CascadiaTools worked example: Two-species conditional occupancy (dominant/subordinate; Richmond et al. 2010, Waddle et al. 2010)
Module: occu-waddle

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 pipe-survey data for Cuban treefrogs and green treefrogs at 180 sites, 5 visits each, in pipe_surveys.csv, and site information (distance to road, canopy cover) in sites.csv. I want to know whether green treefrogs occupy fewer sites where Cuban treefrogs are present, and whether green treefrogs are harder to detect on visits when Cuban treefrogs are found. Cuban treefrog detection probably depends on air temperature. Please run the analysis and give me a report with figures I can use 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/occu-waddle.html
