CascadiaTools worked example: Multispecies occupancy with species interactions (Rota et al. 2016)
Module: occu-rota

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 camera-trap data from 220 stations, 6 weekly occasions in June-July 2024. The files are camera_detections.csv (one row per camera and week: days the camera worked, and 1/0 for coyote, gray fox and bobcat) and camera_sites.csv (forest cover within 500 m, housing units per km2, whether the camera is on a trail). Are gray foxes less likely to occupy sites where coyotes are present, and does that change with housing density? Please account for animals the cameras missed and for cameras that were down. Detection probably depends on days active and on whether the camera faces a trail. I need results and figures for 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-rota.html
