tests/testthat/test-tableUnmappedCodes.R

In CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

test_that("unmapped codes", {

  cdm <- mockVocabRef("database")
  cdm <- omopgenerics::insertTable(cdm, "condition_occurrence",
                                   dplyr::tibble(person_id = NA,
                                                 condition_occurrence_id = NA,
                                                 condition_concept_id = NA,
                                                 condition_start_date = NA,
                                                 condition_type_concept_id = NA,
                                                 condition_source_concept_id = NA))
  cdm <- omopgenerics::insertTable(cdm, "drug_exposure",
                                   dplyr::tibble(person_id = NA,
                                                 drug_exposure_id = NA,
                                                 drug_concept_id = NA,
                                                 drug_exposure_start_date = NA,
                                                 drug_exposure_end_date = NA,
                                                 drug_type_concept_id = NA,
                                                 drug_source_concept_id = NA))
  cdm <- omopgenerics::insertTable(cdm, "observation",
                                   dplyr::tibble(person_id = NA,
                                                 observation_id = NA,
                                                 observation_concept_id = NA,
                                                 observation_date = NA,
                                                 observation_type_concept_id = NA,
                                                 observation_source_concept_id = NA))
  cdm <- omopgenerics::insertTable(cdm, "procedure_occurrence",
                                   dplyr::tibble(person_id = NA,
                                                 procedure_occurrence_id = NA,
                                                 procedure_concept_id = NA,
                                                 procedure_date  = NA,
                                                 procedure_type_concept_id  = NA,
                                                 procedure_source_concept_id = NA))
  cdm <- omopgenerics::insertTable(cdm, "device_exposure",
                                   dplyr::tibble(person_id = NA,
                                                 device_exposure_id = NA,
                                                 device_concept_id = NA,
                                                 device_exposure_start_date  = NA,
                                                 device_type_concept_id  = NA,
                                                 device_source_concept_id = NA))
  cdm <- omopgenerics::insertTable(cdm, "measurement",
                                   dplyr::tibble(person_id = 1,
                                                 measurement_id = 1,
                                                 measurement_concept_id = 0,
                                                 measurement_date  = as.Date("2000-01-01"),
                                                 measurement_type_concept_id  = NA,
                                                 measurement_source_concept_id = 7))
  expect_no_error(unmappedCodes <- summariseUnmappedCodes(
    x = list("cs" = 2),
    cdm = cdm))
  expect_no_error(tableUnmappedCodes(unmappedCodes))
  expect_no_error(tableUnmappedCodes(unmappedCodes, type = "tibble"))
  expect_no_error(tableUnmappedCodes(unmappedCodes, header = NULL))

  expect_no_error(tableUnmappedCodes(unmappedCodes |>
    omopgenerics::suppress()))


})