@@ -7,13 +7,16 @@ library(purrr)
77skip_on_cran()
88
99# Common data ----
10+ set.seed(123 )
11+ stan_seed <- " 123"
1012data(veev2012 )
1113serosurvey <- veev2012
1214
1315suppressWarnings(
1416 seromodel_constant <- fit_seromodel(
1517 serosurvey = serosurvey ,
16- iter = 100
18+ iter = 100 ,
19+ seed = stan_seed
1720 )
1821)
1922
@@ -24,7 +27,8 @@ suppressWarnings(
2427 foi_index = get_foi_index(serosurvey , group_size = 20 , model_type = " age" ),
2528 is_seroreversion = TRUE ,
2629 seroreversion_prior = sf_normal(0 , 1e-4 ),
27- iter = 100
30+ iter = 100 ,
31+ seed = stan_seed
2832 )
2933)
3034
@@ -33,9 +37,11 @@ suppressWarnings(
3337 serosurvey = serosurvey ,
3438 model_type = " time" ,
3539 foi_index = get_foi_index(serosurvey , group_size = 10 , model_type = " time" ),
36- iter = 100
40+ iter = 100 ,
41+ seed = stan_seed
3742 )
3843)
44+ set.seed(Sys.time())
3945
4046create_prepared_serosurvey <- function (actual_serosurvey ) {
4147 prepared_serosurvey <- prepare_serosurvey_for_plot(
@@ -44,6 +50,7 @@ create_prepared_serosurvey <- function(actual_serosurvey) {
4450 return (prepared_serosurvey )
4551}
4652
53+
4754# Test plot_serosurvey ----
4855test_that(" plot_serosurvey creates a ggplot with correct structure" , {
4956 skip_on_cran()
@@ -81,6 +88,7 @@ test_that("plot_serosurvey creates a ggplot with correct structure", {
8188 expect_lists_equal_with_tolerance(expected_plot , actual_plot )
8289})
8390
91+
8492test_that(" plot_serosurvey creates a binned ggplot with correct structure" , {
8593 bin_step <- 10
8694
@@ -325,8 +333,6 @@ test_that("plot_seromodel creates a ggplot with correct structure", {
325333})
326334
327335
328-
329-
330336test_that(" plot_seromodel with age foi creates a ggplot with correct structure" , {
331337 seromodel <- seromodel_age
332338
@@ -380,9 +386,6 @@ test_that("plot_seromodel with age foi creates a ggplot with correct structure",
380386})
381387
382388
383-
384-
385-
386389test_that(" plot_seromodel with time foi creates a ggplot with correct structure" , {
387390 seromodel <- seromodel_time
388391
@@ -436,9 +439,6 @@ test_that("plot_seromodel with time foi creates a ggplot with correct structure"
436439})
437440
438441
439-
440-
441-
442442# Test plot_seroprev_estimates ----
443443test_that(" plot_seroprev_estimates creates a ggplot with correct structure" , {
444444 seromodel <- seromodel_constant
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