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Auteur Meynard, C.N.; Kaplan, D.
Titre Using virtual species to study species distributions and model performance Type Article scientifique
Année 2013 Publication Revue Abrégée Journal of Biogeography
Volume 40 Numéro 1 Pages 1-8
Mots-Clés Auc; predictive ecology; presence-absence; prevalence; Sensitivity; simulations; specificity; threshold; virtual species
Résumé Simulations of virtual species (i.e. species for which the environmentoccupancy relationships are known) are increasingly being used to test the effects of different aspects of modelling and sampling strategy on performance of species distribution models (SDMs). Here we discuss an important step of the simulation process: the translation of simulated probabilities of occurrence into patterns of presence and absence. Often a threshold strategy is used to generate virtual occurrences, where presence always occurs above a specific simulated probability value and never below. This procedure effectively translates any shape of simulated species response into a threshold one and eliminates any stochasticity from the species occupancy pattern. We argue that a probabilistic approach should be preferred instead because the threshold response can be treated as a particular case within this framework. This also allows one to address questions relating to the shape of functional responses and avoids convergence issues with some of the most common SDMs. Furthermore, threshold-based virtual species studies generate over-optimistic performance measures that lack classification error or incorporate error from a mixture of sampling and modelling choices. Incorrect use of a threshold approach can have significant consequences for the practising biogeographer. For example, low model performance may be interpreted as due to sample bias or poor model choice, rather than being related to fundamental biological responses to environmental gradients. We exemplify these shortcomings with a case study where we compare results from threshold and probabilistic simulation approaches.
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ISSN 0305-0270 ISBN Médium
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Auteur Meynard, C.N.; Kaplan, D.M.; Leroy, B.
Titre Detecting outliers in species distribution data: Some caveats and clarifications on a virtual species study Type Article scientifique
Année 2019 Publication Revue Abrégée J. Biogeogr.
Volume 46 Numéro 9 Pages 2141-2144
Mots-Clés enm; observation errors; outliers; prevalence; probabilistic approach; sample bias; simulations; species distribution models; thresholds; virtual ecology; virtual species
Résumé Liu et al. (2018) used a virtual species approach to test the effects of outliers on species distribution models. In their simulations, they applied a threshold value over the simulated suitabilities to generate the species distributions, suggesting that using a probabilistic simulation approach would have been more complex and yield the same results. Here, we argue that using a probabilistic approach is not necessarily more complex and may significantly change results. Although the threshold approach may be justified under limited circumstances, the probabilistic approach has multiple advantages. First, it is in line with ecological theory, which largely assumes non-threshold responses. Second, it is more general, as it includes the threshold as a limiting case. Third, it allows a better separation of the relevant intervening factors that influence model performance. Therefore, we argue that the probabilistic simulation approach should be used as a general standard in virtual species studies.
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Auteur institutionnel Thèse
Editeur Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
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Volume de collection Numéro de collection Edition
ISSN 0305-0270 ISBN Médium
Région Expédition Conférence
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2640
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