test_that("Test that plot works for cases and incidence for tsd, tsd_onset, tsd_onset_and_burden objects", { skip_if_not_installed("withr") withr::local_seed(123) ## Cases # tsd tsd_data_cases <- generate_seasonal_data( years = 3, start_date = as.Date("2023-10-18") ) cases_plot_1 <- plot(tsd_data_cases) expect_contains(names(cases_plot_1$data), "cases") # tsd_onset tsd_onset_cases <- seasonal_onset( tsd = tsd_data_cases ) cases_plot_2 <- plot(tsd_onset_cases) expect_equal(all(cases_plot_2$data$incidence), NA) # tsd_onset_and_burden combined_cases <- combined_seasonal_output(tsd_data_cases) cases_plot_3 <- plot(combined_cases) expect_equal(all(cases_plot_3$data$incidence), NA) ## Incidence # tsd tsd_data_incidence <- to_time_series( time = tsd_data_cases$time, cases = tsd_data_cases$cases, population = 1e+06 ) incidence_plot_1 <- plot(tsd_data_incidence) expect_contains(names(incidence_plot_1$data), "incidence") # tsd_onset tsd_onset_incidence <- seasonal_onset( tsd = tsd_data_incidence ) incidence_plot_2 <- plot(tsd_onset_incidence) expect_false(all(is.na(incidence_plot_2$data$incidence))) # tsd_onset_and_burden combined_incidence <- combined_seasonal_output(tsd_data_incidence, disease_threshold = 2) incidence_plot_3 <- plot(combined_incidence, y_lower_bound = 1) expect_false(all(is.na(incidence_plot_3$data$incidence))) }) test_that("Test that plot works for cases and incidence in `tsd_growth_warning` objects", { skip_if_not_installed("withr") withr::local_seed(123) ## Cases tsd_data_cases <- generate_seasonal_data( years = 3, trend_rate = 0.997, start_date = as.Date("2023-10-18") ) tsd_onset_cases <- seasonal_onset( tsd = tsd_data_cases, season_start = 21, only_current_season = FALSE ) tsd_growth_w_cases <- consecutive_growth_warnings(tsd_onset_cases) cases_plot <- plot(tsd_growth_w_cases) expect_equal(all(cases_plot$data$incidence), NA) ## Incidence tsd_data_incidence <- to_time_series( time = tsd_data_cases$time, cases = tsd_data_cases$cases, population = 1e+06 ) tsd_onset_incidence <- seasonal_onset( tsd = tsd_data_incidence, season_start = 21, only_current_season = FALSE ) tsd_growth_w_incidence <- consecutive_growth_warnings(tsd_onset_incidence) incidence_plot <- plot(tsd_growth_w_incidence) expect_false(all(is.na(incidence_plot$data$incidence))) })