From 9f7b777a786fb38010255453d851fea47e3ee688 Mon Sep 17 00:00:00 2001 From: Pratik Gupte Date: Wed, 20 Mar 2024 11:45:36 +0000 Subject: [PATCH] Update Vacamole double dose vax tests, add snapshot Minor update to Vacamole 2 dose vax snapshot --- tests/testthat/_snaps/model_vacamole.md | 33 +++++++++++++++++++++++++ tests/testthat/test-model_vacamole.R | 15 ++++++++--- 2 files changed, 44 insertions(+), 4 deletions(-) create mode 100644 tests/testthat/_snaps/model_vacamole.md diff --git a/tests/testthat/_snaps/model_vacamole.md b/tests/testthat/_snaps/model_vacamole.md new file mode 100644 index 00000000..cbcafd49 --- /dev/null +++ b/tests/testthat/_snaps/model_vacamole.md @@ -0,0 +1,33 @@ +# Vacamole model: two dose vaccination and stats. correctness + + Code + data[grepl("dose", data$compartment, fixed = TRUE) & time %in% seq(50, 55), ] + Output + time demography_group compartment value + + 1: 50 [0,60) vaccinated_one_dose 2370379.149 + 2: 50 60+ vaccinated_one_dose 638905.568 + 3: 50 [0,60) vaccinated_two_dose 3957.270 + 4: 50 60+ vaccinated_two_dose 1066.626 + 5: 51 [0,60) vaccinated_one_dose 2394121.139 + 6: 51 60+ vaccinated_one_dose 645305.113 + 7: 51 [0,60) vaccinated_two_dose 27700.882 + 8: 51 60+ vaccinated_two_dose 7466.380 + 9: 52 [0,60) vaccinated_one_dose 2417863.063 + 10: 52 60+ vaccinated_one_dose 651704.650 + 11: 52 [0,60) vaccinated_two_dose 51444.480 + 12: 52 60+ vaccinated_two_dose 13866.132 + 13: 53 [0,60) vaccinated_one_dose 2441604.917 + 14: 53 60+ vaccinated_one_dose 658104.178 + 15: 53 [0,60) vaccinated_two_dose 75188.064 + 16: 53 60+ vaccinated_two_dose 20265.882 + 17: 54 [0,60) vaccinated_one_dose 2465346.699 + 18: 54 60+ vaccinated_one_dose 664503.696 + 19: 54 [0,60) vaccinated_two_dose 98931.632 + 20: 54 60+ vaccinated_two_dose 26665.630 + 21: 55 [0,60) vaccinated_one_dose 2489088.407 + 22: 55 60+ vaccinated_one_dose 670903.205 + 23: 55 [0,60) vaccinated_two_dose 122675.184 + 24: 55 60+ vaccinated_two_dose 33065.377 + time demography_group compartment value + diff --git a/tests/testthat/test-model_vacamole.R b/tests/testthat/test-model_vacamole.R index 8a889ff9..c79237f8 100644 --- a/tests/testthat/test-model_vacamole.R +++ b/tests/testthat/test-model_vacamole.R @@ -38,12 +38,12 @@ uk_population <- population( double_vaccination <- vaccination( name = "double_vaccination", nu = matrix( - 1e-3, - nrow = 2, ncol = 2 + c(1e-3, 5e-4), # fewer second doses + nrow = 2, ncol = 2, byrow = TRUE ), time_begin = matrix( - 00, - nrow = 2, ncol = 2 + c(0, 50), + nrow = 2, ncol = 2, byrow = TRUE # second dose given from t = 50 onwards ), time_end = matrix( 100, @@ -336,6 +336,13 @@ test_that("Vacamole model: two dose vaccination and stats. correctness", { expect_true( all(epidemic_size(data_baseline) > epidemic_size(data)) ) + + # expect snapshot for range from t = 50:55 + # second dose begins at t = 50 + expect_snapshot( + data[grepl("dose", data$compartment, fixed = TRUE) & + time %in% seq(50, 55), ] + ) }) test_that("Vacamole model: time dependence", {