COVID-19

A python dashboard for COVID-19 statistics. Deployed at https://worldwide-covid-19.herokuapp.com

History

With the world in the grips of the COVID-19 pandemic, I got tired of looking at daily situation reports from the World Health Organization. I started writing some python code to simply scrape the data from the report pdfs, and plot it. I started to look into producing a dashboard with a map, and eventually landed with Bokeh and GeoPandas. After yet another change to the format of the WHO reports (each requiring new tweaking to the scraper) I found where the data can be directly downloaded, and will rely on that from now on. Similarly, the code's been upgraded to directly access the data from Johns Hopkins, without the need to download manually.

Built With

• Python 3.6.10
  • Bokeh 2.0.1
  • Geopandas 0.7.0

Running

First, obviously get python running with the above libraries. Second, go into the cloned directory and download the COVID-19 data from the WHO website into this directory. It is a csv file found at:

• https://covid19.who.int/

with the 'Download Map Data' button in the bottom right of the map. This file should be named WHO-COVID-19-global-data.csv (rename it if not). The recent code can also use the data from Johns Hopkins, which it pulls directly from their github. Also download, and unzip into this directory, the 110m and 50m shape files from natural earth:

• https://www.naturalearthdata.com/download/110m/cultural/ne_110m_admin_0_countries.zip
• https://www.naturalearthdata.com/download/110m/cultural/ne_50m_admin_0_countries.zip

Finally run:

bokeh serve --show COVID-19.py

Resources

Data from:

• World Health Organization - https://covid19.who.int/
• COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University - https://github.com/CSSEGISandData/COVID-19

Shapefiles for maps:

• Natural Earth - http://www.naturalearthdata.com/

Ideas and code snippets for

• Visualization
  • https://towardsdatascience.com/walkthrough-mapping-basics-with-bokeh-and-geopandas-in-python-43f40aa5b7e9
  • https://towardsdatascience.com/a-complete-guide-to-an-interactive-geographical-map-using-python-f4c5197e23e0
  • https://towardsdatascience.com/data-visualization-with-bokeh-in-python-part-ii-interactions-a4cf994e2512
  • https://jimking100.github.io/2019-09-04-Post-3/
  • http://dmnfarrell.github.io/bioinformatics/bokeh-maps
• Animating
  • https://github.com/bokeh/bokeh/blob/master/examples/app/gapminder/main.py
• Deploying
  • https://blog.thedataincubator.com/2015/09/painlessly-deploying-data-apps-with-bokeh-flask-and-heroku/
  • https://pjandir.github.io/Bokeh-Heroku-Tutorial/
  • https://github.com/datademofun/heroku-basic-flask