covid19

Python scripts for extracting and calculating statistics on Covid-19 data, made available by Johns Hopkins University (JHU): https://github.com/CSSEGISandData/COVID-19

Order of execution matters, since scripts work on CSV data stored in the data folder. Ensure you have data and graphs folders created before running scripts.

Use get_data.py to pull the dataset. Then run compare_countries_confirmed.py and compare_countries_deaths.py to generate the graphs and a CSV files with the related data. Then run predict_daily_growth_confirmed.py and predict_daily_growth_deaths.py to get predictions.

Added run_all_scripts.py to execute all files automatically in order.

Prediction calculates and uses daily change rates from available data to calculate exponential regression and predict future based on calculated coefficients. The number of days regression calculation considers is controlled by a days_for_regression variable in the predict_* files.

Required python3 package libraries:

pandas
matplotlib
numpy
datetime
sklearn
scipy

Animation

Animation it done by running animation_confirmed_new_vs_total.py, this script uses data gathered by get_data.py. It will place individual plots into animation folder. After all plots are created you can run ffmpeg to generate MP4 file. I use the following command embedded in the script (based on MacOS, you may need to tweak for your OS)

ffmpeg -framerate 2 -i %04d_confirmed_new_vs_total.png -vcodec libx264 -crf 25 -pix_fmt yuv420p -movflags +faststart confirmed.mov

I added multiprocessing capability to version 2 (animation_confirmed_new_vs_total_v2.py & animation_deaths_new_vs_total_v2.py)

If you are using MacOS you need to have the following environment variable set in order for this to work: OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES

To run this in Terminal you need to first run: export OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES

Latest graphs (will try to keep updated):

Links to animation of confirmed cases MP4:

Confirmed: https://github.com/dmitripr/covid19/blob/master/animation/confirmed.mov?raw=true

Deaths: https://github.com/dmitripr/covid19/blob/master/animation/deaths.mov?raw=true