Opening the black box: an open‐source release of Maxent |
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| Authors: | Steven J Phillips Robert P Anderson Miroslav Dudík Robert E Schapire Mary E Blair |
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| Institution: | 1. http://orcid.org/0000‐0002‐6991‐608X;2. Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY, USA;3. Dept of Biology, City College of New York, City Univ. of New York, New York, NY, USA;4. Program in Biology, Graduate Center, City Univ. of New York, New York, NY, USA, and Div. of Vertebrate Zoology (Mammalogy), American Museum of Natural History, New York, NY, USA;5. Microsoft Research, New York, NY, USA |
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| Abstract: | This software note announces a new open‐source release of the Maxent software for modeling species distributions from occurrence records and environmental data, and describes a new R package for fitting such models. The new release (ver. 3.4.0) will be hosted online by the American Museum of Natural History, along with future versions. It contains small functional changes, most notably use of a complementary log‐log (cloglog) transform to produce an estimate of occurrence probability. The cloglog transform derives from the recently‐published interpretation of Maxent as an inhomogeneous Poisson process (IPP), giving it a stronger theoretical justification than the logistic transform which it replaces by default. In addition, the new R package, maxnet, fits Maxent models using the glmnet package for regularized generalized linear models. We discuss the implications of the IPP formulation in terms of model inputs and outputs, treating occurrence records as points rather than grid cells and interpreting the exponential Maxent model (raw output) as as an estimate of relative abundance. With these two open‐source developments, we invite others to freely use and contribute to the software. |
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