Jointly estimating spatial sampling effort and habitat suitability for multiple species from opportunistic presence‐only data
Open accessAbstract
Building reliable species distribution models (SDMs) from presence‐only information requires a good understanding of the spatial variation in the sampling effort. However, in most cases, the sampling effort is unknown, leading to biases in SDMs. This study proposes a method to jointly estimate the parameters of sampling effort and species densities to avoid such biases. The method is particularly suited to the analysis of massive but highly heterogeneous presence‐only data. The proposed method is based on estimating the variation in sampling effort over units of a spatial mesh in parallel with the environmental density of multiple species using a marked Poisson process model. Based on simulations with realistic settings, we examined the performance and robustness of parameter estimations. We also analysed a large‐scale citizen science dataset with highly heterogeneous sampling (Pl@ntNet), including around 300,000 occurrences of 150 plant species. We found that sampling effort was correctly estimated when the true sampling effort was constant within the cells of a spatial mesh. Estimation bias arose when sampling effort and environmental drivers strongly covaried within cells. Otherwise, the inference was correct and robust to sampling variation within cells. Running the model on real occurrences of 150 plant species provided an estimated map of relative sampling effort for 15% of French territory. We also found that the density estimated for an exotic invasive plant was consistent with prior data. This is the first method jointly estimating species densities depending on environment, and sampling effort as an explicit spatial function, from occurrence data of multiple species. An asset of the method is that a few frequently observed species greatly contribute to correctly estimate sampling effort, thereby improving density estimation of all other species. This approach can thus provide reliable SDM for large opportunistic presence‐only datasets, with broad spatial variation in sampling effort but also many species, such as datasets from citizen science programmes.
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Deep learning methods have started to be employed to model species' ecological niches, facilitated by the development of machine-learning-ready datasets such as GeoLifeCLEF.
“Recently, DL methods have also started to be employed to model species’ ecological niches82,145, facilitated by the development of machine-learning-ready datasets such as GeoLifeCLEF.”
From Perspectives in machine learning for wildlife conservation (2022) · cites this paper as [145]
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Perspectives in machine learning for wildlife conservation
Tuia, D., Kellenberger, B., Beery, S., Costelloe, B. R., Zuffi, S., Risse, B., Mathis, A., Mathis, M. W., van Langevelde, F., Burghardt, T., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-27980-y · Cited by 740 · see citing works
- Authors
- Botella, C., Joly, A., Bonnet, P., Munoz, F., & Monestiez, P.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Institut national de recherche en sciences et technologies du numérique (FR)
- Laboratoire Interdisciplinaire de Physique (FR)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Corresponding author
- Botella, Christophe
- Venue
- Methods in Ecology and Evolution
- Publisher
- Wiley
- Published
- 2021-02-16
- Volume
- 12
- Issue
- 5
- Pages
- 933-945
- ISSN
- 2041-210X (ISSN-L)
- OpenAlex
- W3127610943
- Cited by
- 17
- References
- 48
- Citations by year
- 2026: 5 · 2025: 2 · 2024: 3 · 2023: 1 · 2022: 6
- FWCI
- 10.75
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Methods in Ecology and Evolution (publishedVersion, cc-by)
- HAL (submittedVersion, cc-by)
- Agritrop (Cirad) (submittedVersion, cc-by)
- Funders
- Agence Nationale de la Recherche (ANR-18-CE02-0010)
- Topics
- Physical Sciences › Environmental Science › Ecological Modeling › Species Distribution and Climate Change
- Physical Sciences › Environmental Science › Nature and Landscape Conservation › Ecology and Vegetation Dynamics Studies
- Physical Sciences › Environmental Science › Ecology › Wildlife Ecology and Conservation
- Keywords
- habitat suitability, species distribution modeling, presence-only data, marked Poisson process, citizen science, Pl@ntNet, plant species, invasive plants, sampling bias
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