CascadiaTools worked example: Jolly-Seber open-population capture-recapture (abundance, survival, recruitment)
Module: jolly-seber

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 eight summers (2015 to 2022) of hoop-trapping data for western pond turtles at one pond complex, in two files: turtle_captures.csv (every capture, with the turtle's ID, the season and its sex; U means we could not sex it) and turtle_seasons.csv (trap-nights of effort in each season). I want to know how many turtles were there each year and in total, how many new turtles joined each year, what share survive from year to year and whether males survive less well than females, and whether the population is declining. 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/jolly-seber.html
