missoula-covid19-website's Introduction

Missoula/Montana Covid-19 Website

www.missoulacovid19.com

Dependencies

Python 3.7.3
scipy
pandas
numpy
streamlit
altair

see requirements.txt for versions

Data sources

New York Times

Montana State Library

Manual labor

In order to get this app running quickly I have not fully automated everything, therefore, it takes a bit of manual labor to update. Here are the current steps I take:

At 4:30 pm the State updates the daily Covid-19 case totals. I add these values to the /data/mt_coronavirus_status.csv file. This file is only used for the latest data because the NYT data seems to lag by 2 days.
I then run the runsir.py file locally which runs the SIR model and saves the results in .csv files. It also archives old model results locally so that we can look back at our predictions at a later date.
I spend a bit of time tuning the model to make sure we get realistic solutions. Because it is still early and the signal is not strong (especially in Missoula) you can get some funky results.
Once I like the model, I run runsir.py one more time to save the preferred model results to the repository.
Commit the changes.
Push to Heroku

The model

Currently, I am using N=10000 for Montana and N=1000 for Missoula and Gallatin counties. Betas and gammas will be reported on the website in future versions.

The code was adapted (hijacked) from the great work of Lewauathe and their blog post. Thank you!

TODOS

Add uncertainty to the model
Report and interpret peak timing, peak magnitude, beta, gamma, R_0 and HIT from the model results.
Add previous model runs
Add other (all) counties in Montana
Improve model: Li et al. 2020

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