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...
R packages on OPSI PCs
if you are having trouble to install packages at the university PCs that run OPSI you can try to follow the guide on this page. Install packages for Advance...
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 | Advanced visualization |
Advanced visualization in R This section offers a practical exercise for those with a solid foundation in spatial data analysis. You will develop an advanc...
| 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...
| 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 |
There are some ecological concepts that are needed to interpret and critically evaluate SDM results, which are going to be discussed here. Write down a one-...
unit02
| LM | Overview |
This unit provides a foundational understanding of how Species Distribution Modeling (SDM) has evolved and the diverse array of algorithms used to map specie...
| LM | Student tutorials on machine learning methods |
This is a collection of sources to obtain various kinds of information on different SDM techniques. These tutorials have been created by students of the Spec...
| EX | A short history of SDM |
Species Distribution Modeling (SDM) has evolved from simple climate “envelopes” to high-dimensional machine learning and deep learning models. Understanding ...
| A | Assignment: 02 |
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...
unit03
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 | 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 | Spatial evaluation |
In the last exercise, you learned how to evaluate your species distribution model by separating the data into training, validation, and testing datasets. W...
| A | Assignment: 03 |
Assignment Follow the entire code in Unit 3 of the SDM workflow. Ensure that all the code runs smoothly and that you have a clear understanding of ea...
unit04
Overview
This unit focuses on modeling acoustic detection probability to understand the dynamic “acoustic phenology” of a species. You will learn to integrate bioacou...
| LM | Fundamentals of Bioacoustics |
Bioacoustics (Laiolo 2010) is an interdisciplinary science dedicated to studying organisms or the environment via sound. It examines both the acoustic signal...
| EX | Bioacoustic and SDM |
Species Distribution Modeling (SDM) utilizing bioacoustic data is a relatively new and evolving field. In this context, we don´t just model the spatial distr...
| EX | Model Training and Prediction |
In this exercise, we move from data preparation to the core of SDM: Model Training and Spatio-Temporal Prediction. We use a Random Forest (RF) classifier and...
| EX | Assignment 04 |
In this assignment, you will apply your knowledge of acoustic modeling to visualize calling probabilities and test the robustness of your predictions. You wi...
unit05
Overview
This unit explores the critical uncertainties inherent in evaluating Species Distribution Models (SDMs) built with presence-only data. You will learn how to ...
| LM | Model evaluation |
Model evaluation is the process of assessing how good or reliable a model as well as its predictions are. Also we want to determine the model’s ability to ...
| EX | Model evaluation |
Most Species Distribution Model (SDM) outputs are continuous probabilities ranging from 0 to 1. A common pitfall for researchers is failing to realize how dr...
| LM | Presence-only SDM model evaluation |
In the last exercise, we calculated some evaluation metrics for the model we created for Aglais caschmirensis in Pakistan. Since we only had presence-only te...
| A | Assignment: 05 |
Today, we learned that evaluation metrics calculated on presence-only data (like AUC or TSS) can deviate from actual model performance. In this assignment, w...
unit06
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...
| LM | Sample Presence-Absence Points |
For the purpose of this course, we want to sample presence-absence points instead of presence-only points for all virtual species. We will again use the virt...
| A | Assignment: 06 |
In this assignment we will use everything we have learnt so far in unit 06 to create virtual species. We will use the bioclim as environmental variables and ...
unit07
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...
| 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...
| EX | Research gaps in SDM |
This exercise is designed to deepen your understanding of current methodological challenges in species distribution modeling (SDM) and to help you identify r...
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 ...
| 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 2026 23...