test_that("summarisePopulationCharacteristics() works", { skip_on_cran() # Load mock database ---- cdm <- cdmEunomia() # Check that works ---- expect_no_error(summarisedPopulation <- summarisePopulationCharacteristics(cdm = cdm)) expect_true(inherits(summarisedPopulation,"summarised_result")) expect_true(all(summarisedPopulation |> dplyr::select("strata_name") |> dplyr::distinct() |> dplyr::pull() == c("overall"))) expect_true(all(summarisedPopulation |> dplyr::filter(variable_name == "Number records") |> dplyr::select("estimate_value") |> dplyr::pull() == 2694)) expect_true(all(summarisedPopulation |> dplyr::filter(variable_name == "Cohort start date" & estimate_name == "min") |> dplyr::select("estimate_value") |> dplyr::pull() == "1908-09-22")) expect_true(summarisedPopulation |> dplyr::filter(variable_name == "Age at end") |> dplyr::tally() |> dplyr::pull() != 0) expect_no_error(summarisedPopulationEqual <- summarisePopulationCharacteristics( cdm = cdm, studyPeriod = NULL) ) expect_equal(summarisedPopulation, summarisedPopulationEqual) # Add date range expect_no_error(summarisedPopulation <- summarisePopulationCharacteristics( cdm = cdm, studyPeriod = c("1900-01-01", "2010-01-01")) ) expect_true(inherits(summarisedPopulation,"summarised_result")) expect_true(all(summarisedPopulation |> dplyr::select("strata_name") |> dplyr::distinct() |> dplyr::pull() == c("overall"))) expect_true(all(summarisedPopulation |> dplyr::filter(variable_name == "Number records") |> dplyr::select("estimate_value") |> dplyr::pull() == 2694)) expect_true(all(summarisedPopulation |> dplyr::filter(variable_name == "Cohort end date" & estimate_name == "max") |> dplyr::select("estimate_value") |> dplyr::pull() == "2010-01-01")) # Add sex and age group strata expect_no_error(summarisedPopulation <- summarisePopulationCharacteristics( cdm = cdm, studyPeriod = c("1950-01-01", NA), sex = TRUE, ageGroup = list(c(0,20),c(21,150))) ) expect_true(inherits(summarisedPopulation,"summarised_result")) expect_true(all(summarisedPopulation |> dplyr::select("strata_name") |> dplyr::distinct() |> dplyr::pull() |> sort() == c("age_group_at_start", "age_group_at_start &&& sex", "overall", "sex"))) expect_true(all(summarisedPopulation |> dplyr::filter(variable_name == "Number records") |> dplyr::select("estimate_value") |> dplyr::pull() |> sort() == c(101,1250,1271,1321,1372,172,2521,2693,71))) expect_true(summarisedPopulation |> dplyr::filter(variable_name == "Age at end" & strata_level == "0 to 20" & estimate_name == "min") |> dplyr::pull("estimate_value") < summarisedPopulation |> dplyr::filter(variable_name == "Age at end" & strata_level == "21 to 150" & estimate_name == "min") |> dplyr::pull("estimate_value")) # Only sex expect_no_error(summarisedPopulation <- summarisePopulationCharacteristics( cdm = cdm, sex = TRUE )) expect_true(inherits(summarisedPopulation,"summarised_result")) expect_true(all(summarisedPopulation |> dplyr::select("strata_name") |> dplyr::distinct() |> dplyr::pull() |> sort() == c("overall", "sex"))) # Only age group expect_no_error(summarisedPopulation <- summarisePopulationCharacteristics( cdm = cdm, ageGroup = list(c(0,1), c(2,Inf)) )) expect_true(inherits(summarisedPopulation,"summarised_result")) expect_true(all(summarisedPopulation |> dplyr::select("strata_name") |> dplyr::distinct() |> dplyr::pull() |> sort() == c("age_group_at_start", "overall"))) # Check result type checkResultType(summarisedPopulation, "summarise_population_characteristics") PatientProfiles::mockDisconnect(cdm = cdm) }) test_that("summarisePopulationCharacteristics() strata works", { skip_on_cran() # Load mock database ---- cdm <- omock::mockCdmReference() |> omock::mockPerson(seed = 1L) |> omock::mockObservationPeriod(seed = 1L) |> copyCdm() # Add sex and age group strata expect_no_error(summarisedPopulation <- summarisePopulationCharacteristics( cdm = cdm, sex = TRUE, ageGroup = list(c(0,20),c(21,150))) ) expect_true(inherits(summarisedPopulation,"summarised_result")) expect_true(all(summarisedPopulation |> dplyr::select("strata_name") |> dplyr::distinct() |> dplyr::pull() |> sort() == c("age_group_at_start", "age_group_at_start &&& sex", "overall", "sex"))) expect_true(all(summarisedPopulation |> dplyr::filter(variable_name == "Number records") |> dplyr::arrange(strata_name, strata_level) |> dplyr::select("estimate_value") |> dplyr::pull() == c(4,6,1,3,4,2,10,5,5))) PatientProfiles::mockDisconnect(cdm = cdm) }) test_that("summarisePopulationCharacteristics() expected errors", { skip_on_cran() # Load mock database ---- cdm <- cdmEunomia() expect_error(summarisePopulationCharacteristics("cdm")) expect_error(summarisePopulationCharacteristics(cdm, studyPeriod = c("2000-01-01", "1990-01-01"))) expect_error(summarisePopulationCharacteristics(cdm, studyPeriod = c(NA, "1990-51-01"))) expect_error(summarisePopulationCharacteristics(cdm, studyPeriod = c("1990-01-01"))) expect_error(summarisePopulationCharacteristics(cdm, studyPeriod = c("01/31/1990", "2000-01-01"))) expect_error(summarisePopulationCharacteristics(cdm, studyPeriod = NULL, sex = "Female")) expect_error(summarisePopulationCharacteristics(cdm, studyPeriod = NULL, ageGroup = c(0,20,40))) PatientProfiles::mockDisconnect(cdm = cdm) }) test_that("tablePopulationCharacteristics() works", { skip_on_cran() # Load mock database ---- cdm <- cdmEunomia() # Check that works ---- x <- summarisePopulationCharacteristics(cdm) expect_no_error(y <- tablePopulationCharacteristics(x)) expect_true(inherits(y,"gt_tbl")) x <- x |> dplyr::filter(.data$result_id == -1) expect_warning(tablePopulationCharacteristics(x)) expect_warning(inherits(tablePopulationCharacteristics(x),"gt_tbl")) PatientProfiles::mockDisconnect(cdm = cdm) }) test_that("summarisePopulationCharacteristics() works with mockOmopSKetch", { skip_on_cran() cdm <- mockOmopSketch(numberIndividuals = 2, seed = 1) expect_no_error(summarisedPopulation <- summarisePopulationCharacteristics( cdm = cdm) ) expect_true(inherits(summarisedPopulation,"summarised_result")) expect_true(all(summarisedPopulation |> dplyr::select("strata_name") |> dplyr::distinct() |> dplyr::pull() == c("overall"))) expect_true(all(summarisedPopulation |> dplyr::filter(variable_name == "Number records") |> dplyr::select("estimate_value") |> dplyr::pull() == 2)) expect_true(all(summarisedPopulation |> dplyr::filter(variable_name == "Cohort start date" & estimate_name == "min") |> dplyr::select("estimate_value") |> dplyr::pull() == "1999-04-05")) expect_true(summarisedPopulation |> dplyr::filter(variable_name == "Age at end", estimate_name == "median") |> dplyr::pull("estimate_value") == as.character(mean(c(40,16)))) expect_true(all(summarisedPopulation |> dplyr::filter(variable_name == "Cohort end date" & estimate_name == "max") |> dplyr::select("estimate_value") |> dplyr::pull() == "2013-06-29")) expect_true(all(summarisedPopulation |> dplyr::filter(variable_name == "Sex", estimate_name == "percentage") |> dplyr::select("estimate_value") |> dplyr::pull() == c(50,50))) expect_true(all(summarisedPopulation |> dplyr::filter(variable_name == "Age at start", estimate_name %in% c("min","max")) |> dplyr::pull("estimate_value") |> sort() == cdm$observation_period |> PatientProfiles::addAge(indexDate = "observation_period_start_date") |> dplyr::pull("age") |> sort())) })