test_that("basic functionality summarise large scale characteristics", { skip_on_cran() person <- dplyr::tibble( person_id = c(1L, 2L), gender_concept_id = c(8507L, 8532L), year_of_birth = c(1990L, 1992L), month_of_birth = c(1L, 1L), day_of_birth = c(1L, 1L), race_concept_id = 0L, ethnicity_concept_id = 0L ) observation_period <- dplyr::tibble( observation_period_id = c(1L, 2L), person_id = c(1L, 2L), observation_period_start_date = as.Date(c("2010-10-01", "2010-10-01")), observation_period_end_date = as.Date(c("2011-10-01", "2011-10-01")), period_type_concept_id = 44814724L ) cohort_interest <- dplyr::tibble( cohort_definition_id = c(1L, 1L), subject_id = c(1L, 2L), cohort_start_date = as.Date(c("2010-10-10", "2010-10-10")), cohort_end_date = as.Date(c("2010-12-01", "2010-12-01")) ) # everyone has 1125315 in drug exposure drug_exposure <- dplyr::tibble( drug_exposure_id = as.integer(1:2), person_id = as.integer(1:2), drug_concept_id = as.integer(c(rep(1125315, 2))), drug_exposure_start_date = as.Date(c("2010-10-01")), drug_exposure_end_date = as.Date(c("2010-12-01")), drug_type_concept_id = 38000177, quantity = 1 ) # only one person has 1125315 in condition occurrence condition_occurrence <- dplyr::tibble( condition_occurrence_id = as.integer(1:2), person_id = as.integer(c(rep(1, 2))), condition_concept_id = as.integer(c(1125315, 378253)), condition_start_date = as.Date(c("2010-10-01", "2010-10-01")), condition_end_date = as.Date(c("2010-10-01", "2010-10-01")), condition_type_concept_id = 32020L ) con <- connection() cdm <- mockCohortCharacteristics( con = con, writeSchema = writeSchema(), person = person, observation_period = observation_period, cohort_interest = cohort_interest, drug_exposure = drug_exposure, condition_occurrence = condition_occurrence ) concept <- dplyr::tibble( concept_id = as.integer(c( 1125315, 1503328, 1516978, 317009, 378253, 4266367 )), domain_id = as.integer(NA), vocabulary_id = as.integer(NA), concept_class_id = as.integer(NA), concept_code = as.integer(NA), valid_start_date = as.Date("1900-01-01"), valid_end_date = as.Date("2099-01-01") ) |> dplyr::mutate(concept_name = paste0("concept: ", .data$concept_id)) name <- CDMConnector::inSchema(schema = "main", table = "concept") DBI::dbWriteTable( conn = con, name = name, value = concept, overwrite = TRUE ) cdm$concept <- dplyr::tbl(con, name) result <- cdm$cohort_interest |> summariseLargeScaleCharacteristics( eventInWindow = c("condition_occurrence", "drug_exposure"), window = c(-Inf, Inf), minimumFrequency = 0 ) expect_no_error(tableLargeScaleCharacteristics(result)) })