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.

• Nice webgui: http://gabgoh.github.io/COVID/index.html
• Another great web based model: https://neherlab.org/covid19/
• rewrite of this project with sophisticated code: https://github.com/cfculhane/coronaSEIR

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

• 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 https://github.com/ExpDev07/coronavirus-tracker-api
• country population data (https://github.com/samayo/country-json)
• can exclude countries, e.g. world without China
• check out screenshots below

Needs Python 3.x installed. Tested on Ubuntu. Should run on Window and Mac, too.

# everything after the hash symbol # is a comment
$ git clone https://github.com/coronafighter/coronaSEIR  # create local copy
$ 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

$ git pull origin master  # update to latest version, might overwrite local changes

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.

• idea: compare optimal fit doubling time for all countries
• idea: compare death rate by testing capacity --> extrapolate fit curve to find real death rate
• idea: calculate for all countries to compare how badly hit (days0 needs to be set manually)
• add data about lockdown starting times, also make it possible to enter as a date
• make R0 and days0 lists to be able to have more than two phases
• add data about intensive care units
• ventilator patients separately?
• make parsing code cleaner / simpler
• be more precise in differentiation between hospitalization and ICU
• X automatic date offset
• X maybe find a better fit with lower R0 - the infectious time seems to be quite short?
• X add proper list of populations
• X use real dates instead of days?

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/
timeline 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/ gamma: Generation time (serial interval): https://www.medrxiv.org/content/10.1101/2020.03.05.20031815v1
also: http://www.cidrap.umn.edu/news-perspective/2020/03/short-time-between-serial-covid-19-cases-may-hinder-containment
Relationship hospitalized/ICU/death https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-COVID19-NPI-modelling-16-03-2020.pdf
r0 ~ 3.0 https://www.newscientist.com/article/2238578-uk-has-enough-intensive-care-units-for-coronavirus-expert-predicts/
r1 (thanks paus-5!) https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3539694 sigma: Infection occurs before symptoms (Drosten): https://www.medrxiv.org/content/10.1101/2020.03.08.20032946v1.full.pdf
Number of asymptomatics: https://www.zmescience.com/medicine/iceland-testing-covid-19-0523/
some more in the source code

MIT license