CascadiaTools worked example: Spatial mark-resight (SMR) and generalized spatial mark-resight (gSMR)
Module: scr-smr

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've put my fisher data in a folder: box-trap captures and trap locations from May, trail camera locations and a photo log from June to August, GPS fixes from 9 collared fishers, and a habitat grid with canopy cover. Some photos show a readable ear tag, some a tag we couldn't read, and most no tag. Please estimate fisher density and abundance, tell me whether density rises with canopy cover, and whether trail cameras get more photos. The box traps were only in the middle of the camera grid. Please check the method works for a design like mine before you trust it, and 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/scr-smr.html
