validateCohortArgument: Validate a cohort table input.

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

Validate a cohort table input.

Description

Validate a cohort table input.

Usage

validateCohortArgument(
  cohort,
  checkEndAfterStart = FALSE,
  checkOverlappingEntries = FALSE,
  checkMissingValues = FALSE,
  checkInObservation = FALSE,
  checkAttributes = FALSE,
  checkPermanentTable = FALSE,
  dropExtraColumns = FALSE,
  validation = "error",
  call = parent.frame()
)

Arguments

cohort	Object to be validated as a valid cohort input.
checkEndAfterStart	If TRUE a check that all cohort end dates come on or after cohort start date will be performed.
checkOverlappingEntries	If TRUE a check that no individuals have overlapping cohort entries will be performed.
checkMissingValues	If TRUE a check that there are no missing values in required fields will be performed.
checkInObservation	If TRUE a check that cohort entries are within the individuals observation periods will be performed.
checkAttributes	Whether to check if attributes are present and populated correctly.
checkPermanentTable	Whether to check if the table has to be a permanent table.
dropExtraColumns	Whether to drop extra columns that are not the required ones.
validation	How to perform validation: "error", "warning".
call	A call argument to pass to cli functions.

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
    )
   ),
   cohortTables = list(
    cohort = dplyr::tibble(
      cohort_definition_id = 1L,
      subject_id = 1L,
      cohort_start_date = as.Date("2020-01-01"),
      cohort_end_date = as.Date("2021-02-10")
    )
  ),
  cdmName = "mock"
)

validateCohortArgument(cdm$cohort)

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