Shifting from closed-source graphical-interface to open-source programming environment: a brief tutorial on running Maxent in R

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1 Institute of Environment, University of Arizona, Tucson, AZ, United States
2 Integrative Biology, Oklahoma State University, Stillwater, OK, United States
DOI
10.7287/peerj.preprints.3346v1
Published
Accepted
Subject Areas
Biogeography, Bioinformatics, Ecology, Zoology, Data Science
Keywords
Maxent, R, ecological niche modeling, open-source, clamping, species distribution modeling
Copyright
© 2017 Feng et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Feng X, Gebresenbet F, Walker C. 2017. Shifting from closed-source graphical-interface to open-source programming environment: a brief tutorial on running Maxent in R. PeerJ Preprints 5:e3346v1

Abstract

Ecological niche modeling (ENM) is increasingly being used in studying the relationship between species distributions and environmental conditions. The development of ENM software/algorithms is heading toward open-source programming, for the advantage of efficiency in handling big data and incorporating new methods. Maxent is one of the commonly used ENM algorithms, but there has been limited information and efforts in implementing Maxent in an open-source programming environment (e.g., R). Therefore, we aim to fill the gap of knowledge for using Maxent in R. More specifically, we demonstrate the general implementation of Maxent in R based on a commonly used ENM procedure, provide a function that bridges the Maxent algorithm and R computing environment for easier use, and demonstrate the manipulation of a few crucial Maxent parameters in R. We expect our efforts will promote a shift of the Maxent user community from a graphical-interface to open-source programming.

Author Comment

This is a preprint submission to PeerJ Preprints.