tests/testthat/test-checkDrugExposureDuration.R

In DrugExposureDiagnostics: Diagnostics for OMOP Common Data Model Drug Records

getTestData <- function() {
  ingredient_drug_records <- tibble::tibble(
    drug_exposure_id = c("1", "2", "3", "4", "5"),
    drug_concept_id = c("1", "1", "2", "2", "3"),
    drug = c("x", "x", "xx", "xx", "xxx"),
    ingredient_concept_id = c("1", "1", "2", "2", "2"),
    ingredient = c("a", "a", "b", "b", "b"),
    person_id = c("1", "2", "3", "4", "5"),
    drug_type_concept_id = c("1", "2", "3", "4", "5"),
    route_concept_id = c("1", "2", "3", "4", "5"),
    lot_number = c("1", "2", "3", "4", "5"),
    provider_id = c("1", "2", "3", "4", "5"),
    visit_occurrence_id = c("1", "2", "3", "4", "5"),
    visit_detail_id = c("1", "2", "3", "4", "5"),
    drug_source_value = c("1", "2", "3", "4", "5"),
    drug_source_concept_id = c("1", "2", "3", "4", "5"),
    route_source_value = c("1", "2", "3", "4", "5"),
    dose_unit_source_value = c("1", "2", "3", "4", "5"),
    drug_exposure_start_date = c(
      as.Date("2010-01-01"), as.Date("2011-01-01"),
      as.Date("2012-01-01"), NA,
      as.Date("2013-01-01")
    ),
    drug_exposure_end_date = c(
      as.Date("2011-01-01"), NA,
      as.Date("2013-01-01"), as.Date("2010-01-01"),
      as.Date("2014-01-01")
    ),
    verbatim_end_date = c(
      as.Date("2011-01-01"), NA,
      as.Date("2013-01-01"), as.Date("2010-01-01"),
      as.Date("2014-01-01")
    ),
    days_supply = c(NA, NA, NA, NA, 366),
    quantity = c(10, 20, 30, 40, 50),
    stop_reason = rep("", 5),
    refills = rep(1, 5),
    sig = rep("", 5)
  )

  mockDrugExposure(ingredient_drug_records = ingredient_drug_records)
}

test_that("summariseDrugExposureDuration test overall", {
  testData <- getTestData()
  result <- summariseDrugExposureDuration(testData, "ingredient_drug_records", byConcept = FALSE)

  expect_equal(nrow(result), 2)
  expect_equal(ncol(result), 17)
  expect_equal(colnames(result), c(
    "ingredient_concept_id", "ingredient", "n_records", "n_sample", "n_person",
    "n_non_negative_days", "n_negative_days", "proportion_negative_days",
    "minimum_drug_exposure_days", "q05_drug_exposure_days",
    "q10_drug_exposure_days", "q25_drug_exposure_days", "median_drug_exposure_days",
    "q75_drug_exposure_days", "q90_drug_exposure_days", "q95_drug_exposure_days",
    "maximum_drug_exposure_days"
  ))

  DBI::dbDisconnect(attr(testData, "dbcon"), shutdown = TRUE)
})

test_that("summariseDrugExposureDuration test by concept", {
  testData <- getTestData()
  resultByconcept <- summariseDrugExposureDuration(testData, "ingredient_drug_records", byConcept = TRUE)
  expect_equal(nrow(resultByconcept), 3)
  expect_equal(resultByconcept$n_records, c(2, 2, 1))

  DBI::dbDisconnect(attr(testData, "dbcon"), shutdown = TRUE)
})