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)PhenotypeR_0.5.0.zip(r-4.6)PhenotypeR_0.5.0.zip(r-4.5)
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:

8.03 score 7 stars 48 scripts 887 downloads 27 exports 54 dependencies

Last updated from:a2835f0499. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK217
source / vignettesOK237
linux-release-x86_64OK204
macos-release-arm64OK96
macos-oldrel-arm64OK128
windows-develOK136
windows-releaseOK151
windows-oldrelOK124
wasm-releaseOK210

Exports:addCodelistAttributebindclinicalDescriptionSpecificationcodelistDiagnosticscohortDiagnosticsdatabaseDiagnosticsdataSourceDescriptionSpecificationdownloadClinicalDescriptionTemplatedownloadDatabaseDescriptionTemplatedraftClinicalDescriptionexportSummarisedResultgetCohortExpectationsimportClinicalDescriptionimportDatabaseDescriptionimportSummarisedResultphenotypeDiagnosticspopulationDiagnosticssettingsshinyClinicalDescriptionsshinyDataSourceDescriptionsshinyDiagnosticssummariseAchillesCodeUsesummariseCodeUsesummariseCohortCodeUsesummariseOrphanCodessuppresstableCohortExpectations

Dependencies:askpassbackportsbitbit64blobCDMConnectorcheckmateclicliprclockCodelistGeneratorCohortCharacteristicsCohortConstructorcpp11crayoncurlDBIdbplyrdplyrDrugUtilisationgenericsgluehmshttr2IncidencePrevalencejsonlitelifecyclemagrittrMeasurementDiagnosticsomopgenericsOmopSketchopensslPatientProfilespillarpkgconfigprettyunitsprogresspurrrR6rappdirsreadrrlangsnakecasestringistringrsystibbletidyrtidyselecttzdbutf8vctrsvroomwithr

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: 2026-05-21
Started: 2025-07-23

CreateDescriptions
Introduction: Create descriptions | Database Descriptions | Clinical Descriptions | Generate clinical descriptions using LLMs
Rendered fromCreateDescriptions.Rmdusingknitr::rmarkdown

Last update: 2026-04-16
Started: 2026-04-16

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