Validate cohortId argument. CohortId can either be a cohort_definition_id value, a cohort_name or a tidyselect expression referinc to cohort_names. If you want to support tidyselect expressions please use the function as: validateCohortIdArgument({{cohortId}}, cohort).

Validate cohortId argument. CohortId can either be a cohort_definition_id value, a cohort_name or a tidyselect expression referinc to cohort_names. If you want to support tidyselect expressions please use the function as: validateCohortIdArgument({{cohortId}}, cohort).

Usage

validateCohortIdArgument(
  cohortId,
  cohort,
  null = TRUE,
  empty = TRUE,
  validation = "error",
  nm = deparse1(substitute(cohortId), backtick = TRUE),
  call = parent.frame()
)

Arguments

cohortId: A cohortId vector to be validated.
cohort: A cohort_table object.
null: Whether NULL is accepted. If NULL all cohortId will be returned.
empty: Whether it can be empty.
validation: How to perform validation: "error", "warning".
nm: Name to use in error messages. Defaults to the expression supplied to cohortId.
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 cast 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 cast column in observation_period as do not match expected column type:
#> • `period_type_concept_id` from numeric to integer

validateCohortIdArgument(NULL, cdm$cohort)
#> [1] 1
validateCohortIdArgument(1L, cdm$cohort)
#> [1] 1
validateCohortIdArgument(2L, cdm$cohort, validation = "warning")
#> Warning: ! cohort definition id: 2 not defined in settings.
#> integer(0)