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, which you will need to download and extract to a new folder 

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 three packages involved: dismo, maptools, and rgdal. 
While the environment we installed in Section 3.2 contains conda packages for dismo and maptools, there is at the moment no conda package available for rgdal because of technical issues the package maintainers have to resolve (see https://github.com/conda-forge/r-rgdal-feedstock/issues/18). We are therefore currently installing the rgdal package in the notebook code itself with the line "%R install.packages('rgdal')" close to the beginning. However, we in the past had a very few cases where this caused problems on some computers. Just in case you find yourself unable to run some of the R commands (starting with %R) in sections 3.1 and 5.2 of the notebook, we are here providing two files that can be used as a workaround. You will then have to place these files in your workspace folder for this walkthrough (just read the corresponding sections in the HTML export of the notebook linked below to see the output produced by the steps you cannot run yourself) and then follow the workaround instructions in the notebook that explain how to continue with the other sections with the help of these two files.

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 of the activities listed there before beginning the next lesson.