checkCohortRequirements {omopgenerics}

Check whether a cohort table satisfies requirements

Description

Check whether a cohort table satisfies requirements

Usage

checkCohortRequirements(
  cohort,
  checkEndAfterStart = TRUE,
  checkOverlappingEntries = TRUE,
  checkMissingValues = TRUE,
  checkInObservation = TRUE,
  type = "error",
  call = parent.frame()
)

Arguments

cohort

cohort_table object.

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.

type

Can be either "error" or "warning". If "error" any check failure will result in an error, whereas if "warning" any check failure will result in a warning.

call

The call for which to return the error message.

Value

An error will be returned if any of the selected checks fail.

Examples

library(omopgenerics)
person <- dplyr::tibble(
  person_id = 1, gender_concept_id = 0, year_of_birth = 1990,
  race_concept_id = 0, ethnicity_concept_id = 0
)
observation_period <- dplyr::tibble(
  observation_period_id = 1, person_id = 1,
  observation_period_start_date = as.Date("2000-01-01"),
  observation_period_end_date = as.Date("2025-12-31"),
  period_type_concept_id = 0
)
cdm <- cdmFromTables(
  tables = list("person" = person, "observation_period" = observation_period),
  cdmName = "test"
)
cdm <- insertTable(cdm, name = "cohort1", table = dplyr::tibble(
  cohort_definition_id = 1, subject_id = 1,
  cohort_start_date = as.Date(c("2020-01-01", "2020-01-10")),
  cohort_end_date = as.Date(c("2020-01-10", "2020-01-25"))
))
cdm$cohort1 <- newCohortTable(cdm$cohort1, .softValidation = TRUE)
# checkCohortRequirements(cdm$cohort1)