CascadiaTools worked example: Joint species distribution model (HMSC)
Module: jsdm

These data are SIMULATED, so the true answer is known. See README_data.md.

To try it:
  1. Unzip this folder somewhere you can find it.
  2. Open the folder in Claude Code (with the CascadiaTools plugin installed).
  3. Paste the prompt below.

Prompt:
I have bird point-count data in this folder: bird_detections.csv (every detection, 3 visits per station), stations.csv (coordinates, July temperature, canopy cover) and bird_traits.csv (body mass and family for each species). How does each species respond to July temperature and canopy cover? Does body size explain who responds how? Which species occur together more or less than the habitat predicts? Please give me a report with figures I can put in a paper.

The analysis settings used for the published example are in config.yaml.
WALKTHROUGH.md shows every step the agent took and the results.
Website: https://cascadiawildlifelab.org/tools/modules/jsdm.html
