covid19_scenarios

COVID-19 Scenarios

Models of COVID-19 outbreak trajectories and hospital demand

covid19-scenarios.org

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Simulator Source code repository Data directory Updates

Overview

This tool is based on the SIR model (see about page for details) that simulates a COVID19 outbreak. The population is initially mostly susceptible (other than for initial cases). Individuals that recover from COVID19 are subsequently immune. Currently, the parameters of the model are _not_ fit to data but are simply defaults. These might fit better for some localities than others. In particular the initial cases counts are often only rough estimates. The primary purpose of the tool is to explore the dynamics of COVID19 cases and the associated strain on the health care system in the near future. The outbreak is influenced by infection control measures such as school closures, lock-down etc. The effect of such measures can be included in the simulation by adjusting the mitigation parameters. Analogously, you can explore the effect of isolation on specific age groups in the column "Isolated" in the table on severity assumptions and age specific isolation. Most parameters can be adjusted in the tool and for many of them we provide presets (scenarios). Input data for the tool and the basic parameters of the populations are collected in the [`/data` directory](https://github.com/neherlab/covid19_scenarios/tree/master/data). Please add data on populations and parsers of publicly available case count data there.

User's Guide

The online application provides a friendly user interface with drop downs to choose model parameters, run the model, and export results in CSV format. A detailed process is below. ### Parameters: population Select the population drop down and select a country/region to auto-populate the model's parameters with respective UN population data. These parameters can be individually updated manually if necessary. ### Parameters: epidemiology The epidemiology parameters are a combination of speed and region - specifying growth rate, seasonal variation, and duration of hospital stay. To choose a preset distribution, select one of the options from the epidemiology drop down to auto-populate the model's parameters with the selected parameters. ### Parameters: mitigation Mitigation parameters represent the reduction of transmission through mitigation (infection control) measures over time. To select a preset, click on the mitigation dropdown and select one of the options. Otherwise, the points on the graph can be dragged and moved with the mouse. The parameter ranges from one (no infection control) to zero (complete prevention of all transmission). ### Running the Model Once the correct parameters are inputted, select the run button located in the Results section of the application. The model output will be displayed in 2 graphs: Cases through time and Distribution across groups and 2 tables: Populations and Totals/Peak. ### Exporting Results The model's results can be exported in CSV format by clicking the "export" button in the right hand corner.

️ Developer's guide

### Quick Start #### Run natively Install the requirements: - git >= 2.0 - node.js >= 10 (we recommend installation through [nvm](https://github.com/nvm-sh/nvm) or [nvm-windows](https://github.com/coreybutler/nvm-windows)) - 1.0 < yarn < 2.0 Then in your terminal type: ```bash git clone --recursive https://github.com/neherlab/covid19_scenarios cd covid19_scenarios/ cp .env.example .env yarn install yarn dev ``` (on Windows, substitute `cp` with `copy`) This will trigger the development server and build process. Wait for the build to finish, then navigate to `http://localhost:3000` in a browser (last 5 versions of Chrome or Firefox are supported in development mode). > ℹ️ Hint: type "rs" in terminal to restart the build > ℹ️ Hit Ctrl+C in to shutdown the server #### Run in docker container Install the requirements: - Docker > 19.0 - docker-compose >= 1.25 Run docker-compose with `docker/docker-compose.dev.yml` file: ``` UID=$(id -u) docker-compose -f docker/docker-compose.dev.yml up --build ``` Variable `UID` should be set to your Unix user ID. On single-user setups these are usually 1000 on Linux and 523 on Mac. ### Directory Structure As a developer you are most likely interested in the actual source code in `src/` directory. | File or directory | Contents | | ---------------------- | --------------------------------------------- | | algorithims/ | Algorithm's implementation | | ├model.ts/ | Model's implementation | | ├run.ts/ | Algorithm's entry point | | assets/ | Input data, images, and text assets | | components/ | React components | | ├Form/ | Form components | | ├Main/ | Simulator's UI main component implementation | | | ├Containment/ | Containment widget | | | ├Results/ | Results panel | | | ├Scenario/ | Scenario panel | | | ├state/ | Main component's state management (hooks) | | | ├validation/ | Form validation | | | ├Main.scss/ | | | | ├Main.tsx/ | Simulator's UI main component entry point | | ├App.tsx/ | App main component | | locales/ | Locales for translation | | pages/ | Application's pages | | server/ | Server that serves production build artifacts | | state/ | App state management (Redux and sagas) | | styles/ | Stylesheets | | types/ | Typescript typings | | index.ejs | HTML template | | index.polyfilled.ts | Entry point wrapper with polyfills | | index.tsx | Real entry point | | links.ts | Navbar links | | routes.ts | Routes (URL-to-page mapping) | ### Production build In order to replicate the production build locally, use this command: ```bash yarn prod:watch ``` This should build the application in production mode and to start static server that will serve the app on `http://localhost:8080` (by default) ### Translations The translation JSON files are in [src/i18n/resources](https://github.com/neherlab/covid19_scenarios/tree/master/src/i18n/resources) You can edit them directly or using GitLocalize. Here are the direct links to GitLocalize for each language that has translations currently: - [:saudi_arabia: ar](https://gitlocalize.com/repo/4360/ar/src/i18n/resources/en/common.json) - [:de: de](https://gitlocalize.com/repo/4360/de/src/i18n/resources/en/common.json) - [:us: en](https://gitlocalize.com/repo/4360/en/src/i18n/resources/en/common.json) - [:es: es](https://gitlocalize.com/repo/4360/es/src/i18n/resources/en/common.json) - [:iran: fa](https://gitlocalize.com/repo/4360/fa/src/i18n/resources/en/common.json) - [:fr: fr](https://gitlocalize.com/repo/4360/fr/src/i18n/resources/en/common.json) - [:india: hi](https://gitlocalize.com/repo/4360/hi/src/i18n/resources/en/common.json) - [:it: it](https://gitlocalize.com/repo/4360/it/src/i18n/resources/en/common.json) - [:jp: ja](https://gitlocalize.com/repo/4360/ja/src/i18n/resources/en/common.json) - [:kr: ko](https://gitlocalize.com/repo/4360/ko/src/i18n/resources/en/common.json) - [:poland: pl](https://gitlocalize.com/repo/4360/pl/src/i18n/resources/en/common.json) - [:portugal: pt](https://gitlocalize.com/repo/4360/pt/src/i18n/resources/en/common.json) - [:ru: ru](https://gitlocalize.com/repo/4360/ru/src/i18n/resources/en/common.json) - [:tr: tr](https://gitlocalize.com/repo/4360/tr/src/i18n/resources/en/common.json) - [:cn: zh](https://gitlocalize.com/repo/4360/zh/src/i18n/resources/en/common.json) ### Schemas The directory `schemas/` contains JSON schemas which serve as a base for type checking, validation and serialization. In particular, some of the types: - are generated from schemas for both Python (as classes) and Typescript (as interfaces) - are validated on runtime using corresponding libraries in these languages - are (when appropriate) serialized a