omock

  1. Overview
    1. Key Features:
  2. Installation
  3. Getting Started
  4. Core API Reference
    1. Modular Mock Table Builders

The omock package enables programmatic creation of synthetic OMOP Common Data Model (CDM) datasets for unit testing, development, and tutorial authoring without requiring access to real patient data.

Overview

Unlike static synthetic database files, omock creates in-memory <cdm_reference> objects on the fly using a pipeable builder pattern. You can specify exact sample sizes, date ranges, and domain tables to tailor synthetic test data to specific unit tests or study designs.

Key Features:

  • Composable Pipe Workflow: Chain mock table generators (mockPerson() $\rightarrow$ mockObservationPeriod() $\rightarrow$ mockConditionOccurrence()).
  • Standardized OMOP Vocabularies: Automatically populates standard vocabularies and concept tables.
  • Fast In-Memory Testing: Integrates with DuckDB and testthat for sub-second test execution.
  • Controlled Seed Reproducibility: Deterministic data simulation via random seed specification.

Installation

Install from CRAN:

install.packages("omock")

Or install the development version from GitHub:

# install.packages("pak")
pak::pkg_install("ohdsi/omock")

Getting Started

Create a customized mock CDM with 500 patients and simulated clinical records:

library(omock)
library(dplyr)
library(CDMConnector)

# Initialize and chain mock generators
cdm <- mockCdmReference() |>
  mockPerson(nPerson = 500, birthRange = as.Date(c("1950-01-01", "2000-01-01"))) |>
  mockObservationPeriod() |>
  mockConditionOccurrence() |>
  mockDrugExposure() |>
  mockMeasurement()

# Verify table record counts
cdm$person |> count() |> collect()
cdm$condition_occurrence |> count() |> collect()

Core API Reference

Modular Mock Table Builders

Function Description
mockCdmReference() Initializes an empty in-memory <cdm_reference> container with standard vocabulary tables.
mockPerson(cdm, nPerson, ...) Generates synthetic patient demographic records in the person table.
mockObservationPeriod(cdm, ...) Generates valid continuous observation intervals in the observation_period table.
mockConditionOccurrence(cdm, ...) Populates the condition_occurrence table with synthetic diagnosis events.
mockDrugExposure(cdm, ...) Simulates prescription and dispensation records in drug_exposure.
mockMeasurement(cdm, ...) Generates lab tests and clinical vital sign measurements in measurement.
mockProcedureOccurrence(cdm, ...) Generates surgical and diagnostic procedures in procedure_occurrence.
mockVisitOccurrence(cdm, ...) Generates inpatient, outpatient, and emergency room encounters in visit_occurrence.
mockDeath(cdm, ...) Simulates mortality records in the death table.
mockCohort(cdm, ...) Creates pre-populated synthetic <cohort_table> objects for testing cohort analytics.