Accounting for preferential sampling in species distribution models

Pennino Maria Grazia, Paradinas Iosu, Illian Janine B., Munoz Facundo, Bellido José María, López‐Quílez Antonio, Conesa David. 2019. Accounting for preferential sampling in species distribution models. Ecology and Evolution, 9 (1) : pp. 653-663.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
Published version - Anglais
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Published version - Anglais
License Licence Creative Commons.

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Quartile : Q2, Sujet : ECOLOGY / Quartile : Q3, Sujet : EVOLUTIONARY BIOLOGY

Abstract : Species distribution models (SDM s) are now being widely used in ecology for management and conservation purposes across terrestrial, freshwater, and marine realms. The increasing interest in SDM s has drawn the attention of ecologists to spatial models and, in particular, to geostatistical models, which are used to associate observations of species occurrence or abundance with environmental covariates in a finite number of locations in order to predict where (and how much of) a species is likely to be present in unsampled locations. Standard geostatistical methodology assumes that the choice of sampling locations is independent of the values of the variable of interest. However, in natural environments, due to practical limitations related to time and financial constraints, this theoretical assumption is often violated. In fact, data commonly derive from opportunistic sampling (e.g., whale or bird watching), in which observers tend to look for a specific species in areas where they expect to find it. These are examples of what is referred to as preferential sampling , which can lead to biased predictions of the distribution of the species. The aim of this study is to discuss a SDM that addresses this problem and that it is more computationally efficient than existing MCMC methods. From a statistical point of view, we interpret the data as a marked point pattern, where the sampling locations form a point pattern and the measurements taken in those locations (i.e., species abundance or occurrence) are the associated marks. Inference and prediction of species distribution is performed using a Bayesian approach, and integrated nested Laplace approximation (INLA ) methodology and software are used for model fitting to minimize the computational burden. We show that abundance is highly overestimated at low abundance locations when preferential sampling effects not accounted for, in both a simulated example and a practical application using fishery data. This highlights that ecologists should be aware of the potential bias resulting from preferential sampling and account for it in a model when a survey is based on non‐randomized and/or non‐systematic sampling.

Mots-clés Agrovoc : Modèle mathématique, Distribution des populations, Espèce, Échantillonnage

Mots-clés complémentaires : Species distribution models (SDMs), Modélisation Bayésienne, Approximation de Laplace emboîtée intégrée (ALEI), Equation stochastique

Mots-clés libres : Bayesian modelling, Integrated nested Laplace approximation (INLA), Point processes, Species distribution models, Stochastic partial differential equations

Classification Agris : U30 - Research methods
U10 - Computer science, mathematics and statistics

Champ stratégique Cirad : CTS 7 (2019-) - Hors champs stratégiques

Agence(s) de financement européenne(s) : European Regional Development Fund

Auteurs et affiliations

  • Pennino Maria Grazia, Instituto Español de Oceanografía (ESP) - auteur correspondant
  • Paradinas Iosu, Universitat de Valencia (ESP)
  • Illian Janine B., Université de St Andrews (GBR)
  • Munoz Facundo, CIRAD-BIOS-UMR ASTRE (FRA) ORCID: 0000-0002-5061-4241
  • Bellido José María, Instituto Español de Oceanografía (ESP)
  • López‐Quílez Antonio, Universitat de Valencia (ESP)
  • Conesa David, Universitat de Valencia (ESP)

Source : Cirad-Agritrop (

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