CohortContrast: Enrichment Analysis of Clinically Relevant Concepts in Common Data Model Cohort Data

Identifies clinically relevant concepts in Observational Medical Outcomes Partnership Common Data Model cohorts using an enrichment-based workflow. Defines target and control cohorts and extracts medical interventions that are over-represented in the target cohort during the observation period. Users can tune filtering and selection thresholds. The workflow includes chi-squared tests for two proportions with Yates continuity correction, logistic tests, and hierarchy and correlation mappings for relevant concepts. The results can be optionally explored using the bundled graphical user interface. For workflow details and examples, see <https://healthinformaticsut.github.io/CohortContrast/>.

Version: 1.0.0
Imports: dplyr (≥ 1.0.4), tibble, purrr, tidyr (≥ 1.0.0), stringr, stats, utils, CDMConnector (≥ 2.0.0), CohortConstructor (≥ 0.6.0), omopgenerics (≥ 1.3.0), lubridate (≥ 1.9.0), doParallel, parallel, foreach, data.table (≥ 1.14.0), cli, jsonlite (≥ 1.8.0), nanoparquet (≥ 0.4.0)
Suggests: testthat (≥ 3.0.0), PatientProfiles (≥ 1.1.0), duckdb, DBI (≥ 1.2.0), RPostgres, readr, knitr, rmarkdown, processx, bit64, reshape2, igraph, Matrix, cluster, vegan, reticulate (≥ 1.26)
Published: 2026-04-16
DOI: 10.32614/CRAN.package.CohortContrast (may not be active yet)
Author: Markus Haug ORCID iD [aut, cre], Raivo Kolde ORCID iD [aut]
Maintainer: Markus Haug <markus.haug at ut.ee>
BugReports: https://github.com/HealthInformaticsUT/CohortContrast/issues
License: Apache License 2.0
URL: https://healthinformaticsut.github.io/CohortContrast/
NeedsCompilation: no
SystemRequirements: Python (>= 3.8)
Materials: README
CRAN checks: CohortContrast results

Documentation:

Reference manual: CohortContrast.html , CohortContrast.pdf
Vignettes: Setup (source, R code)
Execution (source, R code)
Graphical User Interface (source, R code)
Dashboard Composite Plot (source, R code)
Trajectories Tab (source, R code)
Overlap Tab (source, R code)
Mappings Tab (source, R code)
Patient vs Summary Mode (source, R code)
Demographics Tab (source, R code)
Sidepanel Filters and Controls (source, R code)
Air-gapped Server Setup (source, R code)
Interpreting Results with lc500 (source, R code)
Interpreting Summary Results with lc500s (source, R code)

Downloads:

Package source: CohortContrast_1.0.0.tar.gz
Windows binaries: r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

Please use the canonical form https://CRAN.R-project.org/package=CohortContrast to link to this page.