Modelling species distributions with penalised logistic regressions: A comparison with maximum entropy models

• Published in: Ecological modelling 2011-07, Vol.222 (13), p.2037-2041
• Main Authors: GASTON, Aitor, GARCIA-VINAS, Juan I
• Format: Article
• Language: English
• Subjects: Animal, plant and microbial ecology; biogeography; Biological and medical sciences; Calibration; entropy; Fundamental and applied biological sciences. Psychology; General aspects. Techniques; Generalised linear models; Methods and techniques (sampling, tagging, trapping, modelling...); new methods; regression analysis; Regularisation; Species distribution models; trees
• ISSN: 0304-3800; 1872-7026
• DOI: 10.1016/j.ecolmodel.2011.04.015

► Penalised logistic regression outperformed standard logistic regression. ► Penalised logistic regression equalled the performance of Maxent. ► We encourage further use of penalised regression for species distribution modelling. An important aspect of species distribution modelling is the choice of the modelling method because a suboptimal method may have poor predictive performance. Previous comparisons have found that novel methods, such as Maxent models, outperform well-established modelling methods, such as the standard logistic regression. These comparisons used training samples with small numbers of occurrences per estimated model parameter, and this limited sample size may have caused poorer predictive performance due to overfitting. Our hypothesis is that Maxent models would outperform a standard logistic regression because Maxent models avoid overfitting by using regularisation techniques and a standard logistic regression does not. Regularisation can be applied to logistic regression models using penalised maximum likelihood estimation. This estimation procedure shrinks the regression coefficients towards zero, causing biased predictions if applied to the training sample but improving the accuracy of new predictions. We used Maxent and logistic regression (standard and penalised) to analyse presence/pseudo-absence data for 13 tree species and evaluated the predictive performance (discrimination) using presence–absence data. The penalised logistic regression outperformed standard logistic regression and equalled the performance of Maxent. The penalised logistic regression may be considered one of the best methods to develop species distribution models trained with presence/pseudo-absence data, as it is comparable to Maxent. Our results encourage further use of the penalised logistic regression for species distribution modelling, especially in those cases in which a complex model must be fitted to a sample with a limited size.