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.
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)
#>
#> ── # OMOP CDM reference (local) of mock ────────────────────────────────────────
#> • omop tables: person, observation_period
#> • cohort tables: -
#> • achilles tables: -
#> • other tables: -