tests/testthat/test-patterns.R

In DrugUtilisation: Summarise Patient-Level Drug Utilisation in Data Mapped to the OMOP Common Data Model

test_that("create patterns, correct output", {
  skip_on_cran()
  drug_strength <- dplyr::tibble(
    drug_concept_id = c(1, 1, 2),
    ingredient_concept_id = c(13, 14, 15),
    amount_value = c(3, NA, NA),
    amount_unit_concept_id = c(8718, NA, NA),
    numerator_value = c(NA, 20, 10),
    numerator_unit_concept_id = c(NA, 7, 8576),
    denominator_value = c(NA, 100, 100),
    denominator_unit_concept_id = c(NA, 10, 45744809),
    valid_start_date = as.Date("1900-01-01"),
    valid_end_date = as.Date("2100-01-01")
  )
  concept <- dplyr::tibble(
    concept_name = c(
      "Drug1", "Drug2", "Ing1", "Ing2", "Ing3", "AmountUnit", "NumUnit1",
      "NumUnit2", "DenUnit", "DenUnit2", "international unit", "milligram",
      "Actuation"
    ),
    concept_class_id = c(
      rep("Branded drug", 2), rep("Ingredient", 3), rep("Unit", 8)
    ),
    domain_id = c(rep("Drug", 5), rep("Unit", 8)),
    concept_id = c(1, 2, 13, 14, 15, 4, 7, 8, 10, 11, 8718, 8576, 45744809),
    vocabulary_id = 0,
    concept_code = 0,
    valid_start_date = as.Date("1900-01-01"),
    valid_end_date = as.Date("2100-01-01")
  )
  concept_relationship <- dplyr::tibble(
    concept_id_1 = c(1, 2),
    concept_id_2 = c(19016586, 46275062),
    relationship_id = c(rep("RxNorm has dose form", 2)),
    valid_start_date = as.Date("1900-01-01"),
    valid_end_date = as.Date("2100-01-01")
  )

  cdm <- mockDrugUtilisation(
    con = connection(), writeSchema = schema(), drug_strength = drug_strength,
    concept = concept, concept_relationship = concept_relationship
  )

  expect_no_error(patternTab <- patternTable(cdm))
  expect_true(all(colnames(patternTab) == c(
    "pattern_id", "formula_name", "validity", "number_concepts",
    "number_ingredients", "number_records", "amount_numeric",
    "amount_unit_concept_id", "numerator_numeric", "numerator_unit_concept_id",
    "denominator_numeric", "denominator_unit_concept_id"
  )))

  expect_true(nrow(patternTab) == 3)
  expect_true(all(patternTab |> dplyr::select(number_concepts) |> dplyr::pull() == c(1, 1, 1)))
  patternTab |>
    dplyr::filter(.data$validity == "pattern with formula") |>
    nrow() |>
    expect_equal(2)
  patternTab |>
    dplyr::filter(.data$validity != "pattern with formula") |>
    nrow() |>
    expect_equal(1)

  mockDisconnect(cdm = cdm)
})