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Opening the black box: an open‐source release of Maxent
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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“If a predictor value is common, and presence points rarely occur, these values will be down-weighted so that they have a lower probability of occurrence [86].”
From Advancing predictive modeling in archaeology: an evaluation of regression and machine learning methods on the grand staircase-escalante national monument (2020) · cites this paper as [86]
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The art of modelling range-shifting species: The art of modelling range-shifting species
Elith, J., Kearney, M., & Phillips, S. (2010) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2010.00036.x · Cited by 2,813 · cited 2×
“Species distribution models based on Maxent and IPP remain an active area of research, as new methods are developed to accommodate the challenging nature of occurrence data and species distributions (Fithian et al. 2015, Merow et al. 2016). The open-source release of the Maxent Java code, together with the maxnet R pa…”
Self-citationAdvances in global change research require open science by individual researchers
Wolkovich, E. M., Regetz, J., & O'Connor, M. I. (2012) · Global Change Biology · doi:10.1111/j.1365-2486.2012.02693.x · Cited by 111
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Metadata
- Authors
- Phillips, S. J., Anderson, R. P., Dudík, M., Schapire, R. E., & Blair, M. E.
- Affiliations
- Center for Biodiversity and Conservation, American Museum of Natural History New York NY USA
- Dept of Biology, City College of New York City Univ. of New York New York NY USA
- Microsoft Research New York NY USA
- Venue
- Ecography
- Publisher
- Wiley
- Published
- 2017-05-09
- Volume
- 40
- Issue
- 7
- Pages
- 887-893
- ISSN
- 0906-7590
- 1600-0587
- Cited by
- 2,729
- References
- 2
- Language
- en
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