PhenotypeR

Review codelists and cohorts in OMOP CDM

2025-06-26

Introduction

PhenotypeR package is designed to review cohorts in OMOP CDM.

The code is publicly available in OHDSI’s GitHub repository PhenoypeR.

PhenotypeR 0.1.6 is available in CRAN.

Vignettes with further information can be found in the package website.

Set of Functions: Individual Diagnostics Assessment

Database diagnostics
- Summarises the databases metadata and the observation period.
- databaseDiagnostics()

Codelist diagnostics
- Summarises the codelist use associated to our cohort.
- codelistDiagnostics()

Cohort diagnostics
- Summarises baseline characteristics, attrition, overlap, and large-scale characteristics. It also allows to compare our results with a matched cohort.
- cohortDiagnostics()

Population diagnostics
- Incidence and prevalence of our cohort in the database.
- populationDiagnostics()

Set of Functions: Phenotype Diagnostics

Comprises all the diagnostics that are being offered in this package.

result <- phenotypeDiagnostics(
  cohort,
  databaseDiagnostics = TRUE,
  codelistDiagnostics = TRUE,
  cohortDiagnostics = TRUE,
  survival = TRUE,
  match = TRUE,
  matchedSample = NULL,
  populationDiagnostics = TRUE,
  populationSample = NULL,
  populationDateRange = as.Date(c(NA,NA))
)

Create a shiny app to visualize all the results

shinyDiagnostics(result = result, directory = here())

Run Phenotype Diagnostics - Example

library(CDMConnector)
library(CodelistGenerator)
library(CohortConstructor)
library(CohortCharacteristics)
library(dplyr)
library(PhenotypeR)
library(here)
library(omock)
library(duckdb)

# Create mock cdm
datasetName <- "synpuf-1k_5.3"
dbdir <- here(paste0(datasetName, ".duckdb"))
con <- dbConnect(drv = duckdb(dbdir = dbdir))
cdm <- mockCdmFromDataset(datasetName = datasetName)
cdm <- insertCdmTo(cdm = cdm, to = dbSource(con = con, writeSchema = "main"))

cdm <- cdm %>%
  buildAchillesTables()

# Create mock cohorts
drug_codes <- getDrugIngredientCodes(
  cdm = cdm, 
  name = c("diclofenac", "acetaminophen"),
  nameStyle = "{concept_name}"
)

cdm$medications <- conceptCohort(
  cdm = cdm, 
  conceptSet = drug_codes, 
  name = "medications"
)

# Run Phenotype Diagnostics 
result <- phenotypeDiagnostics(cdm$medications,
                               databaseDiagnostics = TRUE,
                               codelistDiagnostics = TRUE,
                               cohortDiagnostics = TRUE,
                               survival = TRUE,
                               match = TRUE,
                               matchedSample = NULL,
                               populationDiagnostics = TRUE,
                               populationSample = NULL,
                               populationDateRange = as.Date(c(NA,NA)))

shinyDiagnostics(result = result, directory = here())

Visualise the results

See the results in the shiny app

PhenotypeR

👉 Packages website
👉 CRAN link
👉 Manual

📧 marta.alcaldeherraiz@ndorms.ox.ac.uk

Extra - PhenotypeR shiny app