update epinow tests

epiforecasts · Oct 21, 2023 · 4eb8f9f · 4eb8f9f
1 parent 5f16fbc
commit 4eb8f9f
Showing 1 changed file with 15 additions and 16 deletions.
diff --git a/tests/testthat/test-epinow.R b/tests/testthat/test-epinow.R
@@ -1,11 +1,10 @@
 skip_on_cran()
 
-# get example delays
-generation_time <- example_generation_time
-incubation_period <- example_incubation_period
+# set example reporting delay
 reporting_delay <- dist_spec(
   mean = convert_to_logmean(2, 1), mean_sd = 0.1,
-  sd = convert_to_logsd(2, 1), sd_sd = 0.1, max = 15
+  sd = convert_to_logsd(2, 1), sd_sd = 0.1,
+  max = 10
 )
 
 reported_cases <- EpiNow2::example_confirmed[1:30]
@@ -20,8 +19,8 @@ expected_out <- c("estimates", "estimated_reported_cases", "summary", "plots", "
 test_that("epinow produces expected output when run with default settings", {
   out <- suppressWarnings(epinow(
     reported_cases = reported_cases,
-    generation_time = generation_time_opts(generation_time),
-    delays = delay_opts(incubation_period + reporting_delay),
+    generation_time = generation_time_opts(example_generation_time),
+    delays = delay_opts(example_incubation_period + reporting_delay),
     stan = stan_opts(
       samples = 25, warmup = 25,
       cores = 1, chains = 2,
@@ -42,8 +41,8 @@ test_that("epinow produces expected output when run with default settings", {
 test_that("epinow runs without error when saving to disk", {
   expect_null(suppressWarnings(epinow(
     reported_cases = reported_cases,
-    generation_time = generation_time_opts(generation_time),
-    delays = delay_opts(incubation_period + reporting_delay),
+    generation_time = generation_time_opts(example_generation_time),
+    delays = delay_opts(example_incubation_period + reporting_delay),
     stan = stan_opts(
       samples = 25, warmup = 25, cores = 1, chains = 2,
       control = list(adapt_delta = 0.8)
@@ -56,8 +55,8 @@ test_that("epinow runs without error when saving to disk", {
 test_that("epinow can produce partial output as specified", {
   out <- suppressWarnings(epinow(
     reported_cases = reported_cases,
-    generation_time = generation_time_opts(generation_time),
-    delays = delay_opts(incubation_period + reporting_delay),
+    generation_time = generation_time_opts(example_generation_time),
+    delays = delay_opts(example_incubation_period + reporting_delay),
     stan = stan_opts(
       samples = 25, warmup = 25,
       cores = 1, chains = 2,
@@ -79,8 +78,8 @@ test_that("epinow can produce partial output as specified", {
 test_that("epinow fails as expected when given a short timeout", {
   expect_error(suppressWarnings(x = epinow(
     reported_cases = reported_cases,
-    generation_time = generation_time_opts(generation_time),
-    delays = delay_opts(incubation_period + reporting_delay),
+    generation_time = generation_time_opts(example_generation_time),
+    delays = delay_opts(example_incubation_period + reporting_delay),
     stan = stan_opts(
       samples = 100, warmup = 100,
       cores = 1, chains = 2,
@@ -95,8 +94,8 @@ test_that("epinow fails as expected when given a short timeout", {
 test_that("epinow fails if given NUTs arguments when using variational inference", {
   expect_error(suppressWarnings(epinow(
     reported_cases = reported_cases,
-    generation_time = generation_time_opts(generation_time),
-    delays = delay_opts(incubation_period + reporting_delay),
+    generation_time = generation_time_opts(example_generation_time),
+    delays = delay_opts(example_incubation_period + reporting_delay),
     stan = stan_opts(
       samples = 100, warmup = 100,
       cores = 1, chains = 2,
@@ -110,8 +109,8 @@ test_that("epinow fails if given NUTs arguments when using variational inference
 test_that("epinow fails if given variational inference arguments when using NUTs", {
   expect_error(suppressWarnings(epinow(
     reported_cases = reported_cases,
-    generation_time = generation_time_opts(generation_time),
-    delays = delay_opts(incubation_period + reporting_delay),
+    generation_time = generation_time_opts(example_generation_time),
+    delays = delay_opts(example_incubation_period + reporting_delay),
     stan = stan_opts(method = "sampling", tol_rel_obj = 1),
     logs = NULL, verbose = FALSE
   )))