Selecting thresholds of occurrence in the prediction of species distributions
TLDR
Twelve approaches to determining thresholds were compared using two species in Europe and artificial neural networks, and the modelling results were assessed using four indices: sensitivity, specificity, overall prediction success and Cohen's kappa statistic.Abstract:
Transforming the results of species distribution modelling from probabilities of or suitabilities for species occurrence to presences/absences needs a specific threshold. Even though there are many approaches to determining thresholds, there is no comparative study. In this paper, twelve approaches were compared using two species in Europe and artificial neural networks, and the modelling results were assessed using four indices: sensitivity, specificity, overall prediction success and Cohen's kappa statistic. The results show that prevalence approach, average predicted probability/suitability approach, and three sensitivity-specificity-combined approaches, including sensitivity-specificity sum maximization approach, sensitivity-specificity equality approach and the approach based on the shortest distance to the top-left corner (0,1) in ROC plot, are the good ones. The commonly used kappa maximization approach is not as good as the afore-mentioned ones, and the fixed threshold approach is the worst one. We also recommend using datasets with prevalence of 50% to build models if possible since most optimization criteria might be satisfied or nearly satisfied at the same time, and therefore it's easier to find optimal thresholds in this situation.read more
Citations
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Novel methods improve prediction of species' distributions from occurrence data
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TL;DR: This work compared 16 modelling methods over 226 species from 6 regions of the world, creating the most comprehensive set of model comparisons to date and found that presence-only data were effective for modelling species' distributions for many species and regions.
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AUC: a misleading measure of the performance of predictive distribution models
TL;DR: The area under the receiver operating characteristic (ROC) curve, known as the AUC, is currently considered to be the standard method to assess the accuracy of predictive distribution models as discussed by the authors.
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Predicting species distributions from small numbers of occurrence records: A test case using cryptic geckos in Madagascar
TL;DR: A novel jackknife validation approach is developed and tested to assess the ability to predict species occurrence when fewer than 25 occurrence records are available and the minimum sample sizes required to yield useful predictions remain difficult to determine.
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A practical guide to MaxEnt for modeling species' distributions: what it does, and why inputs and settings matter
TL;DR: A detailed explanation of how MaxEnt works and a prospectus on modeling options are provided to enable users to make informed decisions when preparing data, choosing settings and interpreting output to highlight the need for making biologically motivated modeling decisions.
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