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geoffroychaussonnet / script_to_monitor_Covid19

Python scripts to monitor Covid-19
BSD 3-Clause "New" or "Revised" License
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COVID-19 Evolution Curves

Scripts to monitor the evolution of COVID-19 propagation for each countries, based on data aggregated by the Johns Hopkins University (https://github.com/CSSEGISandData/COVID-19).

Prerequisites

Scripts were developped with Python 3.6.8, matplotlib 2.2.2, pandas 0.25.3 and scipy 1.2.0.

Installation

To create a new virtual environment:

$ virtualenv venv
$ source venv/bin/activate

To install the dependencies:

$ pip install -r requirements.txt

Getting Started

The two main scripts are:

1/ plot_versus_time.py (see Fig. 1)
-> Plot the usual observables (confirmed cases, deaths, active cases) versus time. The observables can be show in the form of cumulated, daily value (gradient) or daily value variation (curvature)
-> Curves can be smoothed with the Savitzky-Golay filter
-> Exponential extrapolation is proposed based on data before (dashed line) and after (plain line) lockdown, if lockdown date is given.

Fig. 1: Example of curve produced by plotCorrelation.py

2/ plot_phase_portrait.py (see Fig. 2)
-> plot the phase diagram of the usual observables.
-> X-axis is the gradient (=new case/day) and Y-axis is the curvature (=variation of new case/day). The course of the epidemic can be well visualized in this phase diagram.

Fig. 2: Example of curve produced by phase_diagram.py

Authors

License

This project is licensed under the BSD 3 License - see the LICENSE.md file for details