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README.md

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.

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.

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