Entomologia

EXERCISE 107

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A Brief Tutorial on Maxent
Steven Phillips
AT&T Labs-Research, Florham Park, NJ, U.S.A., email phillips@research.att.com

S. Laube

Species’ Distribution Modeling for Conservation Educators and Practitioners

Lessons in Conservation http://ncep.amnh.org/linc

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EXERCISE

A Brief Tutorial on Maxent
Steven Phillips

INTRODUCTION

This tutorial gives abasic introduction to use of the Maxent program for maximum entropy modelling of species’ geographic distributions, written by Steven Phillips, Miro Dudik, and Rob Schapire, with support from AT&T Labs-Research, Princeton University, and the Center for Biodiversity and Conservation, American Museum of Natural History. For more details on the theory maximum entropy modeling as well as a descriptionof the data used and the main types of statistical analysis used here, see: Phillips, S.J., R.P. Anderson, and R.E. Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling 190: 3-4 pp 231-259. A second paper describing more recently-added features of the Maxent software is: Phillips, S.J. and M. Dudik. 2008. Modeling of species distributions with Maxent:new extensions and a comprehensive evaluation. Ecography (31)2: 161-175. The environmental data we will use consist of climatic and elevational data for South America, together with a potential vegetation layer. Our sample species will be Bradypus variegatus, the brown-throated three-toed sloth. This tutorial will assume that all the data files are located in the same directory as the Maxentprogram files; otherwise you will need to use the path (e.g., c:\data\maxent\tutorial) in front of the file names used here.

Species’ Distribution Modeling for Conservation Educators and Practitioners

Lessons in Conservation http://ncep.amnh.org/linc

EXERCISE 109
GETTING STARTED
Downloading

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The software consists of a jar file, maxent.jar, which can be used on any computer runningJava version 1.4 or later. Maxent can be downloaded, along with associated literature, from www.cs.princeton.edu/~schapire/maxent; the Java runtime environment can be obtained from java.sun.com/javase/downloads. If you are using Microsoft Windows (as we assume here), you should also download the file maxent.bat, and save it in the same directory as maxent.jar. The website has a file called“readme.txt”, which contains instructions for installing the program on your computer. Firing up If you are using Microsoft Windows, simply click on the file maxent.bat. Otherwise, enter “java -mx512m -jar maxent.jar” in a command shell (where “512” can be replaced by the megabytes of memory you want made available to the program). The following screen will appear:

Species’ Distribution Modeling forConservation Educators and Practitioners

Lessons in Conservation http://ncep.amnh.org/linc

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EXERCISE
To perform a run, you need to supply a file containing presence localities (“samples”), a directory containing environmental variables, and an output directory. In our case, the presence localities are in the file “samples\bradypus.csv”, the environmental layers are in the directory“layers”, and the outputs are going to go in the directory “outputs”. You can enter these locations by hand, or browse for them. While browsing for the environmental variables, remember that you are looking for the directory that contains them – you don’t need to browse down to the files in the directory. After entering or browsing for the files for Bradypus, the program looks like this:

The file“samples\bradypus.csv” contains the presence localities in .csv format.The first few lines are as follows: species,longitude,latitude bradypus_variegatus,-65.4,-10.3833 bradypus_variegatus,-65.3833,-10.3833 bradypus_variegatus,-65.1333,-16.8 bradypus_variegatus,-63.6667,-17.45 bradypus_variegatus,-63.85,-17.4

Species’ Distribution Modeling for Conservation Educators and Practitioners...