PhenotypeR: Assess Study Cohorts Using a Common Data Model
Phenotype study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model. Diagnostics are run at the database, code list, cohort, and population level to assess whether study cohorts are ready for research.
| Version: | 0.3.3 |
| Depends: | R (≥ 4.1.0) |
| Imports: | cli, clock, CodelistGenerator (≥ 4.0.2), CohortCharacteristics (≥ 1.1.0), CohortConstructor (≥ 0.5.0), dplyr, DrugUtilisation (≥ 1.1.0), IncidencePrevalence (≥ 1.2.0), MeasurementDiagnostics (≥ 0.3.0), omopgenerics (≥ 1.2.0), OmopSketch (≥ 1.0.1), PatientProfiles (≥ 1.4.5), purrr, readr, rlang, vctrs |
| Suggests: | CDMConnector (≥ 1.6.1), duckdb, DBI, gt, omock, testthat (≥ 3.0.0), knitr, glue, RPostgres, ggplot2, ggpubr, stringr, shiny (≥ 1.11.1), DiagrammeR, DiagrammeRsvg, reactable, reactablefmtr, rsvg, sortable, shinycssloaders, here, DT, bslib, shinyWidgets, plotly, tidyr, scales, usethis, rmarkdown, CohortSurvival (≥ 1.1.0), ellmer, htmltools, visOmopResults (≥ 1.4.2), rsconnect, cpp11, progress, qs2, lubridate, systemfonts |
| Published: | 2026-02-23 |
| DOI: | 10.32614/CRAN.package.PhenotypeR |
| Author: | Edward Burn  [aut,
cre],
Martí Català
[aut],
Xihang Chen [aut],
Marta Alcalde-Herraiz
[aut],
Nuria Mercade-Besora
[aut],
Albert Prats-Uribe
[aut] |
| Maintainer: | Edward Burn <edward.burn at ndorms.ox.ac.uk> |
| BugReports: | https://github.com/OHDSI/PhenotypeR/issues |
| License: | Apache License (≥ 2) |
| URL: | https://ohdsi.github.io/PhenotypeR/ |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | PhenotypeR results [issues need fixing before 2026-03-30] |
Documentation:
| Reference manual: | PhenotypeR.html , PhenotypeR.pdf |
| Vignettes: |
CodelistDiagnostics (source, R code) CohortDiagnostics (source, R code) DatabaseDiagnostics (source, R code) PhenotypeDiagnostics (source, R code) PhenotypeExpectations (source, R code) PopulationDiagnostics (source, R code) ShinyDiagnostics (source, R code) |
Downloads:
| Package source: | PhenotypeR_0.3.3.tar.gz |
| Windows binaries: | r-devel: PhenotypeR_0.3.3.zip, r-release: PhenotypeR_0.3.3.zip, r-oldrel: PhenotypeR_0.3.3.zip |
| macOS binaries: | r-release (arm64): PhenotypeR_0.3.3.tgz, r-oldrel (arm64): PhenotypeR_0.3.3.tgz, r-release (x86_64): PhenotypeR_0.3.3.tgz, r-oldrel (x86_64): PhenotypeR_0.3.3.tgz |
| Old sources: | PhenotypeR archive |
Linking:
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