3.11 Walkthrough: Species distribution modeling with Jupyter

You now have a basic understanding of the species distribution modeling task we want to solve in this lesson's walkthrough as well as the different Python packages that will play a role in preparing the data, running the model, and visualizing the result. Since all of this will take place within a Jupyter notebook, the remainder of this section will consist of the notebook itself exported to html and embedded into the Drupal pages for this lesson. Here is the link to the data you need for this walkthrough:

Link to L3 Walkthrough data

Instead of just reading through the HTML version of the notebook content linked below, you should download the notebook, extract the contained .ipynb notebook file, place it in your user home or documents folder, open it with Jupyter and work through it step-by-step following the instructions given in the notebook itself, executing the code cells, and trying to understand the code sections and the output they produce.

Important note: Sections 3.1 and 5.2 of the notebook will use the Python-to-R interface (Section 3.7 of the lesson materials). On the R side, there are two packages involved: dismo and terra. Only if you have the time, this Notebook uses the AC311_WLKTGH environment discussed earlier in the lesson in section 3.2. You will need to switch environments for this Notebook.

Here is the link to html export of the notebook if you want to have a look at it outside of Jupyter Notebook: HTML export of the walkthrough notebook

You have finished the Lesson 3 course materials. On the next pages, you will find a few practice exercises and the instructions for the Lesson 3 homework assignment. Double-check the list of requirements on the Lesson 3 Checklist page to make sure you have completed all activities listed there before beginning the next lesson.