CascadiaTools worked example: Cormack-Jolly-Seber apparent survival
Module: cjs

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 nine years of song sparrow banding data from my station (2016 to 2024) in three files: sosp_captures.csv (every capture, with band number and date), sosp_birds.csv (sex and body mass of each bird when first banded) and sosp_years.csv (mean January minimum temperature for each winter). I want annual adult survival, whether it differs between males and females, and whether it is related to winter cold and body mass. Many birds are only caught once; I think some are migrants passing through. Please analyse this 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/cjs.html
