DARWIN-EU Mock Data Tutorial

This tutorial demonstrates Drug Utilisation and Survival Analysis workflows on synthetic OMOP CDM data.

Scenario: Understand how two drugs (Acetaminophen and Simvastatin) are used, and how mock cohorts differ in time-to-event outcomes.

We will:

Summarize patterns of drug use
Estimate survival probabilities using synthetic cohort data

library(duckdb)          # Lightweight embedded database, supports SQL querying

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# Load packages
# Required libraries for OMOP CDM-based analysis
library(DrugUtilisation) # Drug exposure analysis
library(CohortSurvival)  # Survival estimation and plotting
library(PatientProfiles) # Adding demographic attributes
library(visOmopResults) # Visualization tools for OMOP results
library(duckdb)          # Lightweight embedded database, supports SQL querying
library(ggplot2)         # Grammar of graphics for data visualization
library(gt)              # Generate presentation-ready tables
 
 
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# Generate synthetic CDM data
# This creates 1000 synthetic patients and assigns them randomly to 3 cohorts
message("Generating synthetic CDM data using mockDrugUtilisation()...")
cdm <- DrugUtilisation::mockDrugUtilisation(numberIndividuals = 1000)
message("Mock CDM loaded.")
 
 
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# Inspect mock cohort distribution
# Each person is randomly assigned to a `cohort_definition_id` of 1, 2, or 3
message("Cohort counts (cohort1 and cohort2):")
print(cohortCount(cdm$cohort1))
print(cohortCount(cdm$cohort2))
 
 
הההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההה
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1. Drug Utilisation Profiling

We analyze exposure patterns to:

Acetaminophen (acute)
Simvastatin (chronic)

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# Define ingredients of interest
# Use mock concept IDs for Acetaminophen and Simvastatin
ingredientIds <- c(1125315, 1503297)
 
 
הההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההה
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# Summarise drug utilisation (restricted to cohort_definition_id = 1)
message("Summarizing drug utilization metrics for selected drugs...")
drug_utilisation_result_full <- DrugUtilisation::summariseDrugUtilisation(
  cohort = cdm$cohort1, # Target population for DUS
  cohortId = 1,
  ingredientConceptId = ingredientIds, # Drugs to analyze
  strata = list(),
  estimates = c("mean", "median", "q25", "q75", "min", "max", "count", "count_missing", 
"percentage_missing"),
  restrictIncident = TRUE, # Include only first-ever exposures per person (incident use)
 
 
הההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההה
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# View summary table of drug use
drug_table_full <- DrugUtilisation::tableDrugUtilisation(drug_utilisation_result_full)
print(drug_table_full)
 
 
הההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההה
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# Plot: Mean number of exposures
message("Plotting mean number of exposures across cohorts...")
plot_data <- drug_utilisation_result_full[
  drug_utilisation_result_full$variable_name == "number exposures" &
    drug_utilisation_result_full$estimate_name == "mean",
]
print(DrugUtilisation::plotDrugUtilisation(plot_data, variable = "number exposures"))
 
 
הההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההה
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2. Survival Analysis

Estimate survival time for cohort1, using events from cohort2, filtered to cohort_definition_id = 1.

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# Estimate survival (basic)
message("Estimating survival: target = cohort1, outcome = cohort2, cohort_definition_id = 1")
survival_analysis_basic <- CohortSurvival::estimateSingleEventSurvival(
  cdm = cdm,
  targetCohortTable = "cohort1",
  outcomeCohortTable = "cohort2",
  targetCohortId = 1,
  outcomeCohortId = 1,
  censorOnCohortExit = TRUE,
  eventGap = 30,
 
 
הההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההה
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# Plot: Overall survival curve
print(CohortSurvival::plotSurvival(survival_analysis_basic))
 
 
הההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההה
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# Add demographics to cohort1 for stratified analysis
cdm$cohort1_demographics <- cdm$cohort1 |>
  PatientProfiles::addDemographics(
    indexDate = "cohort_start_date", # Use the cohort start date as the index point for age 
calculation
    age = TRUE,
    sex = TRUE,
    ageGroup = list(
      "Age_18_to_39" = c(18, 39),
      "Age_40_to_59" = c(40, 59),
 
 
הההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההה
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# Estimate survival stratified by sex
message("Survival stratified by sex")
survival_sex_stratified <- CohortSurvival::estimateSingleEventSurvival(
  cdm = cdm,
  targetCohortTable = "cohort1_demographics",
  outcomeCohortTable = "cohort2",
  targetCohortId = 1,
  outcomeCohortId = 1,
  strata = list("sex"),
  censorOnCohortExit = TRUE, # Limit follow-up time to the target cohort's observation period 
(until cohort_end_date)
 
 
הההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההה
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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# Estimate survival stratified by age group
message("Survival stratified by age group")
survival_age_stratified <- CohortSurvival::estimateSingleEventSurvival(
  cdm = cdm,
  targetCohortTable = "cohort1_demographics",
  outcomeCohortTable = "cohort2",
  targetCohortId = 1,
  outcomeCohortId = 1,
  strata = list("age_group"),
  censorOnCohortExit = TRUE,
 
 
הההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההה
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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# Display stratified survival tables
print(CohortSurvival::tableSurvival(survival_sex_stratified))
print(CohortSurvival::tableSurvival(survival_age_stratified))
 
 
הההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההה
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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# Plot: Stratified survival by sex and age
print(CohortSurvival::plotSurvival(survival_sex_stratified, colour = "sex", ribbon = FALSE))
print(CohortSurvival::plotSurvival(survival_age_stratified, colour = "age_group", ribbon = FALSE))
 
 
הההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההההה
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

This script covers:

Mock CDM generation
Drug utilization analysis
Survival analysis with stratification

All data is synthetic. For demonstration purposes only.

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