Long Covid DALYs

A research project to explore how different public health interventions could improve or worsen the burden of long covid, as measured in Disability Adjusted Life Years

Affiliated Organizations

• PolyBio
• University of California, San Francisco

Prerequisites

• Install Node (if you don't have it): https://nodejs.org/en/download

• Set up Git (if you haven't) https://docs.github.com/en/get-started/git-basics/set-up-git

Setup

1. Fork the repository https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo#forking-a-repository

2. Clone the repo to your local machine https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo#cloning-your-forked-repository

3. (if you're going to contribute back to this repo) Add this repo as the "upstream" https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo#configuring-git-to-sync-your-fork-with-the-upstream-repository

4. Install dependencies

     cd long-covid-dalys/

     npm install

5. Preview:

    npm run dev

   The site will be available at http://localhost:5173

📈 Data overview

• Data lives in src/data/ directory
  • DALYs.json - Baseline DALY projections (main chart data)
• Configuration lives in src/config
  • scenarios.ts defines the various public health scenarios and their data structure

Update DALYs

Format for src/data/DALYS.json:

[
  {
    "year": 1,
    "baseline": 258,
    "HEPAMostCommonSpaces": 246,
    "HEPASchoolsAndDaycare": 233,
    "HEPAAllPublicIndoor": 162,
    "farUVCMostCommonSpaces": 240,
    "farUVCSchoolsAndDaycare": 226,
    "farUVCAllPublicIndoor": 131
  },
  {
    "year": 2,
    "baseline": 258,
    "HEPAMostCommonSpaces": 246,
    "HEPASchoolsAndDaycare": 233,
    "HEPAAllPublicIndoor": 162,
    "farUVCMostCommonSpaces": 240,
    "farUVCSchoolsAndDaycare": 226,
    "farUVCAllPublicIndoor": 131
  },
  ...
]

• year: number 1-10, for number of years of the projection
• baseline: baseline scenario, and each further scenario.
• numbers are the resultant DALYs

To update: Replace src/data/DALYS.json with your updated projections that match the above format. The chart will use the new data.

• Easiest method: use the GitHub web interface to replace the src/data/DALYS.json file.

Testing Your Changes (if working locally)

After updating data files:

1. Development mode: npm run dev - See changes immediately with hot reload
2. Production build: npm run build - Create optimized build for deployment
3. Preview build: npm run preview - Test the production build locally

Deployment

After updating data files and verifying they work:

1. Commit your changes: git add . && git commit -m "a message describing your changes, such as: Update DALY projections"
2. Push to your repository: git push
3. Open a pull request against the "upstream" repo: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork
4. Once merged, the application will automatically rebuild and deploy to Netlify

React + TypeScript + Vite

This project bootstrapped from the following Vite template: React + TypeScript + Vite

This template provides a minimal setup to get React working in Vite with HMR and some ESLint rules.

Currently, two official plugins are available:

• @vitejs/plugin-react uses Babel for Fast Refresh
• @vitejs/plugin-react-swc uses SWC for Fast Refresh

Expanding the ESLint configuration

If you are developing a production application, we recommend updating the configuration to enable type aware lint rules:

• Configure the top-level parserOptions property like this:

export default tseslint.config({
  languageOptions: {
    // other options...
    parserOptions: {
      project: ["./tsconfig.node.json", "./tsconfig.app.json"],
      tsconfigRootDir: import.meta.dirname,
    },
  },
});

• Replace tseslint.configs.recommended to tseslint.configs.recommendedTypeChecked or tseslint.configs.strictTypeChecked
• Optionally add ...tseslint.configs.stylisticTypeChecked
• Install eslint-plugin-react and update the config:

// eslint.config.js
import react from "eslint-plugin-react";

export default tseslint.config({
  // Set the react version
  settings: { react: { version: "18.3" } },
  plugins: {
    // Add the react plugin
    react,
  },
  rules: {
    // other rules...
    // Enable its recommended rules
    ...react.configs.recommended.rules,
    ...react.configs["jsx-runtime"].rules,
  },
});

Prior Art and Libraries Used

• UI components from Shadcn, OriginUI
• Charts built using Recharts