Introduction
CohortDiagnostics is an R utility package for the development and evaluation of phenotype algorithms for OMOP CDM compliant data sets. This package provides a standard, end to end, set of analytics for understanding patient capture including data generation and result exploration through an R Shiny interface. Analytics computed include cohort characteristics, record counts, index event misclassification, captured observation windows and basic incidence proportions for age, gender and calendar year. Through the identification of errors, CohortDiagnostics enables the comparison of multiple candidate cohort definitions across one or more data sources, facilitating reproducible research.
Features
- Show cohort inclusion rule attrition.
- List all source codes used when running a cohort definition on a specific database.
- 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 gender.
- Break down index events into the specific concepts that triggered them.
- 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 cohort.
Installation
See the instructions here for configuring your R environment, including Java.
In R, use the following commands to download and install CohortDiagnostics:
remotes::install_github("OHDSI/CohortDiagnostics")User Documentation
Documentation can be found on the package website.
PDF versions of the documentation are also available:
- Package manual: CohortDiagnostics manual
- Vignette: What is Cohort Diagnostics
- Vignette: Running Cohort Diagnostics
- Vignette: Viewing Results Using Diagnostics Explorer
Support
- Developer questions/comments/feedback: OHDSI Forum
- We use the GitHub issue tracker for all bugs/issues/enhancements
Contributing
Read here how you can contribute to this package.