Measuring COVID-19 real-time transmission rate (Rt)

A collection of work related to COVID-19

These are modified versions of Kevin Systrom's and William Farr's models for estimating Covid-19 Rt (transmission rate of Covid-19 in real-time.) Nothing is changed in the way the models themselves operate.

Modifications

• method for dealing with negative case count on consequtive days (which, of course, is an impossibility, caused by non-linear case reporting and/or errors in reports
• layout implemented and streamlined across notebooks, now using the color scheme featured on https://rt.live
• plotting function for Stan R0 notebooks
• Stan notebooks rewritten to use pyplot + numPy instead of pyLab
• extended save and load functions for processed data
• models processing EU data as well as US data, with possibility of expanding to any country reported on https://ourworldindata.org
• high resolution png files of the last runs (residing in imagefolder)

Notebooks

These are the notebooks containing the aforementioned modifications:

• Realtime Rt mcmc EUW.ipynb
• Realtime Rt mcmc US.ipynb
• Stan R0 EUW.ipynb
• Stan R0 US.ipynb

The original notebooks have not been modified.