Public Health Environmental Surveillance Evaluation Framework (PHES-EF)

An international consensus study developing evaluation standards for wastewater-based surveillance using a multidisciplinary, multinational approach.

Website: https://big-life-lab.github.io/PHES-EF/

About PHES-EF

The Public Health Environmental Surveillance Evaluation Framework (PHES-EF) is developing a consensus-driven evaluation framework for public health environmental surveillance, using wastewater surveillance as the primary example.

Key Features:

• Open science approach (CC-BY-SA-4.0 license)
• eDelphi consensus methodology
• International, multidisciplinary collaboration
• Emphasis on equity, diversity, and inclusion
• Registered protocol (Ottawa Health Science Network REB #20230428-01H)

Repository Structure

PHES-EF/
├── _quarto.yml           # Quarto website configuration
├── *.qmd                 # Content pages (index, about, methods, delphi, etc.)
├── assets/               # Images, logos, SCSS themes, CSL files
├── data/                 # CSV data files (schema, example terms)
├── references.bib        # Bibliography
├── llm.md               # AI assistant instructions
└── docs/                 # Build output (auto-generated, do not edit)

Requirements

Software

• Quarto (latest version recommended)
• TinyTeX: quarto install tinytex
• R >= 4.2.0 (compatibility floor for StatsCan/ICES environments)

R Environment

This project uses renv for package management:

# After cloning the repository
renv::restore()

# After adding new packages
renv::snapshot()

Note: Commit renv.lock, .Rprofile, and renv/activate.R. Do NOT commit renv/library/, renv/staging/, or renv/local/.

Development Workflow

Local Preview

quarto preview

Opens a live preview that updates as you make changes.

Build Locally

quarto render

Generates static files in the docs/ directory.

Publishing

• Automatic: GitHub Actions publishes to GitHub Pages on push to main branch
• Manual Setup: Configure GitHub Pages to use gh-pages branch, root folder
  • Settings → Pages → Branch: gh-pages, Folder: /
  • The gh-pages branch appears after first successful publish

Data Files

• data/PHES-EF-schema.csv - Framework schema definition
• data/PHES-ef-example-terms.csv - Example terminology

Continuous Integration

• Pull Requests: Build check only (not published)
• Main Branch: Automatic deployment to GitHub Pages
• See .github/workflows/ for workflow details

Contributing

See llm.md for AI assistant guidelines and development standards.

Funding & Acknowledgments

This project is funded by:

• Canadian Institutes for Health Research (CoVaRR-Net, FRN: 175622)
• Health Canada (Safe Restart Agreement, #2223-HQ-000098)

The views expressed do not necessarily represent those of the funding organizations.

License

CC-BY-SA-4.0 - See LICENSE.md for details.

Contact

Visit the Contact page or the Team page for more information.