doglaw1993/coronaseir

Simple SEIR model Python script for the COVID-19 pandemic with real world data comparison.

coronavirus SEIR model

An SEIR model of the COVID-19 pandemic. Heavily based off a fork of coronafighters work here

Disclaimer

This is not a scientific or medical tool. Use at your own risk.

Features

• SEIR epidemic model
• Reduced R0 after a certain amount of days to account for containment measures.
• Delays to allow for lagging official data etc.
• Real world data automatically updated every three hours from Johns Hopkins CSSE (https://github.com/CSSEGISandData/2019-nCoV) via https://github.com/ExpDev07/coronavirus-tracker-api
• country population data (https://github.com/samayo/country-json)
• check out screenshots below

Installation / Requirements / Documentation

Needs Python 3.x installed.

Note: Make sure you got correct number for population and available ICU units for your country.

ToDo

• ventilator patients separately?
• be more precise in differentiation between hospitalization and ICU

Credits

Based on:
https://github.com/ckaus/EpiPy
https://scipython.com/book/chapter-8-scipy/additional-examples/the-sir-epidemic-model/

API/Data: https://github.com/ExpDev07/coronavirus-tracker-api https://github.com/samayo/country-json

Formulas:
https://hal.archives-ouvertes.fr/hal-00657584/document
https://institutefordiseasemodeling.github.io/Documentation/general/model-seir.html

Parameters:
Master CoVidActNow CoVid-19 Model - https://docs.google.com/spreadsheets/d/1YEj4Vr6lG1jQ1R3LG6frijJYNynKcgTjzo2n0FsBwZA/htmlview?#

https://www.medrxiv.org/content/10.1101/2020.03.05.20031815v1

Country Data: https://github.com/porimol/countryinfo

Examples

Without any lockdown or testing delays:

With lockdown reducing R0 to halve intital R0

License

MIT license