CascadiaTools worked example: Effective population size and relatedness
Module: popgen-ne

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 microsatellite genotypes for bull trout from Upper Elk Creek in bulltrout_microsats.csv: 50 adults sampled in 2014 and 50 in 2024, 16 loci, two columns per locus, 0 = missing. There are also 12 juveniles from 2024, two from each of six redds; known_relationships.csv lists the nest-mate pairs. Generation time is about 5 years and redd counts suggest about 120 adults. Please estimate the effective population size and how fast the population is losing genetic diversity, and tell me whether the markers can identify relatives. I'd like a report with figures for 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/popgen-ne.html
