Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions

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Royle, J. Andrew, Chandler, Richard B., Yackulic, Charles, and Nichols, James D.

Understanding the factors affecting species occurrence is a pre-eminent focus of applied ecological research. However, direct information about species occurrence is lacking for many species. Instead, researchers sometimes have to rely on so-called presence-only data (i.e. when no direct information about absences is available), which often results from opportunistic, unstructured sampling. maxent is a widely used software program designed to model and map species distribution using presence-only data. We provide a critical review of maxent as applied to species distribution modelling and discuss how it can lead to inferential errors. A chief concern is that maxent produces a number of poorly defined indices that are not directly related to the actual parameter of interest – the probability of occurrence (ψ). This focus on an index was motivated by the belief that it is not possible to estimate ψ from presence-only data; however, we demonstrate that ψ is identifiable using conventional likelihood methods under the assumptions of random sampling and constant probability of species detection. The model is implemented in a convenient r package which we use to apply the model to simulated data and data from the North American Breeding Bird Survey. We demonstrate that maxent produces extreme under-predictions when compared to estimates produced by logistic regression which uses the full (presence/absence) data set. We note that maxent predictions are extremely sensitive to specification of the background prevalence, which is not objectively estimated using the maxent method. As with maxent, formal model-based inference requires a random sample of presence locations. Many presence-only data sets, such as those based on museum records and herbarium collections, may not satisfy this assumption. However, when sampling is random, we believe that inference should be based on formal methods that facilitate inference about interpretable ecological quantities instead of vaguely defined indices.


Royle, J. A., R. B. Chandler, C. Yackulic, and J. D. Nichols. 2012. Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions. Methods in Ecology and Evolution 3:545–554.