CascadiaTools worked example: Community composition - ordination, RDA and variation partitioning, PERMANOVA with dispersion test, beta-diversity partitioning, indicator species
Module: community

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 bird point counts from 60 forest stations (cascades_bird_counts.csv, one column per species) and a station table with stand type, elevation and canopy cover (cascades_stations.csv). How much of the variation in the bird community goes with elevation versus canopy cover, do old growth, thinned and young plantation stands hold different communities, is it turnover or nestedness, and which species are indicators of each stand type? Please give me a report and 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/community.html
