Package: CohortContrast
Type: Package
Title: Enrichment Analysis of Clinically Relevant Concepts in Common
        Data Model Cohort Data
Version: 1.0.0
Maintainer: Markus Haug <markus.haug@ut.ee>
Authors@R: c(
    person("Markus", "Haug", , "markus.haug@ut.ee", 
    role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0935-3307")),
    person("Raivo", "Kolde", , "raivo.kolde@ut.ee", 
    role = c("aut"), comment = c(ORCID = "0000-0003-2886-6298"))
    )
Description: 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/>.
License: Apache License 2.0
Encoding: UTF-8
RoxygenNote: 7.3.3
SystemRequirements: Python (>= 3.8)
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), icd.data,
        duckdb, DBI (>= 1.2.0), RPostgres, readr, knitr, rmarkdown,
        processx, bit64, reshape2, igraph, Matrix, cluster, vegan,
        reticulate (>= 1.26)
Config/testthat/edition: 3
Config/testthat/parallel: false
URL: https://healthinformaticsut.github.io/CohortContrast/,
        https://CRAN.R-project.org/package=CohortContrast,
        https://github.com/HealthInformaticsUT/CohortContrast
BugReports: https://github.com/HealthInformaticsUT/CohortContrast/issues
VignetteBuilder: knitr
Config/pak/sysreqs: libicu-dev libssl-dev python3 libx11-dev
Repository: https://healthinformaticsut.r-universe.dev
Date/Publication: 2026-08-25 09:05:38 UTC
RemoteUrl: https://github.com/healthinformaticsut/cohortcontrast
RemoteRef: HEAD
RemoteSha: 658d6971d921eed2734cd7a440d41ed589264969
NeedsCompilation: no
Packaged: 2026-08-25 10:07:36 UTC; root
Author: Markus Haug [aut, cre] (ORCID: <https://orcid.org/0000-0003-0935-3307>),
  Raivo Kolde [aut] (ORCID: <https://orcid.org/0000-0003-2886-6298>)