getTestData <- function() { ingredient_drug_records <- tibble::tibble( drug_exposure_id = c(1, 2, 3, 0, 5), drug_concept_id = c(0, 0, 2, 2, 3), drug = c("x", "x", "x", "x", "x"), ingredient_concept_id = c(1, 1, 1, 1, 1), ingredient = c("a", "a", "a", "a", "a"), person_id = c(1, 2, 3, 4, 0), drug_type_concept_id = c(1, 2, 3, 4, 0), route_concept_id = c(1, 2, 3, 4, 0), lot_number = seq(1, 5), provider_id = seq(1, 5), visit_occurrence_id = seq(1, 5), visit_detail_id = seq(1, 5), drug_source_value = seq(1, 5), drug_source_concept_id = seq(1, 5), route_source_value = seq(1, 5), dose_unit_source_value = seq(1, 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("getDrugMissings overall", { testData <- getTestData() result <- getDrugMissings(testData, "ingredient_drug_records", byConcept = FALSE, sampleSize = 100 ) expect_equal(nrow(result), 15) expect_equal(ncol(result), 9) expect_equal(colnames(result), c( "ingredient_concept_id", "ingredient", "variable", "n_records", "n_sample", "n_person", "n_records_not_missing_value", "n_records_missing_value", "proportion_records_missing_value" )) missingDaysSupply <- result %>% dplyr::filter(variable == "n_missing_days_supply") expect_equal(missingDaysSupply %>% dplyr::pull(n_records_missing_value), 4) expect_equal(missingDaysSupply %>% dplyr::pull(proportion_records_missing_value), 0.8) missingDrugConcept <- result %>% dplyr::filter(variable == "n_missing_drug_concept_id") expect_equal(missingDrugConcept %>% dplyr::pull(n_records_missing_value), 2) expect_equal(missingDrugConcept %>% dplyr::pull(proportion_records_missing_value), 0.4) missingDrugType <- result %>% dplyr::filter(variable == "n_missing_drug_type_concept_id") expect_equal(missingDrugType %>% dplyr::pull(n_records_missing_value), 1) expect_equal(missingDrugType %>% dplyr::pull(proportion_records_missing_value), 0.2) missingRoute <- result %>% dplyr::filter(variable == "n_missing_route_concept_id") expect_equal(missingRoute %>% dplyr::pull(n_records_missing_value), 1) expect_equal(missingRoute %>% dplyr::pull(proportion_records_missing_value), 0.2) missingDrugExposure <- result %>% dplyr::filter(variable == "n_missing_drug_exposure_id") expect_equal(missingDrugExposure %>% dplyr::pull(n_records_missing_value), 1) expect_equal(missingDrugExposure %>% dplyr::pull(proportion_records_missing_value), 0.2) missingPerson <- result %>% dplyr::filter(variable == "n_missing_person_id") expect_equal(missingPerson %>% dplyr::pull(n_records_missing_value), 1) expect_equal(missingPerson %>% dplyr::pull(proportion_records_missing_value), 0.2) DBI::dbDisconnect(attr(testData, "dbcon"), shutdown = TRUE) }) test_that("getDrugMissings byConcept", { testData <- getTestData() result <- getDrugMissings(testData, "ingredient_drug_records", byConcept = TRUE, sampleSize = 100 ) expect_equal(nrow(result), 45) expect_equal(ncol(result), 11) expect_equal(colnames(result), c( "drug_concept_id", "drug", "ingredient_concept_id", "ingredient", "variable", "n_records", "n_sample", "n_person", "n_records_not_missing_value", "n_records_missing_value", "proportion_records_missing_value" )) missingDaysSupply <- result %>% dplyr::filter(variable == "n_missing_days_supply") %>% dplyr::arrange(drug_concept_id) expect_equal(missingDaysSupply %>% dplyr::pull(n_records_missing_value), c(2, 2, 0)) expect_equal(missingDaysSupply %>% dplyr::pull(proportion_records_missing_value), c(1, 1, 0)) DBI::dbDisconnect(attr(testData, "dbcon"), shutdown = TRUE) })