Species Distribution Models

An introductory course at SFU Jena

Author

Emilio Berti

Course overview

This course introduces Ecological Niche Modeling (ENM) and Species Distribution Modeling (SDM) using the R programming language.

Important

This course assumes basic R knowledge.

In the first # days, etc.

Note

A basic knowledge of Geographic Information Systems is required for ENM/SDM. I will introduce basic concepts and operations of of GIS, but this is not a course about GIS.

I lecture a GIS course every year at iDiv in Leipzig: GIS course. SFU Jena also offers GIS courses: MSc Environmental and Georesources Management, MSc Geoinformatic, and BSc Geography.

Learning objectives

  • Understand the theory behind ENM/SDM.
  • Perform ENM/SDM in R.
  • Apply ENM/SDM to real data.
  • Produce maps.

Software

We will use two extremely popular R package: terra and mgcv. For terra, you might want to install also codetools, which performs checks on the C++ code of terra.

install.packages(c("codetools", "terra"))

For mgcv, you might want to install also gratia, which provides functionality to plot and inspect the output of mgcv.

install.packages(c("mgcv", "gratia"))
Note

terra is still in active development and some functionalities change with newer releases.