diff --git a/README.md b/README.md index bf848b63..c1a3ec1c 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,102 @@ -# Epiverse developer website +# Epiverse-TRACE Website -This repository contains all the code, markdown files, scripts, assets, and so on used to create [the Epiverse website](https://epiverse-trace.github.io). +This repository contains the source code for the [Epiverse-TRACE website](https://epiverse-trace.github.io), showcasing our ecosystem of tools for epidemic analytics and outbreak response preparedness. -## Rendering the website +## About Epiverse-TRACE -Please ensure you have Quarto installed on your command line. You should be able to run the following and render the entire website: +Epiverse-TRACE develops **robust, validated, and reliable** software tools for epidemic analytics, helping to transform how we respond to infectious disease outbreaks globally. Our mission is to build integrated, generalisable, and scalable community-driven software that addresses gaps identified during the COVID-19 pandemic. + +### Our Ecosystem + +We maintain R packages covering the complete epidemiological analysis pipeline: + +- **Data Management**: Import ([`readepi`](https://epiverse-trace.github.io/readepi)), clean ([`cleanepi`](https://epiverse-trace.github.io/cleanepi)), simulate ([`simulist`](https://epiverse-trace.github.io/simulist)), and validate ([`linelist`](https://epiverse-trace.github.io/linelist)) epidemiological data +- **Parameter Estimation**: Access epidemiological parameters ([`epiparameter`](https://epiverse-trace.github.io/epiparameter)), estimate case fatality ratios ([`cfr`](https://epiverse-trace.github.io/cfr)), and analyze seroprevalence ([`serofoi`](https://epiverse-trace.github.io/serofoi)) +- **Modeling & Analysis**: Simulate epidemic dynamics ([`epidemics`](https://epiverse-trace.github.io/epidemics)), calculate final outbreak size ([`finalsize`](https://epiverse-trace.github.io/finalsize)), and assess vaccine efficacy ([`vaccineff`](https://epiverse-trace.github.io/vaccineff)) +- **Specialized Tools**: Analyze transmission chains ([`epichains`](https://epiverse-trace.github.io/epichains)), superspreading events ([`superspreading`](https://epiverse-trace.github.io/superspreading)), and vector-borne diseases ([`epiCo`](https://epiverse-trace.github.io/epiCo)) + +All packages are built on methods validated through real epidemic responses including cholera, COVID-19, dengue, Ebola, and Zika outbreaks. + +## Repository Structure + +This website is built with [Quarto](https://quarto.org/) and features: + +- **Blog**: Technical articles, package releases, and community updates +- **Documentation**: Getting started guides and learning materials +- **Resources**: How-to guides and tutorials +- **Community**: Contributor profiles and team information +- **Presentations**: Conference talks and workshop materials ``` -quarto render -# individual pages -quarto render +├── _components/ # React components for interactive elements +├── _data/ # CSV files with contributor and package data +├── posts/ # Blog posts and articles +├── slides/ # Presentation materials +├── resources/ # Documentation and guides +├── _scripts/ # Data collection and automation scripts +└── _templates/ # Content generation templates ``` -## Scheduling pull requests +## Development Setup + +### Prerequisites + +- [Quarto](https://quarto.org/docs/get-started/) CLI installed +- [R](https://cran.r-project.org/) (for content generation scripts) + +### Getting Started + +1. **Clone the repository** + ```bash + git clone https://github.com/epiverse-trace/epiverse-trace.github.io.git + cd epiverse-trace.github.io + ``` + +2. **Render the website** + ```bash + # Render entire website + quarto render + + # Render individual pages + quarto render + + # Preview locally + quarto preview + ``` + +### Content Management + +- **Blog posts**: Add new `.qmd` files to `posts/` directory +- **Release posts**: Automatically upon release on GitHub +- **Contributor data**: Automatically updated via `_scripts/collect_contributor_data.R` +- **Package information**: Pulled from `_data/epiverse_pkgs.csv` + +## Contributing + +We welcome contributions! Feel encouraged to open up pull requests for small changes or existing issues. If you want to discuss a new package, [please use our discussion board first](https://github.com/orgs/epiverse-trace/discussions). + +### Scheduling Pull Requests +For time-sensitive content (e.g., blog posts), you can schedule merges by adding `/schedule ` at the end of your PR description using ISO8601 format (e.g., `/schedule 2024-12-25T10:00:00Z`). + +## Community + +Epiverse-TRACE is a collaborative effort involving: + +- **London School of Hygiene & Tropical Medicine (LSHTM)** +- **MRC Unit The Gambia at LSHTM** +- **Universidad Javeriana** (Colombia) +- **Universidad de los Andes** (Colombia) + +Supported by the **Wellcome Trust**, **Rockefeller Foundation**, and **IDRC Canada** as part of the data.org Epiverse initiative. + +### Connect With Us + +- **Bluesky**: [@epiverse-trace.bsky.social](https://bsky.app/profile/epiverse-trace.bsky.social) +- **GitHub**: [@epiverse-trace](https://github.com/epiverse-trace) +- **R Universe**: [epiverse-trace.r-universe.dev](https://epiverse-trace.r-universe.dev/packages) +- **Twitter**: [@Epiverse_TRACE](https://twitter.com/Epiverse_TRACE) +- **Website**: [epiverse-trace.github.io](https://epiverse-trace.github.io) + +## License -Given that we sometimes want to merge pull requests at specific times, especially for blog posts, there is the option to schedule a merge attempt. To do so, add an ISO8601 compliant datetime command as such at the end of the first post in the PR: `/schedule ` (e.g., `/schedule 2026-01-01` for January 1st, 2026). \ No newline at end of file +This website content is licensed under [Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0/). Website code is licensed MIT. Individual software packages maintain their own licenses.