coronavirus SEIR model

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

Purpose is to easily be able to experiment and better understand what is happening currently and what might happen in the near future.

What I learned: Activating containment measures early can save lives.

Disclaimer

This is not a scientific or medical tool. Use at your own risk. BETA! There might be serious bugs.

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.
• hopefully easily readable code
• Real world data automatically updated every three hours from Johns Hopkins CSSE (https://github.com/CSSEGISandData/2019-nCoV) via 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. Tested on Ubuntu. Should run on Window and Mac, too.

$ pip3 install --upgrade numpy scipy matplotlib python-dateutil  # might need sudo -H pip3 ...
$ python3 ./main_coronaSEIR.py
read data: 843103 bytes
r0: 5.20    r1: 1.30
doubling0 every ~3.4 days
day 60
 Infected: 119363 0.2
 Infected found: 1085 0.0
 Hospital: 787 0.0
 Recovered: 44584 0.1
 Deaths: 17 0.0
data points for Italy: 40
first data: 2020-01-31
latest data: 2020-03-10 (you can update the data manually by running fetch_data.py)

$python3 ./world_data.py  # to just plot current numbers

$python3 ./deaths_per_capita.py  # might be a better measure than cases per capita

No GUI, you need to alter the script and run again to experiment.

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

ToDo

• automatic date offset
• maybe find a better fit with lower R0
• add proper list of populations
• add data about intensive care units
• use real dates instead of days?
• ventilator patients separately?
• make parsing code cleaner / simpler
• 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:
https://www.reddit.com/r/COVID19/comments/fbdzc1/coronavirus_epidemiology_metaanalysis_and/ https://www.reddit.com/r/COVID19/comments/fbxk43/update_open_source_simple_coronavirus_modeling/ https://www.reddit.com/r/COVID19/comments/fd6lmg/infectionfatalityratio_ifr_of_covid19_is/
https://www.reddit.com/r/COVID19/comments/ffzqzl/estimating_the_asymptomatic_proportion_of_2019/
https://www.reddit.com/r/Coronavirus/comments/f8k2nj/why_sarscov2_is_not_just_the_flu_with_sources/ https://www.medrxiv.org/content/10.1101/2020.03.05.20031815v1
http://www.cidrap.umn.edu/news-perspective/2020/03/short-time-between-serial-covid-19-cases-may-hinder-containment
some more in the source code

Screenshots

License

MIT license