International course of the Department of Physical Geography at Marburg University

Species distribution modelling (SDM) is a key competence for ecogeographical research and applied nature conservation. It allows researchers to estimate current distributions of species and to also predict their future distributions under climate change scenarios. SDM encompasses various area-wide spatial predictions techniques and requires profound skills related to organizing, handling, analyzing and visualizing geodata.

By using the programming environment R, this course will open the door to the cosmos of SDM techniques and will provide a flexible baseline for workflow automation in various research projects. Special emphasis will be on R Markdown and GitHub for proper documentation and reproducibility.

Intended learning outcomes

At the end of this course you should be able to

  • feel comfortable with the usage of R and GitHub,
  • distinguish between and apply major SDM techniques,
  • analyse, share and reproduce your spatial data with R Markdown,
  • use open GIS to manage, visualize and georeference your spatial data,
  • include and process remote sensing data in your workflow,
  • learn how to implement a research project in a collaborative approach, and last but not least to
  • critically evaluate your analyses and results.

Course features

This course is intended as a blended learning module in our study program although the provided introductions, explanations and examples might be useful for self-study, too. Given the enormous body of literature and methods available for SDM, it can only be an entry point for more sophisticated and project-specific modelling techniques. Each course aims to create area-wide species distribution maps for a group of organisms and a particular area of the world for which hitherto no species richness maps exist.

This course will take place in a hybrid setting (except for the first session) with a digital classroom and additional students being present in person in the physical classroom (F 14 | 00A12). Details on this synchronous hybrid classroom format will be provided in the first session, which will take place in presence only on Tuesday 19.04.2022 at 10:15 am. The link to the digital classroom will be provided in the Ilias course environment (only accessible for members of the course who are logged-in into Ilias). Please also seriously check and follow the Information on the Coronavirus of the University of Marburg.

Course times

Tuesdays 10:15 - 12:45.

Syllabus

Session Date Topic Content
    Basics  
01 19.04.2022 The very basics Course introduction, expectations, organisational matters, R, R Studio, R Markdown, GitHub
02 26.04.2022 More basics Data types, object types, indexing, work environment, data input and output
03 03.05.2022 Working with spatial data Raster data, vector data, coordinate reference systems, reading and writing spatial data, spatial operators, mapping
04 10.05.2022 Session cancelled  
05 17.05.2022 SDM Basics Why SDM?, applicability of SDM, ecological concepts, SDM modelling cycle. Student tutorial assignment
    Digitizing distribution records  
06 24.05.2022 Software development I Project introduction, objectives, testing software for digitizing species records
07 31.05.2022 Software development II Work on projects
08 07.06.2022 Applying the software Use the digitizer for extracting butterfly distribution records across Asia
09 14.06.2022 Project week Department of Geography Session cancelled
    Species Distribution Modelling  
10 21.06.2022 SDM methods I Student tutorials presentations: Bioclim, GAM
11 28.06.2022 SDM methods II Student tutorials presentations: Random forest, SVM
12 05.07.2022 SDM methods III Student tutorials presentations: Neural networks, MaxEnt/BRT
13a 12.07.2022 SDM methods IV Student tutorials presentations: XG Boost, Model averaging
    Synthesis  
13b 12.07.2022 Wrap up Get feedback from your peers and instructors, tell us how you self-assess your skills, and happy holidays

Deliverables

The course certificate will be based on individual assignments written in R Markdown and published on GitHub. Participants will prepare a graded student tutorial about an SDM method of their choice, which will be published on this page.

Preparation and prerequisites

Basic knowledge of R and of handling spatial data is beneficial, but not required. All software needed for this course is free and open source.

This course uses additionally provided material for teaching basic R skills, which can be found here.

Instructor

Dirk Zeuss

University of Marburg