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:

8.11 score 10 stars 66 scripts 820 downloads 30 exports 53 dependencies

Last updated from:f9092f582e. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE175
source / vignettesOK410
linux-releaseNOTE146
macos-releaseNOTE124
macos-oldrelNOTE139
windows-develNOTE106
windows-releaseNOTE104
windows-oldrelNOTE96
wasm-releaseOK136

Exports:addCodelistAttributebindclinicalDescriptionSpecificationcodelistDiagnosticscohortDiagnosticsdatabaseDiagnosticsdataSourceDescriptionSpecificationdownloadClinicalDescriptionTemplatedownloadDatabaseDescriptionTemplatedraftClinicalDescriptionexportCohortExpectationsexportSummarisedResultgetCohortExpectationsimportClinicalDescriptionimportCohortExpectationsimportDatabaseDescriptionimportSummarisedResultphenotypeDiagnosticspopulationDiagnosticsreviewCohortConceptssettingsshinyClinicalDescriptionsshinyDataSourceDescriptionsshinyDiagnosticssummariseAchillesCodeUsesummariseCodeUsesummariseCohortCodeUsesummariseOrphanCodessuppresstableCohortExpectations

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