Sitemap
A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
A flexible two-column Jekyll theme. Perfect for personal sites, blogs, and portfolios hosted on GitHub or your own server. Latest release v4.9.1
(Advanced) Species Distribution Modeling
Create virtual species, dive deep into the world of SDM and work on experimental research questions.
Splash Page
Bacon ipsum dolor sit amet salami ham hock ham, hamburger corned beef short ribs kielbasa biltong t-bone drumstick tri-tip tail sirloin pork chop.
Posts
unit00
Learning Environment
This course is intended as a blended learning module, although the provided introductions, explanations and examples might be useful for self-study only, too.
Deliverables
In this section of the course, you will find all essential information on organizational matters, including details on your deliverables and frequently asked...
Frequently Asked Questions
Course requirements What is the expected workload for this course? This course gives 6 (ECTS) credit points, making up a total of 180 hours workload. 180 ho...
unit01
Overview
Go through a brute force introduction into R, R Markdown, the RStudio IDE to get ready for solving the upcoming assignment problems and submitting your solut...
| LM | The very basics |
Start learning (or recap) the essentials for working with R and RStudio to create species distribution models.
| EX-A | Advanced visualization (optional / advanced) |
This is an optional exercise intended for advanced course participants. Advanced visualization in R This section offers a practical exercise for those with ...
| LM | SDM basics |
Obviously, there are too many species on Earth to know them all, not to say their distributional ranges. To make things even more complicated, a species does...
| EX-A | Further background knowledge (optional / advanced) |
This is an optional exercise intended for advanced course participants. To deepen your understanding of species distribution modeling (SDM) and its associat...
| LM | Key ecological concepts |
This section of the course outlines essential ecological concepts that are important to fully understand SDM and species interactions with the environment. S...
| A | Assignment: 01 |
Until next session: Select one paper from the list provided below. Read the selected paper carefully. Summarize the main topic of the paper in a...
unit02
Overview
This unit provides an introduction to species distribution modeling, covering key steps from data preparation and model training to model quality assessment....
| LM | SDM workflow |
If you are already experienced with SDM, you may be familiar with this workflow. However, please take a moment to recap it and refresh your knowledge.
| LM | Input data |
This unit guides you through the entire process of creating a species distribution model, step by step. We will begin with the essential data needed for the ...
| LM | Training, validation and test data |
The data of the species occurrence are referred to as training data, usually machine learning models are not trained with all data but only with a subset of ...
| EX | Get your training data |
Exercise: Create your training data The with code below, you can prepare predictors and training data for species distribution modeling. We will use the butt...
| EX | Model training |
Last week we prepared the training data we will use for our species distribution modeling task. The training dataset as well as the background points will be...
| EX | Assessment & predictions |
Predictions Now we create a spatial prediction with our model and do a visual inspection of the map we created. Load the pre-trained model using the readRDS...
| EX-A | Spatial evaluation (optional / advanced) |
This is an optional exercise intended for advanced course participants. In the last session, you learned how to evaluate your species distribution model by ...
| A | Assignment: 02 |
Assignment for Bachelor Students Follow the entire code in Unit 2 of the SDM workflow. Ensure that all the code runs smoothly and that you have a cle...
unit03
Overview
In this unit, you will generate artificial landscapes as environmental variables for SDM. You will learn how to construct neutral landscape models (NLMs) and...
| LM | Artificial landscapes |
In this unit, you will learn how to generate environmental data using Neutral Landscape Models (NLMs), which we will later use in the next unit to create vir...
| Ex | Artificial landscapes |
Exercise: Create Environmental Variables Now it’s your turn! Use the code in the gist below to generate six different environmental variables. Ensure each v...
| A | Assignment: 03 |
In this assignment you will use your knowledge from the previous session to create your own little kingdom. Which mean you will now create a country with neu...
unit04
Overview
In this unit, we will focus on virtual species as a tool for testing species distribution models. You will learn how to generate virtual species by defining ...
| LM | Virtual species |
Here, you’ll learn how to generate virtual species for modeling purposes, which will later allow us to conduct a comprehensive comparison of species distribu...
| EX | Virtual species |
Exercise Plot the habitat suitability response curves for different transformation functions and observe how they change as you adjust the values. Each cour...
| A | Assignment: 04-01 |
In this assignment we will use everything we have learnt so far in unit 02 to create virtual species. We will use the NLMs as environmental variables and the...
| LM | Sample Presence-Absence Points |
For this course, we want to sample presence-absence points instead of presence-only points for all virtual species. We will again use the virtualspecies R pa...
| A | Assignment: 04-02 |
For all virtual species created during this session, generate a dataset containing sampled presence-absence points. Follow these steps: Sample Prese...
unit05
Overview
This unit is all about your final team project. Think about your research question and create a project outline as basis for your project. To finish this cou...
Your research project
Now, you will create your own research project. Decide on a question and answer it by modeling species distributions with virtual species. This project will ...
| LM | Research gaps in SDM |
This page serves as a resource to inspire your research projects in the field of SDM. You will find an overview of key research gaps, relevant studies, and m...
| A | Assignment: 05-1 |
Write your project outline. Therefore find your group members and get to know each other, choose a research question, strictly follow the points ...
Final project
After you have written your project outline and have received feedback on it, it will be your task to realize a full research project on the basis of your p...
| A | Assignment: 05-2 |
Bring it to an end. Therefore implement the feedback into your outline, realize your team project, and upload your pdf until 30 September 2025 23...