The CohortDiagnostics package allows one to generate a wide set of
diagnostics to evaluate cohort definitions against a database in the
Common Data Model (CDM). These diagnostics include incidence rates
(optionally stratified by age, gender, and calendar year), cohort
characteristics (comorbidities, drug use, etc.), and the codes found in
the data triggering the various rules in the cohort definitions.
The CohortDiagnostics package in general works in two steps:
- Generate the diagnostics against a database in the CDM.
- Explore the generated diagnostics in a Shiny app included in the
The use of Cohort Diagnostics is a recommended best practice to help
improve the confidence in your cohort definitions.
- Show cohort inclusion rule attrition.
- List all source codes used when running a cohort definition on a
- Find orphan codes, (source) codes that should be, but are not
included in a particular concept set.
- Compute cohort incidence across calendar years, age, and
- Break down index events into the specific concepts that triggered
- Compute overlap between two cohorts.
- Characterize cohorts, and compare these characterizations. Perform
cohort comparison and temporal comparisons.
- Explore patient profiles of a random sample of subjects in a