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https://github.com/neherlab/covid19_scenarios

Models of COVID-19 outbreak trajectories and hospital demand
https://github.com/neherlab/covid19_scenarios
coronavirus covid covid-19 data hospital model modelling ncov neherlab open-source opensource outbreak population research sars-cov-2 science simulation ventilator
Last synced: 3 months ago
JSON representation
Models of COVID-19 outbreak trajectories and hospital demand
Host: GitHub
URL: https://github.com/neherlab/covid19_scenarios
Owner: neherlab
License: mit
Created: 2020-02-29T14:53:31.000Z (over 4 years ago)
Default Branch: master
Last Pushed: 2022-02-15T19:04:38.000Z (over 2 years ago)
Last Synced: 2024-04-11T00:26:42.806Z (3 months ago)
Topics: coronavirus, covid, covid-19, data, hospital, model, modelling, ncov, neherlab, open-source, opensource, outbreak, population, research, sars-cov-2, science, simulation, ventilator
Language: JavaScript
Homepage: https://covid19-scenarios.org
Size: 56.5 MB
Stars: 1,362
Watchers: 50
Forks: 355
Open Issues: 44
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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awesome-stars - neherlab/covid19_scenarios - Models of COVID-19 outbreak trajectories and hospital demand (JavaScript)
awesome-stars - neherlab/covid19_scenarios - Models of COVID-19 outbreak trajectories and hospital demand (JavaScript)
README

        


  COVID-19 Scenarios





Models of COVID-19 outbreak trajectories and hospital demand





  

    🌐 covid19-scenarios.org

  





  

    

  







  

    

  

  

    

  

  

    

  

  

    

  





  

    

  

  

    

  

  

    

  

  

    

  

  

    

  



  

    

  

  

    

  

  

    

  

  

    

  





  

    

  

  

    

  

  

    

  

  

    

  

  

    

  





  

    

  

  

    

  





  

    

  







Got questions or suggestions?





  

    

  







🔍 Discover







    

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 and deserialized using generated serialization/deserialized functions

We make emphasis on types that are shared across languages (e.g. Python to Typescript) as well as on types that

participate in input-output (e.g. URLs, Local Storage, File I/O) and require particularly careful validation and

serialization.

If you are planning to change one of the types that happens to be generated, you need to modify the corresponding schema

first and them re-run the type generation.

#### See also:

- [JSON Schema website](https://json-schema.org/)

- [Understanding JSON Schema](https://json-schema.org/understanding-json-schema/)

### Release cycle, continuous integration and deployment

TODO

### Getting Started

For new contributers, follow the guide below to learn how to install required software, fork & clone, and submit changes

using a pull request.

#### ✨ Installing Required Software

1. Install Git by following GitHub's instructions

   [here](https://help.github.com/en/github/getting-started-with-github/set-up-git)

2. Node.js can be installed using nvm on [Mac/Linux](https://gist.github.com/d2s/372b5943bce17b964a79) and nvm-windows

   on [Windows](https://docs.microsoft.com/en-us/windows/nodejs/setup-on-windows).

3. Yarn can be globally installed following [these steps](https://classic.yarnpkg.com/en/docs/install/#mac-stable)

#### 🍴 Forking the Repo

Click the Fork button on the upper right-hand side of the repository’s page.

#### 👯 Clone Forked Repository

Clone this repository to your local machine. You can use the URL of your repo inside git command, for example:

```bash

git clone https://github.com//covid19_scenarios

```

#### 🔨 Start coding!

#### 💻 Updating the Forked Repository

To ensure that the forked code stays updated, you’ll need to add a Git remote pointing back to the original repository

and create a local branch.

```

git remote add upstream https://github.com/neherlab/covid19_scenarios

```

To create and checkout a branch,

1. Create and checkout a branch

```

git checkout -b 

```

2. Make changes to the files

3. Commit your changes to the branch using `git add` and then `git commit`

#### 💪 Submitting changes using a Pull Request

To submit your code to the repository, you can

[submit a pull request](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request).





🙏 Acknowledgements



### Initial development

Initially, the development was started in the [Research group of Richard Neher](https://neherlab.org) at the

[Biozentrum, University of Basel](https://www.biozentrum.unibas.ch/home/) (Basel, Switzerland) by Richard Neher

([@rneher](https://github.com/rneher)), Ivan Aksamentov ([@ivan-aksamentov](https://github.com/ivan-aksamentov)) and

Nicholas Noll ([@nnoll](https://github.com/nnoll)).

[Jan Albert](https://ki.se/en/mtc/jan-albert-group) from [Karolinska Institute](https://ki.se/en) (Stockholm, Sweden)

had the initial idea to develop this tool and suggested features and parameters, and

[Robert Dyrdak](https://staff.ki.se/people/robdyr) provided initial parameter estimates.








