weatherxbiodiversity-lizards

Erosion of Lizard Diversity by Climate Change and Altered Thermal Niches — replication study.

Reference paper: Sinervo et al. (2010)

This repository is a self-contained replication of the headline claim from the reference paper above. It produces:

• A reproducible computational pipeline (Snakefile + notebooks).

• A FORRT-tagged nanopublication chain on the Science Live platform, documenting the claim, the replication design, and the outcome with full provenance.

• A Zenodo-archived release (source + container image) with a citable DOI.

Quick start¶

git clone https://github.com/annefou/weatherxbiodiversity-lizards.git
cd weatherxbiodiversity-lizards
mamba env create -f environment.yml
mamba activate weatherxbiodiversity-lizards
snakemake --cores 1

Or with Docker:

docker run --rm ghcr.io/annefou/weatherxbiodiversity-lizards:latest

Structure¶

• paper/ — the source paper PDF (drop yours in there).

• notebooks/ — jupytext .py notebooks that drive the pipeline.

• data/ — downloaded by notebooks/01_data_download.py, never committed.

• nanopubs/ — drafts of the FORRT chain field-by-field, plus the published-URI registry.

• docs/ — operating manuals (FORRT form fields, chain decision tree, claim-type vocabulary).

• figures/ — curated figures used in the Jupyter Book.

Nanopublication chain¶

The published chain is listed in nanopubs/PUBLISHED.md. Each step links to its viewer URL on the Science Live platform.

Citation¶

If you use this work, please cite both:

• This software: CITATION.cff → DOI Fouilloux (2026).

• The original paper: Sinervo et al. (2010).