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), 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/
BugReports: https://github.com/HealthInformaticsUT/CohortContrast/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-04-09 14:28:29 UTC; markushaug
Author: Markus Haug [aut, cre] (ORCID: <https://orcid.org/0000-0003-0935-3307>),
  Raivo Kolde [aut] (ORCID: <https://orcid.org/0000-0003-2886-6298>)
Repository: CRAN
Date/Publication: 2026-04-16 09:12:17 UTC
Built: R 4.6.0; ; 2026-04-30 22:28:16 UTC; unix
