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UBC Ecological Niche Modeling Workshop

In this workshop we will cover the basics of building an ecological niche model. You will specifically learn how to use R to generate niche models with the MAXENT algorithm.

Course Outline

Day 1: Overview and Data Preparation
Day 2: Model Calibration
Day 3: Model Evaluation and Prediction

Important Information

Prior to the start of the workshop, please do the following:

  1. Free up as much space on your hard-drive as possible (preferrably 15-20 GB but at least 10 GB)
  2. Download the "Data" folder (and extract the zipped files) from: https://github.com/jullee/UBC-ENM-Workshop-Fall-2016/tree/master/Data
  3. Download and install R (or make sure you have a fairly recent version)
  4. Download MAXENT from here: https://www.cs.princeton.edu/~schapire/maxent/
  5. Install the following R packages and any dependancies:
  • raster
  • maptools
  • dismo
  • spThin
  • rgeos
  • adehabitatHR
  • spatial.tools
  • PresenceAbsence

In R, you can install packages using the following command:

install.packages("<PACKAGE_NAME>") # replace <PACKAGE_NAME> with the name of the package you wish to install

You may need to update Java. You also need to follow the instructions for the dismo package carefully: put a copy of the maxent.jar file into the dismo "java" folder (you need to locate your R libraries on your computer).

If you can't figure all this out before the first class, please plan to stay a bit longer at the end of the class so we can get you set up.

Questions?

Contact Julie:
lee-yaw [at] zoology [dot] ubc [dot] ca