_{Richard Neher}




@rneher










_{Ivan Aksamentov}




@ivan-aksamentov










_{Nicholas Noll}




@nnoll










_{Jan Albert}




 










_{Robert Dyrdak}




 



### Contributors ✨

We are thankful to all our contributors, no matter how they contribute: in ideas, science, code, documentation or

otherwise. Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):

  

    
_{Aditya Sharad}
💻 🔧

    
_{Agon Hasani}
💻 🔣

    
_{Alexis Iglauer}
💻 🔣 🚧

    
_{Andrew McKeever}
💻 💬

    
_{Anson Chong}
💻 🎨

    
_{Arkadiusz Goralski}
💻 🌍

    
_Arnaud
💻 👀

  

  

    
_{Ashwin Gokhale}
💻

    
_{Bradley Betts}
💻 🔧

    
_{Bruno RZN}
💻 💬 👀

    
_{Christian Wienbruch}
💻 🔣

    
_{Christian-G-UT}
💻 🔣

    
_{Danko Kozar}
💻 🎨

    
_{Danny Sepler}
💻 💬 👀

  

  

    
_{Darío Hereñú}
📖 🌍 💻 🔣

    
_{David Hansen}
💻

    
_{Di Guan}
💻

    
_{Emmanuel Murillo Sánchez}
💻 💬 🌍

    
_{Evan Krell}
💻 🔣

    
_{Fabio Zanini}
💻 🔣

    
_{Gabriel Homsi}
💻 🔣

  

  

    
_{Gavin Jefferies}
💻 📖 🔣 ⚠️ 👀

    
_{Gustavo Ribeiro}
💻 🔣

    
_{Hannes Granström}
💻 💬 🌍

    
_{Hui Xiang Chua}
💻 🔣 🔧

    
_{Igor Savin}
💻 💬 👀

    
_{Ivan Aksamentov}
💻 📖 🚇 🚧 💬 👀

    
_{Iván Yepes}
💻 💬

  

  

    
_{Jacob Smith}
💻 💬 👀

    
_{Jill Adona}
💻 🔣

    
_{John Yani}
💻 🔣

    
_{Joram van den Boezem}
💻 🔣

    
_{Jose Eduardo Kimura}
💻 🎨

    
_Joël
💻 💬 🚧

    
_Juha
🖋 🌍

  

  

    
_{Kamil Bobrowski}
💻 ⚠️ 🚧

    
_Kartik
💻 🔣

    
_{Manuel Blechschmidt}
💻 💬 ⚠️

    
_{Maoz Gelbart}
💻 🔣

    
_{Martin Vejmelka}
💻 💬 🔣

    
_{Max Tarsis}
💻 💬 ⚠️

    
_{Mickey Pearce}
💻 🚧

  

  

    
_{Miguel Serrano}
💻 💬 📖 🚧

    
_{Mika Laaksonen}
💻 🎨

    
_MikaMaracuja
💻 🔣

    
_{Nataliya Karatkova}
💻 🎨

    
_{Nathan Springman}
💻 🎨

    
_{Nicholas Noll}
💻 📖 🔣 🚧 👀

    
_{Nils Ole Tippenhauer}
💻 🔣

  

  

    
_{Patrick Assaf}
💻 🎨

    
_{Patrik Varga}
💻 🚧 💬

    
_{Pete Bacon Darwin}
💻 💬

    
_{Rachel Harvill}
💻 💬 📖

    
_{Rebecca Mullin}
💻 💬

    
_{Rich Evans}
💻 📖 🔣

    
_{Richard Neher}
💻 📖 🔣 🚧 🛡️ 👀

  

  

    
_{Rizky Maulana Nugraha}
💻 🚧

    
_{Rui Lima}
💻 💬 🌍

    
_{Rui Saraiva}
💻 📖 💬 🚧

    
_Sam
📖 🖋

    
_{Sebastian Gierth}
💻 💬 👀 🌍

    
_{TIAGO ANDRES VAZ}
💻 🔣 🤔

    
_TeepaBlue
💻

  

  

    
_{Thomas Eckert}
💻 📖

    
_{Tryggvi Gylfason}
💻 🎨

    
_{Valentin Druelle}
💻 🔣 🤔 📢

    
_{Victor Cordova}
💻 🎨

    
_{William Hiver}
💻 🌍

    
_abrie
💻 📖 ⚠️ 👀

    
_alebrand
💻 🔣

  

  

    
_arieltonglet
💻 🎨

    
_aschelch
💻 💬 🌍

    
_bharath6365
💻 💬

    
_btoo
💻 📖 🚧

    
_ceporche
🌍

    
_joaopn
💻 🌍

    
_kmid5280
💻 🎨

  

  

    
_kupad95
💻 🔣

    
_nono
💻 💬 🌍

    
_pvillamartin
💻 🔣 🎨

    
_r-s-rai
💻 🎨

    
_thoo1
💻 🎨

  

This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification.

Contributions of any kind welcome!

## License

[MIT License](LICENSE)

Copyright (c) 2020 neherlab