Jointly estimating spatial sampling effort and habitat suitability for multiple species from opportunistic presence-only data

Botella Christophe, Joly Alexis, Bonnet Pierre, Munoz François, Monestiez Pascal. 2021. Jointly estimating spatial sampling effort and habitat suitability for multiple species from opportunistic presence-only data. Methods in Ecology and Evolution, 12 (5) : pp. 933-945.

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Abstract : 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.

Mots-clés Agrovoc : Distribution des populations, Botanique, Participation communautaire, Participation publique, Distribution spatiale, Échantillonnage, Analyse de données, Plante sauvage

Mots-clés géographiques Agrovoc : France

Mots-clés complémentaires : science participative

Mots-clés libres : Citizen science, Multi-species data, Presence-only data, Species distribution models, Pl@ntNet

Classification Agris : F70 - Plant taxonomy and geography
U10 - Computer science, mathematics and statistics

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Auteurs et affiliations

  • Botella Christophe, INRIA (FRA) - auteur correspondant
  • Joly Alexis, INRIA (FRA)
  • Bonnet Pierre, CIRAD-BIOS-UMR AMAP (FRA) ORCID: 0000-0002-2828-4389
  • Munoz François, Université Grenoble Alpes (FRA)
  • Monestiez Pascal, INRAE (FRA)

Source : Cirad-Agritrop (

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