test_that("summariseMeasurementUse works", { skip_on_cran() cdm <- testMockCdm() cdm <- copyCdm(cdm) res <- summariseMeasurementUse( cdm = cdm, codes = list("test" = 3001467L, "test2" = 1L, "test3" = 45875977L), bySex = TRUE, ageGroup = list(c(0, 17), c(18, 64), c(65, 150)) ) expect_equal( omopgenerics::settings(res), dplyr::tibble( result_id = 1:3L, result_type = c("measurement_timings", "measurement_value_as_numeric", "measurement_value_as_concept"), package_name = "MeasurementDiagnostics", package_version = as.character(utils::packageVersion("MeasurementDiagnostics")), group = c("codelist_name", "codelist_name &&& concept_name &&& unit_concept_name", "codelist_name &&& concept_name"), strata = c(rep("sex &&& age_group", 3)), additional = c("", "concept_id &&& unit_concept_id &&& domain_id", "concept_id &&& value_as_concept_id &&& domain_id"), min_cell_count = "0" ) ) expect_equal( res |> omopgenerics::filterSettings(result_type == "measurement_timings") |> dplyr::filter(strata_name == "overall") |> dplyr::pull(estimate_value) |> sort(), c('0', '0', '100', '1426.75', '14973', '3521.5', '5334', '64', '96') ) expect_equal( res |> omopgenerics::filterSettings(result_type == "measurement_timings") |> dplyr::filter(strata_name == "overall") |> dplyr::pull(variable_name) |> sort(), c(rep("number records", 2), rep("number subjects", 2), rep("time", 5)) ) expect_equal( res |> omopgenerics::filterSettings(result_type == "measurement_timings") |> dplyr::filter(strata_name == "overall") |> dplyr::pull(estimate_name) |> sort(), c(rep("count", 4), "max", "median", "min", "q25", "q75") ) expect_equal( res |> omopgenerics::filterSettings(result_type == "measurement_value_as_numeric") |> dplyr::filter(strata_name == "overall") |> dplyr::pull(estimate_value) |> sort(), c('114.848484848485', '114.848484848485', '115.580808080808', '115.580808080808', '12.3232323232323', '12.3232323232323', '13.7878787878788', '13.7878787878788', '148.535353535354', '148.535353535354', '150', '150', '2', '2', '3', '3', '4', '4', '46.7424242424242', '46.7424242424242', '47.4747474747475', '47.4747474747475', '50', '50', '50', '50', '6', '6', '81.1616161616162', '81.1616161616162', '81.1616161616162', '81.1616161616162') ) expect_equal( res |> omopgenerics::filterSettings(result_type == "measurement_value_as_numeric") |> dplyr::filter(strata_name == "overall") |> dplyr::pull(estimate_name) |> sort(), c('count', 'count', 'count', 'count', 'count_missing', 'count_missing', 'count_missing', 'count_missing', 'max', 'max', 'max', 'max', 'median', 'median', 'median', 'median', 'min', 'min', 'min', 'min', 'percentage_missing', 'percentage_missing', 'percentage_missing', 'percentage_missing', 'q25', 'q25', 'q25', 'q25', 'q75', 'q75', 'q75', 'q75') ) expect_equal( res |> omopgenerics::filterSettings(result_type == "measurement_value_as_concept") |> dplyr::filter(strata_name == "overall") |> dplyr::pull(estimate_value) |> sort(), c('33', '33', '33', '33', '33', '33', '33', '33', '34', '34', '34', '34') ) expect_equal( res |> omopgenerics::filterSettings(result_type == "measurement_value_as_concept") |> dplyr::filter(strata_name == "overall") |> dplyr::pull(estimate_name) |> sort(), c('count', 'count', 'count', 'count', 'count', 'count', 'percentage', 'percentage', 'percentage', 'percentage', 'percentage', 'percentage') ) # suppress resSup <- res |> omopgenerics::suppress(minCellCount = 68) expect_equal(resSup$estimate_value |> unique(), c("100", "-", "81", "0")) }) test_that("summariseMeasurementUse straifications work", { skip_on_cran() cdm <- testMockCdm() cdm <- copyCdm(cdm) res <- summariseMeasurementUse( cdm = cdm, codes = list("test" = 3001467L, "test2" = 1L, "test3" = 45875977L), bySex = TRUE, byYear = TRUE, ageGroup = NULL, dateRange = as.Date(c("2000-01-01", "2005-01-01")) ) expect_equal( res$strata_level |> unique(), c("overall", "Female", "Male", "2000", "2001", "2002", "2003", "2004") ) expect_equal( res |> dplyr::filter(strata_level == "2000", result_id == 3, estimate_name == "count") |> dplyr::pull(estimate_value) |> sort(), c("1", "1", "1", "1") ) expect_true(unique(omopgenerics::settings(res)$date_range) == "2000-01-01 to 