Tsimane Oral Health Heatmap

TL;DR

This static site publishes an oral-health heatmap (oral-health-heatmap.png) and summary page (index.md) covering 28 permanent teeth across 1,176 Tsimane adults in Bolivia. Local scripts rasterize the committed source figure (Figure2-Teeth_v4.1.pdf) into a 200 DPI PNG, validate repository links and site metadata, and smoke-test the rendered HTML page.

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Live Site

View the published page and full-resolution figure at:

https://mschwar.github.io/data-visualization/

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Inputs, Checks, and Outputs

• Inputs: Narrative copy in index.md, site settings in _config.yml, custom styles in assets/css/style.scss.css, and the committed figure Figure2-Teeth_v4.1.pdf. The raw source dataset behind the figure is not published in this repository.
• Checks: Structural and link validation via scripts/validate_repo.py, documentation hygiene checks via tests/test_doc_hygiene.py, and rendered HTML checks via scripts/check_homepage.py.
• Outputs: The 1700 x 2200 raster image oral-health-heatmap.png and the static Jekyll site rendered into _site/index.html.

For the contributor branch and verification workflow, read docs/agentic-first-buildout-plan.md and AGENTS.md.

About the Visualization

The heatmap displays dental status across 1,176 adults (543 men and 633 women) from the Tsimane Health and Life History Project. Over 32,000 tooth-level observations are organized across four visual dimensions:

• 28 permanent teeth: Incisors, canines, premolars, and first and second molars.
• Age groups: Adults sorted from ages 15-24 through 75+.
• Sex: Side-by-side panels comparing men and women.
• Anatomy: Separate upper (maxilla) and lower (mandible) dental arches.

A five-point ordinal color scale encodes tooth condition from healthy (blue) to missing (dark red).

Repository Contents

• index.md: Main GitHub Pages content and figure narrative.
• oral-health-heatmap.png: Published 200 DPI heatmap image.
• Figure2-Teeth_v4.1.pdf: Committed vector source figure used to regenerate the PNG.
• _config.yml: Jekyll theme, metadata, and public-site file exclusions.
• Gemfile and .ruby-version: Pinned Ruby 3.3.4 and github-pages 232 build toolchain.
• scripts/validate_repo.py: Repository structure, config, and local link validator.
• scripts/render_heatmap.py: PDF-to-PNG rasterization script for the heatmap image.
• scripts/check_homepage.py: Smoke test for rendered homepage HTML.
• tests/test_doc_hygiene.py: Zero-dependency standard-library documentation hygiene test suite.
• CURRENT_STATE.md: Operational status, verification evidence, and known constraints.
• docs/heatmap-provenance.md: Figure provenance boundary and local rebuild notes.
• docs/historical-artifacts.md: Retention policy for historical repository snapshots.
• README.CRAWL.md: Retained historical crawl snapshot kept for audit comparison only.

Historical Artifacts

README.CRAWL.md is retained as a historical snapshot, not as active documentation. _config.yml excludes it from the public site, and docs/historical-artifacts.md defines the retention rules.

Validate the Repository

Run the structure validator and documentation hygiene gate from the repository root:

python scripts/validate_repo.py
/usr/bin/python3 -m unittest tests/test_doc_hygiene.py -v

After building the Jekyll site, run the homepage HTML smoke test:

bundle exec jekyll build
python scripts/check_homepage.py

You can also pass an explicit HTML file path or live site URL:

python scripts/check_homepage.py _site/index.html
python scripts/check_homepage.py https://mschwar.github.io/data-visualization/

Rebuild Locally

This repository pins Ruby 3.3.4 and github-pages 232 to match GitHub Pages. Run these commands to build the site or regenerate the PNG locally:

bundle install
bundle exec jekyll build
bundle exec jekyll serve --baseurl=""
python scripts/render_heatmap.py

scripts/render_heatmap.py exports Figure2-Teeth_v4.1.pdf at 200 DPI to match the published 1700 x 2200 pixel PNG. Only PNG encoder metadata headers differ across PDF rasterizers.

On an earlier Windows audit host, MiKTeX pdftoppm failed with temporary log permission errors. Read docs/heatmap-provenance.md for the exact provenance boundary and rebuild details.

Publication Context

This figure accompanies the published study:

Trumble, B., Schwartz, M., Kaplan, H., Gurven, M., and coauthors (2024). Poor Oral Health Is Associated With Inflammation, Aortic Valve Calcification, and Brain Volume Among Forager-Farmers. The Journals of Gerontology. Digital Object Identifier (DOI): 10.1093/gerona/glae013

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Created by Matthew Schwartz.