test_that("check for incidence", { inc <- tibble::tibble( incidence_analysis_id = c("1", "2", "3"), n_persons = c(4, 6, 200), n_events = c(3, 3, 100), person_days = 100, person_years = 1, incidence_100000_pys = c(1, 25, 50), incidence_100000_pys_95CI_lower = c(0.1, 20, 50), incidence_100000_pys_95CI_upper = c(10, 30, 50) ) inc <- obscureCounts(inc, minCellCount = 5) expect_true(is.na(inc$n_persons[1])) expect_true(is.na(inc$person_days[1])) expect_true(is.na(inc$person_years[1])) expect_true(is.na(inc$n_events[1])) expect_true(is.na(inc$incidence_100000_pys[1])) expect_true(is.na(inc$incidence_100000_pys_95CI_lower[1])) expect_true(is.na(inc$incidence_100000_pys_95CI_upper[1])) expect_true(!is.na(inc$n_persons[2])) # should still report n_persons expect_true(!is.na(inc$person_days[2])) expect_true(!is.na(inc$person_years[2])) expect_true(is.na(inc$n_events[2])) expect_true(is.na(inc$incidence_100000_pys[2])) expect_true(is.na(inc$incidence_100000_pys_95CI_lower[2])) expect_true(is.na(inc$incidence_100000_pys_95CI_upper[2])) expect_true(!is.na(inc$n_persons[3])) expect_true(!is.na(inc$person_days[3])) expect_true(!is.na(inc$person_years[3])) expect_true(!is.na(inc$n_events[3])) expect_true(!is.na(inc$incidence_100000_pys[3])) expect_true(!is.na(inc$incidence_100000_pys_95CI_lower[3])) expect_true(!is.na(inc$incidence_100000_pys_95CI_upper[3])) }) test_that("check for prevalence", { prev <- tibble::tibble( incidence_analysis_id = c("1", "2", "3"), n_population = c(4, 6, 100), n_cases = c(3, 4, 100), prevalence = c(0.05, 0.55, 0.55), prevalence_95CI_lower = c(0.1, 0.5, 0.5), prevalence_95CI_upper = c(0.15, 0.60, 0.60) ) prev <- obscureCounts(prev) expect_true(is.na(prev$n_population[1])) expect_true(is.na(prev$n_cases[1])) expect_true(is.na(prev$prevalence[1])) expect_true(is.na(prev$prevalence_95CI_lower[1])) expect_true(is.na(prev$prevalence_95CI_upper[1])) expect_true(!is.na(prev$n_population[2])) expect_true(is.na(prev$n_cases[2])) expect_true(is.na(prev$prevalence[2])) expect_true(is.na(prev$prevalence_95CI_lower[2])) expect_true(is.na(prev$prevalence_95CI_upper[2])) expect_true(!is.na(prev$n_population[3])) expect_true(!is.na(prev$n_cases[3])) expect_true(!is.na(prev$prevalence[3])) expect_true(!is.na(prev$prevalence_95CI_lower[3])) expect_true(!is.na(prev$prevalence_95CI_upper[3])) })