2005-01-01") expect_equal( res |> dplyr::filter(group_name == "codelist_name", result_id != 1) |> dplyr::select(strata_name, strata_level, variable_name, variable_level, estimate_name, estimate_type, estimate_value), res |> dplyr::filter(group_name == "codelist_name &&& concept_name") |> dplyr::select(strata_name, strata_level, variable_name, variable_level, estimate_name, estimate_type, estimate_value) ) res <- summariseMeasurementUse( cdm = cdm, codes = list("test" = 3001467L, "test2" = 1L, "test3" = 45875977L), byConcept = FALSE, bySex = FALSE, byYear = FALSE, ageGroup = NULL ) expect_equal( omopgenerics::settings(res), dplyr::tibble( result_id = 1:3L, result_type = c("measurement_timings", "measurement_value_as_numeric", "measurement_value_as_concept"), package_name = "MeasurementDiagnostics", package_version = as.character(utils::packageVersion("MeasurementDiagnostics")), group = c("codelist_name", "codelist_name &&& unit_concept_name", "codelist_name"), strata = c(rep("", 3)), additional = c("", "unit_concept_id", "value_as_concept_id"), min_cell_count = "0" ) ) expect_equal( res |> dplyr::filter(group_level == "test3") |> dplyr::pull("estimate_value"), c("0", "0") ) }) test_that("summariseMeasurementUse expected fails", { skip_on_cran() cdm <- testMockCdm() cdm <- copyCdm(cdm) expect_error(summariseMeasurementUse( cdm = cdm, codes = list("test" = 3001467L, "test2" = 1L, "test3" = 45875977L), bySex = TRUE, byYear = TRUE, ageGroup = NULL, dateRange = as.Date(c("2006-01-01", "2005-01-01")) )) expect_error(summariseMeasurementUse( cdm = cdm, codes = list("test" = 3001467L, "test2" = 1L, "test3" = 45875977L), bySex = TRUE, byYear = 0, ageGroup = NULL, dateRange = as.Date(c("2000-01-01", "2005-01-01")) )) expect_error(summariseMeasurementUse( cdm = cdm, codes = list("test" = 3001467L, "test2" = 1L, "test3" = 45875977L), bySex = TRUE, byYear = TRUE, ageGroup = "0 to 10", dateRange = as.Date(c("2000-01-01", "2005-01-01")) )) expect_error(summariseMeasurementUse( cdm = cdm, codes = list("test" = 3001467L, "test2" = 1L, "test3" = 45875977L), bySex = TRUE, byYear = TRUE, ageGroup = NULL, dateRange = c(0, as.Date("2005-01-01")) )) expect_error(summariseMeasurementUse( cdm = cdm, codes = list("test" = 3001467L, "test2" = 1L, "test3" = 45875977L), bySex = TRUE, byYear = TRUE, ageGroup = NULL, checks = "measurement_records" )) }) test_that("summariseMeasurementUse checks", { skip_on_cran() cdm <- testMockCdm() cdm <- copyCdm(cdm) res <- summariseMeasurementUse( cdm = cdm, codes = list("test" = 3001467L, "test2" = 1L, "test3" = 45875977L), bySex = FALSE, byYear = FALSE, ageGroup = NULL, dateRange = as.Date(c("2000-01-01", "2005-01-01")), checks = "measurement_timings" ) expect_true(unique(res$result_id) == 1) expect_true(omopgenerics::settings(res)$result_type == "measurement_timings") res <- summariseMeasurementUse( cdm = cdm, codes = list("test" = 3001467L, "test2" = 1L, "test3" = 45875977L), bySex = FALSE, byYear = FALSE, ageGroup = NULL, dateRange = as.Date(c("2000-01-01", "2005-01-01")), checks = c("measurement_value_as_numeric", "measurement_value_as_concept") ) expect_true(all(omopgenerics::settings(res)$result_type %in% c("measurement_value_as_numeric", "measurement_value_as_concept"))) expect_null( summariseMeasurementUse( cdm = cdm, codes = list("test" = 3001467L, "test2" = 1L, "test3" = 45875977L), bySex = FALSE, byYear = FALSE, ageGroup = NULL, dateRange = as.Date(c("2000-01-01", "2005-01-01")), checks = character() ) ) }) test_that("summariseMeasurementUse observation domain", { skip_on_cran() cdm <- testMockCdm() cdm <- copyCdm(cdm) res <- summariseMeasurementUse( cdm = cdm, codes = list("mix" = c(3001467, 45875977, 194152, 4092121, 1033535)), bySex = FALSE, byYear = FALSE, ageGroup = NULL, dateRange = as.Date(c("2000-01-01", "2005-01-01")), checks = c("measurement_value_as_numeric", "measurement_value_as_concept") ) tab <- res |> visOmopResults::splitAdditional() |> dplyr::filter(result_id == 2) |> dplyr::distinct(concept_id, domain_id) expect_equal( tab$concept_id |> sort(), c("3001467", "4092121", "overall") ) expect_equal( tab$domain_id |> sort(), c("Measurement", "Observation", "overall") ) })