CascadiaTools worked example: Multistate and multievent capture-recapture (Arnason-Schwarz / Pradel multievent)
Module: multistate

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 years (2015-2022) of capture data for a PIT-tagged frog population in three files: frog_captures.csv (each capture with the frog's id, year and Bd swab result: uninfected, infected, or U when the swab was lost or inconclusive), frog_individuals.csv (snout-vent length of each frog) and survey_years.csv (mean water temperature and survey effort in person-hours for each year). I want to know whether infected frogs survive less well, how often frogs become infected or clear the infection each year, whether water temperature is related to infection and clearance, and whether bigger frogs survive better. 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/multistate.html
