Michael P. Family Name: Nobis Affiliation: WSL DataCRediT: Validation
  • Email: philipp.brunfoo(at) ORCID: Given Name: Philipp Family Name: Brun Affiliation: Swiss Federal Institute for Forest, Snow and Landscape Research WSL DataCRediT: Software
  • Email: lisha.lyufoo(at) ORCID: 0000-0001-7855-8109 Given Name: Lisha Family Name: Lyu Affiliation: ETH Zürich DataCRediT: Validation
  • Email: loic.pellissierfoo(at) ORCID: 0000-0002-2289-8259 Given Name: Loïc Family Name: Pellissier Affiliation: Ecosystems and Landscape Evolution, Dep. of Environmental Systems Science, ETH Zurich DataCRediT: Supervision
  • Email: katalin.csilleryfoo(at) ORCID: 0000-0003-0039-9296 Given Name: Katalin Family Name: Csilléry Affiliation: Swiss Federal Institute for Forest, Snow and Landscape Research WSL | Unit of Land Change Science DataCRediT: Supervision
Contact Person Given Name: Yohann Family Name: Chauvier Email: yohann.chauvierfoo(at) Affiliation: Swiss Federal Institute for Forest, Snow and Landscape Research WSL | Unit of Biodiversity and Conservation Biology ORCID: 0000-0001-9399-3192
Publication Publisher: EnviDat Year: 2022
  • Type: Created Date: 2022-10-17
Version 0.2
Type software
General Type Software
Language English
Location WORLD
Content License Creative Commons Attribution Share-Alike (CC-BY-SA)    [Open Data]
Last Updated April 24, 2024, 09:01 (UTC)
Created October 24, 2022, 11:16 (UTC)