Center for Quality, Safety & Value Analytics

SupplyDemand

A python-based application for predicting changes in COVID-19 cases, hospital visits, admits, ICU needs, and protective equipment

Contributors

Developer

Kenneth J. Locey, PhD Biology, Data Science Analyst

Rush Site Architect and Administrator

Jawad Khan, AVP, Advanced Analytics & Knowledge Management

Center for Quality, Safety & Value Analytics Leadership

Thomas A. Webb, MBA, Associate Vice President Bala N. Hota, MD, MPH, Vice President, Chief Analytics Officer

Software used

We tried to keep the required software to a minimum. Most are standard python libraries.

• python 3.7.4
• numpy 1.18.1
• voila 0.1.21
  • The engine that converts jupyter notebooks to dashboard-like environments https://voila.readthedocs.io/en/stable/index.html
• matplotlib 3.2.1
• pandas 1.0.3
• ipywidgets 7.5.1
• IPython 7.13.0
• scipy 1.4.1

Websites

The source code in this repository is deployed to two different websites:

1. Primary: Rush University Medical Center website http://covid19forecast.rush.edu/ maintained by Jawad Khan
2. Testing: A heroku deployed app used for development and testing https://rush-covid19.herokuapp.com/ maintained by Ken Locey and Tom Webb

Contents

We have endeavored to keep the contents uncomplicated

• Procfile -- A file used by voila and heroku to set the environment. This file contains the following information and nothing else: web: voila --port=$PORT --no-browser --enable_nbextensions=True --theme=light notebooks/dashboard.ipynb

• requirements.txt -- A file used by voila and heroku to determine the packages to download and install. The current contents of the file are:

   voila
   voila-material
   matplotlib
   pandas
   ipywidgets
   numpy
   IPython
   scipy
   datetime
  

• runtime.txt -- A file needed to specify the python version used. The following is the only content of the file:

   python-3.7.4. 
   
  

• notebooks -- A directory containing the following:

  • app_class.py: A highly commented python script containing functions used to construct the application's features (plots, tables, interactive widgets, etc.). This file is imported by dashboard.ipynb.

  • model_fxns.py: A highly commented python script containing fxns needed for modeling and statistical analyses. This file is imported by app_class.py

  • get_dataframe_dailyreports.py: A python script that obtains and aggregates data from daily reports provided by the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE) https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_daily_reports

  • COVID-CASES-DF.txt: The text file produced by get_dataframe_dailyreports.py. This file is used by app_class.py as the application's primary dataframe.

  • dashboard.ipynb: A jupyter notebook comprising the code that voila uses to generate a dashboard-like application. This file imports app_class.py.