Use broadcasting vs loop in day of week (#746)

* use broadcasting vs loop

* add tests for some obs models stan fns

* Update NEWS.md

NEWS.md

@@ -12,6 +12,7 @@
 - The interface for defining delay distributions has been generalised to also cater for continuous distributions
 - When defining probability distributions these can now be truncated using the `tolerance` argument
 - Ornstein-Uhlenbeck and 5 / 2 Matérn kernels have been added. By @sbfnk in # and reviewed by @.
+- Switch to broadcasting the day of the week effect. By @seabbs in #746 and reviewed by @jamesmbaazam.
 - A warning is now thrown if nonparametric PMFs passed to delay options have consecutive tail values that are below a certain low threshold as these lead to loss in speed with little gain in accuracy. By @jamesmbaazam in #752 and reviewed by @seabbs.
 
 ## Bug fixes

inst/stan/functions/observation_model.stan

@@ -10,16 +10,9 @@
  * @return A vector of reports adjusted for day of the week effects.
  */
 vector day_of_week_effect(vector reports, array[] int day_of_week, vector effect) {
-  int t = num_elements(reports);
   int wl = num_elements(effect);
-  // scale day of week effect
   vector[wl] scaled_effect = wl * effect;
-  vector[t] scaled_reports;
-  for (s in 1:t) {
-    // add reporting effects (adjust for simplex scale)
-    scaled_reports[s] = reports[s] * scaled_effect[day_of_week[s]];
-   }
-  return(scaled_reports);
+  return reports .* scaled_effect[day_of_week];
 }
 
 /**

tests/testthat/test-stan-observation_model.R

@@ -0,0 +1,37 @@
+skip_on_cran()
+skip_on_os("windows")
+
+test_that("day_of_week_effect applies day of week effect correctly", {
+  reports <- c(100, 200, 300, 400, 500, 600, 700, 800, 900, 1000)
+  day_of_week <- c(1, 2, 3, 1, 2, 3, 1, 2, 3, 1)
+  effect <- c(1.0, 1.1, 1.2)
+
+  expected <- reports * effect[day_of_week] * 3
+  result <- day_of_week_effect(reports, day_of_week, effect)
+
+  expect_equal(result, expected)
+})
+
+test_that("scale_obs scales reports by fraction observed", {
+  reports <- c(100, 200, 300, 400, 500, 600, 700, 800, 900, 1000)
+  frac_obs <- 0.5
+
+  expected <- c(50, 100, 150, 200, 250, 300, 350, 400, 450, 500)
+  result <- scale_obs(reports, frac_obs)
+
+  expect_equal(result, expected)
+})
+
+test_that("truncate_obs truncates reports correctly", {
+  reports <- c(100, 200, 300, 400, 500, 600, 700, 800, 900, 1000)
+  trunc_rev_cmf <- c(1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1)
+
+  expected_truncate <- c(100, 180, 240, 280, 300, 300, 280, 240, 180, 100)
+  result_truncate <- truncate_obs(reports, trunc_rev_cmf, reconstruct = 0)
+
+  expect_equal(result_truncate, expected_truncate)
+
+  result_reconstruct <- truncate_obs(expected_truncate, trunc_rev_cmf, reconstruct = 1)
+
+  expect_equal(result_reconstruct, reports)
+})