freemansoft/covid-vaccinations-python

Basic python program that loads covid vaccination data sets available on Kaggle and shows national progress

Covid Vaccinations vs population

Tracking Covid vaccinations across the globe. How far have we travelled along the vaccination journey?

Datasets

• Our world in Data
  • https://github.com/owid/covid-19-data/tree/master/public/data/vaccinations
  • https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/vaccinations/vaccinations.csv
  • https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/vaccinations/us_state_vaccinations.csv
• Original vaccination dataset before I found our world of data This data set combines multiple data cents from the our world in data repository.
  • https://www.kaggle.com/gpreda/covid-world-vaccination-progress by https://www.kaggle.com/gpreda

Platform

I used the Kaggle Python Container Image. It is way overkill for this task.

• Kaggle Python Container Image data science docker container to rule them all
• Any reasonable anaconda or Jupyter notebook environment your link here. You can use any Anaaconda / Jupyter Notebook environment.

Genesis / Credits

• Kenny Freeman covid project that got me interested
• Our world in data
• Gabriel Preda Kaggle datsethttps://www.kaggle.com/gpreda

Execution with provided script

The included bash script will download the data and run the server.

1. Open a terminal and cd to this directory
2. execute bash start-kaggle-container.sh It will
   1. download the data
   2. download the docker image
   3. run the container and Jupyter notebook server
3. Open a browser to http://localhost:8080/
4. Open and run code/vaccinations_by_country.ipynb in the Jupyter Notebook browser view in the left pane.
   1. It will prompt you for city or state and pick the correct data file based on your prompt

Manual Execution

1. Open a terminal and cd to this directory

2. Make a directory in this directory called data

3. Blah blah the csv files from Github and put it in data/vaccinations.csv

4. Download the global vaccination data and the us state vaccination data. This can be done from inside the notebook or the command line

   curl https://covid.ourworldindata.org/data/vaccinations/vaccinations.csv -o data/vaccinations_world.csv
   curl https://covid.ourworldindata.org/data/vaccinations/us_state_vaccinations.csv -o data/vaccinations_state.csv

5. Start your Jupyter server

   1. You can use any environment, local, docker, etc
   2. I use the Kaggle Python Docker image by running bash start-kaggle-container.sh in this directory. It will download the container 18GB and start the Jupyter server.

6. Open Jupyter Notebook server.

   1. Open a browser to http://localhost:8080/ or wherever your notbook server is locate
   2. Open and run vaccinations_by_country.ipynb in the Jupyter Notebook browser view in the left pane.

Shutting down the server

There are a couple ways to terminate the server

1. ctrl-c in the terminal window and answer Y
2. Terminate the server in the Jupyter Notebook menu in the browser window

Demo: order of operations

Source data may be missing days and columns

We add missing days and interpolate or fill missing cell values vaccinations_by_country.ipynb

Sample results from various data phases 19 Feb 2021 data set

Phase	Number of Records	Daily Vaccinations (populated)	Total Vaccinations (populated)	Vaccinated per 100 (populated)
Initial Load	3679	3542	2461	1367
Post row fill	6831	3432	2461	1367
Post value interpolation	6831	3868	4008	1837