R Shiny application to view weekly influenza surveillance data
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R Shiny Application for Weekly Influenza Data

The Cook County Department of Public Health collects and analyzes data on local influenza activity year-round. During periods when higher influenza activity is expected (from MMWR Week 40 through MMWR Week 20), this information is compiled into a weekly surveillance report that is distributed to our partners in the healthcare community, schools, community groups, and the public. This application was created as a companion to our weekly surveillance report to give users greater access to the data.

Data sources include:

  • emergency room activity from CCDPH's syndromic surveillance system: ESSENCE,
  • laboratory testing by local sentinel laboratories and CDC's ILINet sentinel laboratories,
  • mandatory reporting of flu-associated intensive care unit (ICU) hospitalizations, and,
  • mortality data from the Illinois Vital Records System.

Data is not included in the repository; however, visitors are welcome to view and borrow code.

The application is live here, but still under development so errors/inefficiencies might be noted. Feedback to improve the code is welcome.

Questions and comments on this project can be directed to kbemis@cookcountyhhs.org.