update news and tests

NEWS.md

@@ -5,7 +5,7 @@
 * The functions `get_dist`, `get_generation_time`, `get_incubation_period` have been deprecated and replaced with examples. By @sbfnk in #481 and reviewed by @seabbs.
 * The utility function `update_list()` has been deprecated in favour of `utils::modifyList()` because it comes with an installation of R. By @jamesmbaazam in #491 and reviewed by @seabbs.
 * The `fixed` argument to `dist_spec` has been deprecated and replaced by a `fix_dist()` function. By @sbfnk in #503 and reviewed by @seabbs.
-* Updated `estimate_infections()` so that rather than imputing missing data, it now skips these data points in the likelihood. This is a breaking change as it changes the behaviour of the model when dates are missing from a time series but are known to be zero. We recommend that users check their results when updating to this version. By @seabbs in # and reviewed by @sbfnk.
+* Updated `estimate_infections()` so that rather than imputing missing data, it now skips these data points in the likelihood. This is a breaking change as it alters the behaviour of the model when dates are missing from a time series but are known to be zero. We recommend that users check their results when updating to this version but expect this to in most cases improve performance. By @seabbs in # and reviewed by @sbfnk.
 
 ## Documentation
 

tests/testthat/test-create_clean_reported_cases.R

@@ -15,7 +15,9 @@ test_that("create_clean_reported_cases filters leading zeros correctly", {
 
   result <- create_clean_reported_cases(modified_data, 7)
   # Check if the first row with non-zero cases is retained
-  expect_equal(result$date[1], min(modified_data$date[modified_data$confirm > 0]))
+  expect_equal(
+    result$date[1], min(modified_data$date[modified_data$confirm > 0])
+  )
 })
 
 test_that("create_clean_reported_cases replaces zero cases correctly", {

tests/testthat/test-estimate_infections.R

@@ -36,6 +36,14 @@ test_that("estimate_infections successfully returns estimates using default sett
   test_estimate_infections(reported_cases)
 })
 
+test_that("estimate_infections successfully returns estimates when passed NA values", {
+  skip_on_cran()
+  reported_cases_na <- data.table::copy(reported_cases)
+  reported_cases_na[sample(1:30, 5), confirm := NA]
+  test_estimate_infections(reported_cases_na)
+})
+
+
 test_that("estimate_infections successfully returns estimates using no delays", {
   skip_on_cran()
   test_estimate_infections(reported_cases, delay = FALSE)