test_that("test summariseCharacteristics", { person <- dplyr::tibble( person_id = c(1, 2, 3), gender_concept_id = c(8507, 8532, 8532), year_of_birth = c(1985, 2000, 1962), month_of_birth = c(10, 5, 9), day_of_birth = c(30, 10, 24), race_concept_id = 0, ethnicity_concept_id = 0 ) dus_cohort <- dplyr::tibble( cohort_definition_id = c(1, 1, 1, 2), subject_id = c(1, 1, 2, 3), cohort_start_date = as.Date(c( "1990-04-19", "1991-04-19", "2010-11-14", "2000-05-25" )), cohort_end_date = as.Date(c( "1990-04-19", "1991-04-19", "2010-11-14", "2000-05-25" )) ) comorbidities <- dplyr::tibble( cohort_definition_id = c(1, 2, 2, 1), subject_id = c(1, 1, 3, 3), cohort_start_date = as.Date(c( "1990-01-01", "1990-06-01", "2000-01-01", "2000-06-01" )), cohort_end_date = as.Date(c( "1990-01-01", "1990-06-01", "2000-01-01", "2000-06-01" )) ) medication <- dplyr::tibble( cohort_definition_id = c(1, 1, 2, 1), subject_id = c(1, 1, 2, 3), cohort_start_date = as.Date(c( "1990-02-01", "1990-08-01", "2009-01-01", "1995-06-01" )), cohort_end_date = as.Date(c( "1990-02-01", "1990-08-01", "2009-01-01", "1995-06-01" )) ) observation_period <- dplyr::tibble( observation_period_id = c(1, 2, 3), person_id = c(1, 2, 3), observation_period_start_date = as.Date(c( "1985-01-01", "1989-04-29", "1974-12-03" )), observation_period_end_date = as.Date(c( "2011-03-04", "2022-03-14", "2023-07-10" )), period_type_concept_id = 0 ) cdm <- mockPatientProfiles( connectionDetails, dus_cohort = dus_cohort, person = person, comorbidities = comorbidities, medication = medication, observation_period = observation_period, cohort1 = emptyCohort, cohort2 = emptyCohort ) cdm$dus_cohort <- omopgenerics::newCohortTable( table = cdm$dus_cohort, cohortSetRef = dplyr::tibble( cohort_definition_id = c(1, 2), cohort_name = c("exposed", "unexposed") )) cdm$comorbidities <- omopgenerics::newCohortTable( table = cdm$comorbidities, cohortSetRef = dplyr::tibble( cohort_definition_id = c(1, 2), cohort_name = c("covid", "headache") )) cdm$medication <- omopgenerics::newCohortTable( table = cdm$medication, cohortSetRef = dplyr::tibble( cohort_definition_id = c(1, 2, 3), cohort_name = c("acetaminophen", "ibuprophen", "naloxone") ), cohortAttritionRef = NULL ) expect_no_error(result <- summariseCharacteristics( cdm$dus_cohort, cohortIntersect = list( "Medications" = list( targetCohortTable = "medication", value = "flag", window = c(-365, 0) ), "Comorbidities" = list( targetCohortTable = "comorbidities", value = "flag", window = c(-Inf, 0) ) ) ) |> suppress(minCellCount = 1)) expect_true(inherits(result, "summarised_result")) expect_identical( result %>% dplyr::filter(group_level == "exposed") %>% dplyr::filter(variable_name == "Covid") %>% dplyr::filter(estimate_name == "count") %>% dplyr::pull("estimate_value") %>% as.numeric(), 2 ) expect_identical( result %>% dplyr::filter(group_level == "exposed") %>% dplyr::filter(variable_name == "Headache") %>% dplyr::filter(estimate_name == "count") %>% dplyr::pull("estimate_value") %>% as.numeric(), 1 ) expect_identical( result %>% dplyr::filter(group_level == "exposed") %>% dplyr::filter(variable_name == "Acetaminophen") %>% dplyr::filter(estimate_name == "count") %>% dplyr::pull("estimate_value") %>% as.numeric(), 2 ) expect_identical( result %>% dplyr::filter(group_level == "exposed") %>% dplyr::filter(variable_name == "Ibuprophen") %>% dplyr::filter(estimate_name == "count") %>% dplyr::pull("estimate_value") %>% as.numeric(), 0 ) expect_identical( result %>% dplyr::filter(group_level == "exposed") %>% dplyr::filter(variable_name == "Naloxone") %>% dplyr::filter(estimate_name == "count") %>% dplyr::pull("estimate_value") %>% as.numeric(), 0 ) expect_identical( result %>% dplyr::filter(group_level == "unexposed") %>% dplyr::filter(variable_name == "Covid") %>% dplyr::filter(estimate_name == "count") %>% dplyr::pull("estimate_value") %>% as.numeric(), 0 ) expect_identical( result %>% dplyr::filter(group_level == "unexposed") %>% dplyr::filter(variable_name == "Headache") %>% dplyr::filter(estimate_name == "count") %>% dplyr::pull("estimate_value") %>% as.numeric(), 1 ) expect_identical( result %>% dplyr::filter(group_level == "unexposed") %>% dplyr::filter(variable_name == "Acetaminophen") %>% dplyr::filter(estimate_name == "count") %>% dplyr::pull("estimate_value") %>% as.numeric(), 0 ) expect_identical( result %>% dplyr::filter(group_level == "unexposed") %>% dplyr::filter(variable_name == "Ibuprophen") %>% dplyr::filter(estimate_name == "count") %>% dplyr::pull("estimate_value") %>% as.numeric(), 0 ) expect_identical( result %>% dplyr::filter(group_level == "unexposed") %>% dplyr::filter(variable_name == "Naloxone") %>% dplyr::filter(estimate_name == "count") %>% dplyr::pull("estimate_value") %>% as.numeric(), 0 ) expect_no_error(result <- summariseCharacteristics( cdm$dus_cohort, cohortIntersect = list( "Medications" = list( targetCohortTable = "medication", value = "flag", window = list( "short" = c(-30, 0), "long" = c(-365, 0) ) ), "Comorbidities" = list( targetCohortTable = "comorbidities", value = "flag", window = c(-Inf, 0) ) ) )|> suppress(minCellCount = 1)) expect_true(inherits(result, "summarised_result")) expect_true( result %>% visOmopResults::splitAdditional() |> dplyr::filter(window == "short") %>% dplyr::tally() %>% dplyr::pull() == omopgenerics::settings(cdm$medication) |> nrow() * 4 # 2 group_level 4 estimate type ) expect_true( result %>% visOmopResults::splitAdditional() |> dplyr::filter(window == "long") %>% dplyr::tally() %>% dplyr::pull() == omopgenerics::settings(cdm$medication) |> nrow() * 4 # 2 group_level 4 estimate type ) expect_true( result %>% visOmopResults::splitAdditional() |> dplyr::filter(table == "medication") %>% dplyr::tally() %>% dplyr::pull() == omopgenerics::settings(cdm$medication) |> nrow() * 8 # 2 group_level 4 estimate type 2 window ) expect_true( result %>% visOmopResults::splitAdditional() |> dplyr::filter(table == "comorbidities") %>% dplyr::tally() %>% dplyr::pull() == omopgenerics::settings(cdm$comorbidities) |> nrow() * 4 # 2 group_level 4 estimate type ) result_notables <- summariseCharacteristics( cdm$dus_cohort, cohortIntersect = list(), tableIntersect = list() )|> suppress(minCellCount = 1) expect_true(inherits(result, "summarised_result")) # demographics expect_no_error(result <- summariseCharacteristics( cdm$dus_cohort, demographics = TRUE, cohortIntersect = list( "Medications" = list( targetCohortTable = "medication", value = "flag", window = c(-365, 0) ) ) )) expect_true(all( c("Cohort start date", "Cohort end date", "Age", "Sex", "Prior observation", "Future observation") %in% result$variable_name )) expect_no_error(result <- summariseCharacteristics( cdm$dus_cohort, demographics = TRUE )) expect_true(all( c("Cohort start date", "Cohort end date", "Age", "Sex", "Prior observation", "Future observation") %in% result$variable_name )) expect_no_error(result <- summariseCharacteristics( cdm$dus_cohort, demographics = FALSE, cohortIntersect = list( "Medications" = list( targetCohortTable = "medication", value = "flag", window = c(-365, 0) ) ) )) expect_false(any( c("Cohort start date", "Cohort end date", "Age", "Sex", "Prior observation", "Future observation") %in% result$variable_name )) expect_error(summariseCharacteristics( cdm$dus_cohort, demographics = FALSE )) }) test_that("test empty cohort", { cdm <- mockPatientProfiles(connectionDetails = connectionDetails) expect_no_error( cdm$cohort1 %>% dplyr::filter(cohort_definition_id == 0) %>% summariseCharacteristics(cohortIntersect = list( "Medications" = list( targetCohortTable = "cohort2", value = "flag", window = c(-365, 0) ), "Comorbidities" = list( targetCohortTable = "cohort2", value = "flag", window = c(-Inf, 0) ) )) ) expect_no_error( cdm$cohort1 %>% summariseCharacteristics(cohortIntersect = list( "Medications" = list( targetCohortTable = "cohort2", value = "flag", window = c(-365, 0), targetCohortId = 1 ), "Comorbidities" = list( targetCohortTable = "cohort2", value = "flag", window = c(-Inf, 0) ) )) ) expect_no_error( x1 <- cdm$cohort1 %>% summariseCharacteristics(tableIntersect = list("Visits" = list( tableName = "visit_occurrence", value = "flag", window = c(-365, 0) ))) ) expect_no_error( x3 <- cdm$cohort1 %>% summariseCharacteristics(tableIntersect = list("Visits" = list( tableName = "visit_occurrence", value = "visit_concept_id", window = c(-Inf, Inf) ))) ) })