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"
)
#> Warning: ! 5 casted column in person as do not match expected column type:
#> • `person_id` from numeric to integer
#> • `gender_concept_id` from numeric to integer
#> • `year_of_birth` from numeric to integer
#> • `race_concept_id` from numeric to integer
#> • `ethnicity_concept_id` from numeric to integer
#> Warning: ! 1 casted column in observation_period as do not match expected column type:
#> • `period_type_concept_id` from numeric to integer

validateCohortArgument(cdm$cohort)
#> # A tibble: 1 × 4
#>   cohort_definition_id subject_id cohort_start_date cohort_end_date
#>                  <int>      <int> <date>            <date>         
#> 1                    1          1 2020-01-01        2021-02-10