CascadiaTools worked example: Integrated population model (counts + capture-recapture + productivity)
Module: ipm

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 15 years (2006-2020) of data on red-backed shrikes from my study plot, in four files: shrike_counts.csv (breeding females counted each June; no count in 2013), shrike_captures.csv (every ringed bird each year it was caught, ringed as a nestling or as a breeding female), shrike_broods.csv (fledglings from each monitored nest, with the mother's age, yearling or older) and sahel_rainfall.csv (July-September rainfall in the Sahel each year). I want to know how the number of breeding females changed, which vital rates drove the ups and downs, how many breeders are immigrants, and whether first-year survival is higher after wet years in the Sahel. I only have data on females. 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/ipm.html
