Read case data

  • Use rio, io, readr and {ImportExport} to read data from individual files.
  • Use {readepi} to read data form HIS APIs and RDBMS.

Clean case data

  • Use cleanepi package to clean and standardize epidemic and outbreak data
  • Understand how to use cleanepi to perform common data cleansing tasks and epidemiology related operations
  • View the data cleaning report in a browser, consult it and make decisions.

Validate case data

  • Use linelist package to tag, validate, and prepare case data for downstream analysis.

Aggregate and visualize

  • Use simulist package to generate synthetic outbreak data
  • Use incidence2 package to aggregate case data based on a date event, and produce epidemic curves.
  • Use ggplot2 package to produce better annotated epicurves.