validateCdmArgument: Validate if an object in a valid cdm_reference.

In omopgenerics: Methods and Classes for the OMOP Common Data Model

Validate if an object in a valid cdm_reference.

Description

Validate if an object in a valid cdm_reference.

Usage

validateCdmArgument(
  cdm,
  checkOverlapObservation = FALSE,
  checkStartBeforeEndObservation = FALSE,
  checkPlausibleObservationDates = FALSE,
  checkPerson = FALSE,
  requiredTables = character(),
  validation = "error",
  call = parent.frame()
)

Arguments

cdm	A cdm_reference object
checkOverlapObservation	TRUE to perform check on no overlap observation period
checkStartBeforeEndObservation	TRUE to perform check on correct observational start and end date
checkPlausibleObservationDates	TRUE to perform check that there are no implausible observation period start dates (before 1800-01-01) or end dates (after the current date)
checkPerson	TRUE to perform check on person id in all clinical table are in person table
requiredTables	Name of tables that are required to be part of the cdm_reference object.
validation	How to perform validation: "error", "warning".
call	A call argument to pass to cli functions.

Value

A cdm_reference object

Examples

cdm <- cdmFromTables(
  tables = list(
    "person" = dplyr::tibble(
      person_id = c(1, 2, 3), gender_concept_id = 0, year_of_birth = 1990,
      race_concept_id = 0, ethnicity_concept_id = 0
    ),
    "observation_period" = dplyr::tibble(
      observation_period_id = 1:3, person_id = 1:3,
      observation_period_start_date = as.Date("2000-01-01"),
      observation_period_end_date = as.Date("2023-12-31"),
      period_type_concept_id = 0
    )
  ),
  cdmName = "mock"
)

validateCdmArgument(cdm)

omopgenerics documentation built on April 3, 2025, 8:47 p.m.