Week 1: Orientation, connecting to HPC, setting up git, and intro to geopandas
Introductory Business
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Icebreaker Questions:
- Name
- Preferred pronouns
- Study system
- Which biome do you think you'd thrive in?
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Review syllabus
- Let's generate an acceptable use of AI policy for ourselves.
- R vs python discussion and horserace
Core Questions
- Why does geography matter in ecology and evolution?
- How do spatial scale, extent, and grain shape biodiversity inference?
- How can we generate hypotheses about spatial patterns of biodiversity?
- How can we create reproducible spatial biodiversity workflows?
Python Tools for today
- Jupyter
- pandas
- GeoPandas
Applied Lab
Brief intro to jupyter notebooks, python, and the geopandas package. Start with a few simple dataset containing species, latitude, longitude. Create a occurrence record maps per species, merge two species geodataframes, and calculate convex hulls.
The goal of this lab is to just get the feel for working in jupyter notebooks with python geospatial libraries.
Assignment
Submit a reproducible notebook which demonstrates reinforcement of several concepts from the lab assignment.
Additionally, please watch this (short) video about Species Distribution Models: Ecological Explanation
And here is the article for paper discussion this week, it is a simple application of SDMs to N. American snake species: