Week 2: Species Distribution Modeling Step 1 (Biodiversity data acquisition)

Icebreaker question

What is one thing you wish you understood but don't?

Introductory business

Introduce the FAQ page
NY-SDM Symposium 9/18
I added the UMaine CloudBank JupyterHub link to the course home page.
- Exercise 1: Pull the latest version of the class github repository. Launch your jupyterhub, open a terminal and see if you can remember how to do this yourself before checking the answer in the box below.

Commands to pull the latest version of the class repository

Change directory to your local copy of the course repo
Pull the latest copy of 'upstream' which is my copy of the class website

Push the changes to your own github repo

cd ~/BIO597-SpatialBiodiversity/`  
git upstream 
git push

Review Assignment-01-Geopandas

Core Questions

What are Species Distribution Models and what are the major steps in constructing them?
Where to obtain biodiversity occurrence records at scale? (hint: GBIF)
How do I use python to programatically fetch occurence data?

Paper discussion

Applied Lab

Students use pygbif to search GBIF for Storeria dekayi, inspect the returned list and dictionary objects, save the GBIF species key, count matching occurrence records, fetch up to 100 georeferenced records, convert those records to a DataFrame and then a GeoDataFrame, and map the points with .explore().

The lab also introduces simple summaries and filters, including grouping records by year and selecting records by location.

Lab Concepts

GBIF as a source of biodiversity occurrence data.
Scientific names and 'taxon keys'.
Occurrence records with coordinates.
Converting and plotting GBIF records with GeoDataFrames
Simple record summaries using grouping and filtering.

Python Tools

pygbif
GeoPandas

Homework

Register for the symposium next week: NY-SDM Emerging Frontiers Symposium: AI, Genomics & Community Science in Biogeography

Complete and submit these two assignment:

docs/assignments/Assignment-02-PythonCollections.ipynb
docs/assignments/Assignment-02-pygbif.ipynb

Paper discussion leader next week: John! Please select a paper for the group to discuss before Sunday 09/13 6pm and send it around to the class email list: bio597-fall2026-group@maine.edu

Be prepared to lead a brief discussion on this paper next Friday 09/18, following the guidelines in the Paper Discussion section on the assignments page.