Read case data

  • Use rio, io, readr or {ImportExport} to read data from individual files.
  • Use readepi to read data from RDBMS and HIS.
  • The {rio} package supports a wide range of file formats including CSV, TSV, XLSX, and compressed files.
  • Use readepi::login() to establish connections to RDBMS, DHIS2, or SORMAS systems.
  • The readepi package currently supports importing data from DHIS2 and SORMAS health information systems.

Clean case data

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

Validate case data

  • Use the 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 other variables to produce epidemic curves.
  • Use ggplot2 package to produce better annotated epicurves.