Return epinow()'s "timing" output as <difftime> (#688)

* Print units of model run time * Add NEWS item * Fix tests * Make "timing" output a difftime object * Use purrr::map_vec to preserve difftime class * Test for the class instead of the type * Improve NEWS item * Import map_vec * Add reviewer Co-authored-by: Sebastian Funk <[email protected]> --------- Co-authored-by: Sebastian Funk <[email protected]>
epiforecasts · Jun 7, 2024 · 916a988 · 916a988
1 parent 4915906
commit 916a988
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Showing 6 changed files with 12 additions and 6 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -197,6 +197,7 @@ importFrom(purrr,map2_dbl)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_dbl)
 importFrom(purrr,map_dfc)
+importFrom(purrr,map_vec)
 importFrom(purrr,pmap_dbl)
 importFrom(purrr,quietly)
 importFrom(purrr,reduce)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,9 @@
 # EpiNow2 (development version)
 
+## Model changes
+
+- `epinow()` now returns the "timing" output in a "time difference"" format that is easier to understand and work with. By @jamesmbaazam in #688 and reviewed by @sbfnk.
+
 # EpiNow2 1.5.2
 
 A patch release to further fix an issue with the date in the package citation. This has now been addressed by removing `inst/CITATION`.

diff --git a/R/epinow.R b/R/epinow.R
@@ -286,7 +286,7 @@ epinow <- function(data,
 
   # log timing if specified
   if (output["timing"]) {
-    out$timing <- round(as.numeric(end_time - start_time), 1)
+    out$timing <- difftime(end_time, start_time)
     if (!is.null(target_folder)) {
       saveRDS(out$timing, file.path(target_folder, "runtime.rds"))
     }

diff --git a/R/summarise.R b/R/summarise.R
@@ -503,7 +503,7 @@ summarise_key_measures <- function(regional_results = NULL,
 #' @return A data.table of region run times
 #' @export
 #' @importFrom data.table data.table fwrite
-#' @importFrom purrr map safely
+#' @importFrom purrr map safely map_vec
 #' @keywords internal
 #' @examples
 #' regional_out <- readRDS(system.file(
@@ -530,7 +530,8 @@ regional_runtimes <- function(regional_output = NULL,
   if (!is.null(regional_output)) {
     timings <- data.table::data.table(
       region = names(regional_output),
-      time = unlist(purrr::map(regional_output, ~ .$timing))
+      # purrr::map_vec will preserve the difftime class
+      time = unlist(purrr::map_vec(regional_output, ~ .$timing))
     )
   } else {
     if (is.null(target_date)) {

diff --git a/tests/testthat/test-regional_epinow.R b/tests/testthat/test-regional_epinow.R
@@ -36,7 +36,7 @@ test_that("regional_epinow produces expected output when run with default settin
     "summarised_measures", "reported_cases", "high_plots", "plots"
   ))
   expect_equal(names(out$regional$realland), c("estimates", "estimated_reported_cases", "summary", "plots", "timing"))
-  expect_type(out$regional$realland$timing, "double")
+  expect_s3_class(out$regional$realland$timing, "difftime")
   df_non_zero(out$regional$realland$estimates$samples)
   df_non_zero(out$regional$realland$estimates$summarised)
   df_non_zero(out$regional$realland$estimated_reported_cases$samples)
@@ -101,7 +101,7 @@ test_that("regional_epinow produces expected output when run with region specifi
     "summarised_measures", "reported_cases", "high_plots", "plots"
   ))
   expect_equal(names(out$regional$realland), c("estimates", "estimated_reported_cases", "summary", "plots", "timing"))
-  expect_type(out$regional$realland$timing, "double")
+  expect_s3_class(out$regional$realland$timing, "difftime")
   df_non_zero(out$regional$realland$estimates$samples)
   df_non_zero(out$regional$realland$estimates$summarised)
   df_non_zero(out$regional$realland$estimated_reported_cases$samples)

diff --git a/tests/testthat/test-regional_runtimes.R b/tests/testthat/test-regional_runtimes.R
@@ -27,5 +27,5 @@ test_that("regional_runtimes produces expected output when with input", {
   runtimes <- regional_runtimes(out$regional)
   expect_equal(names(runtimes), c("region", "time"))
   df_non_zero(runtimes)
-  expect_type(runtimes$time, "double")
+  expect_s3_class(runtimes$time, "difftime")
 })