CascadiaTools worked example: Open-population spatial capture-recapture (Jolly-Seber SCR)
Module: scr-open

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 five summers (2020-2024) of marten hair-snare data from 49 snares on a 1-km grid, each checked 5 times a summer. hair_snares.csv has the snare locations (UTM) and which checks each snare was working; marten_genotypes.csv has one row per genotyped sample with year, check, snare and marten ID; and habitat_grid.csv has canopy cover on a 400 m grid around the snares. I want to know how many martens there are each year, whether they are declining, annual survival and recruitment, and whether density is higher under denser canopy. Please 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/scr-open.html
