Package: PhenotypeR 0.5.0

Edward Burn

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.

Authors:Edward Burn [aut, cre], Martí Català [aut], Xihang Chen [aut], Marta Alcalde-Herraiz [aut], Nuria Mercade-Besora [aut], Albert Prats-Uribe [aut]

PhenotypeR_0.5.0.tar.gz
PhenotypeR_0.5.0.zip(r-4.7-any)PhenotypeR_0.5.0.zip(r-4.6-any)PhenotypeR_0.5.0.zip(r-4.5-any)
PhenotypeR_0.5.0.tgz(r-4.6-any)PhenotypeR_0.5.0.tgz(r-4.5-any)
PhenotypeR_0.5.0.tar.gz(r-4.7-any)PhenotypeR_0.5.0.tar.gz(r-4.6-any)
PhenotypeR_0.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
PhenotypeR/json (API)

# Install 'PhenotypeR' in R:
install.packages('PhenotypeR', repos = c('https://ohdsi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ohdsi/phenotyper/issues

Pkgdown/docs site:https://ohdsi.github.io

On CRAN:

Conda:

7.96 score 9 stars 52 scripts 855 downloads 27 exports 53 dependencies

Last updated from:60f6ebf37d. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK208
source / vignettesOK303
linux-releaseOK160
macos-releaseOK91
macos-oldrelOK137
windows-develOK104
windows-releaseOK102
windows-oldrelOK89
wasm-releaseOK162

Exports:addCodelistAttributebindclinicalDescriptionSpecificationcodelistDiagnosticscohortDiagnosticsdatabaseDiagnosticsdataSourceDescriptionSpecificationdownloadClinicalDescriptionTemplatedownloadDatabaseDescriptionTemplatedraftClinicalDescriptionexportSummarisedResultgetCohortExpectationsimportClinicalDescriptionimportDatabaseDescriptionimportSummarisedResultphenotypeDiagnosticspopulationDiagnosticssettingsshinyClinicalDescriptionsshinyDataSourceDescriptionsshinyDiagnosticssummariseAchillesCodeUsesummariseCodeUsesummariseCohortCodeUsesummariseOrphanCodessuppresstableCohortExpectations

Dependencies:askpassbackportsbitbit64blobCDMConnectorcheckmateclicliprclockCodelistGeneratorCohortCharacteristicsCohortConstructorcpp11crayoncurlDBIdbplyrdplyrDrugUtilisationgenericsgluehmshttr2IncidencePrevalencejsonlitelifecyclemagrittrMeasurementDiagnosticsomopgenericsOmopSketchopensslPatientProfilespillarpkgconfigprettyunitsprogresspurrrR6readrrlangsnakecasestringistringrsystibbletidyrtidyselecttzdbutf8vctrsvroomwithr

Phenotype diagnostics
Introduction | Running PhenotypeDiagnostics | Database diagnostics | Codelist diagnostics | Cohort diagnostics | Modify windows, event in windows, and episodes in window | Population diagnostics | Save the results | Visualisation of the results
Rendered fromPhenotypeDiagnostics.Rmdusingknitr::rmarkdown

Last update: 2026-08-02
Started: 2025-07-23

Shiny diagnostics
Introduction: Run ShinyDiagnostics | Shiny App Overview | Special cases
Rendered fromShinyDiagnostics.Rmdusingknitr::rmarkdown

Last update: 2026-04-16
Started: 2025-07-23

Phenotype expectations
Comparing phenotype diagnostic results against phenotype expectations | Creating phenotype expectations | Using an LLM to draft your phenotype expectations
Rendered fromPhenotypeExpectations.Rmdusingknitr::rmarkdown

Last update: 2026-04-14
Started: 2025-07-24