Opening the black box: an open-source release of Maxent

9 March 2017

Phillips, Steven; Anderson, Robert P.; Dudik, Miro; Schapire, Robert; Blair, Mary

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 (Version 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