CascadiaTools worked example: Spatial, multi-species and integrated occupancy (spOccupancy)
Module: occu-spatial

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 fisher camera-trap data from 160 stations in the western Cascades, summer 2024, up to 6 weekly occasions per camera (some cameras died early). fisher_detections.csv has one row per station-week (station, week, start date, days the camera worked, detected 1/0). camera_stations.csv has UTM coordinates, canopy cover (%), elevation (m) and ownership. prediction_grid_1km.csv is a 1-km grid with the same covariates. Is fisher occupancy related to canopy cover and elevation? Please account for fishers we missed and for spatial clustering, and make a map of predicted occupancy. 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-spatial.html
