#2146 Fix Time Imputation Flag

pharmaverse · Oct 26, 2023 · 28ebe05 · 28ebe05
1 parent dd8f8d9
commit 28ebe05
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Showing 5 changed files with 56 additions and 22 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -201,12 +201,15 @@ importFrom(lubridate,date)
 importFrom(lubridate,days)
 importFrom(lubridate,duration)
 importFrom(lubridate,floor_date)
+importFrom(lubridate,hour)
 importFrom(lubridate,hours)
 importFrom(lubridate,is.Date)
 importFrom(lubridate,is.POSIXct)
 importFrom(lubridate,is.instant)
+importFrom(lubridate,minute)
 importFrom(lubridate,minutes)
 importFrom(lubridate,rollback)
+importFrom(lubridate,second)
 importFrom(lubridate,time_length)
 importFrom(lubridate,weeks)
 importFrom(lubridate,years)
@@ -220,6 +223,7 @@ importFrom(purrr,keep)
 importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,map_chr)
+importFrom(purrr,map_dbl)
 importFrom(purrr,map_if)
 importFrom(purrr,map_lgl)
 importFrom(purrr,modify_at)

diff --git a/R/admiral-package.R b/R/admiral-package.R
@@ -14,13 +14,14 @@
 #'   warn as_data_mask list2
 #' @importFrom utils capture.output str file.edit
 #' @importFrom purrr map map2 map_chr map_lgl reduce walk keep map_if transpose
-#'             flatten every modify_at modify_if reduce compose pmap
+#'             flatten every modify_at modify_if reduce compose pmap map_dbl
 #' @importFrom stringr str_c str_count str_detect str_extract str_glue
 #'   str_length str_locate str_locate_all str_match str_remove str_remove_all
 #'   str_replace str_replace_all str_split str_starts str_sub str_subset
 #'   str_trim str_to_lower str_to_title str_to_upper
 #' @importFrom lubridate as_datetime ceiling_date date days duration floor_date is.Date is.instant
-#'             rollback time_length %--% ymd ymd_hms weeks years hours minutes is.POSIXct
+#'             rollback time_length %--% ymd ymd_hms weeks years hours minutes is.POSIXct hour
+#'             minute second
 #' @importFrom tidyr crossing drop_na fill nest pivot_longer pivot_wider unnest
 #' @importFrom tidyselect all_of any_of contains matches vars_select
 #' @importFrom hms as_hms

diff --git a/R/derive_date_vars.R b/R/derive_date_vars.R
@@ -1207,25 +1207,40 @@ compute_dtf <- function(dtc, dt) {
 #' @export
 #'
 #' @examples
-#' compute_tmf(dtc = "2019-07-18T15:25", dtm = as.POSIXct("2019-07-18T15:25:00"))
-#' compute_tmf(dtc = "2019-07-18T15", dtm = as.POSIXct("2019-07-18T15:25:00"))
-#' compute_tmf(dtc = "2019-07-18", dtm = as.POSIXct("2019-07-18"))
+#' library(lubridate)
+#'
+#' compute_tmf(dtc = "2019-07-18T15:25", dtm = ymd_hms("2019-07-18T15:25:00"))
+#' compute_tmf(dtc = "2019-07-18T15", dtm = ymd_hms("2019-07-18T15:25:00"))
+#' compute_tmf(dtc = "2019-07-18", dtm = ymd("2019-07-18"))
+#' compute_tmf(dtc = "2022-05--T00:00", dtm = ymd_hms("2022-05-15T23:59:59"))
+#' compute_tmf(dtc = "2022-05--T23:00", dtm = ymd_hms("2022-05-15T23:59:59"))
+#' compute_tmf(dtc = "2022-05--T23:59:00", dtm = ymd_hms("2022-05-15T23:59:59"))
 compute_tmf <- function(dtc,
                         dtm,
                         ignore_seconds_flag = FALSE) {
   assert_date_vector(dtm)
   assert_character_vector(dtc)
   assert_logical_scalar(ignore_seconds_flag)
 
+  valid_dtc <- is_valid_dtc(dtc)
+  warn_if_invalid_dtc(dtc, valid_dtc)
+
   partial <- get_partialdatetime(dtc)
   highest_miss <- convert_blanks_to_na(vector("character", length(dtc)))
-  for (c in c("hour", "minute", "second")) {
+  hms <- c("hour", "minute", "second")
+  time_part <-
+    map(set_names(hms), \(y) map_dbl(dtm, \(x) do.call(y, as.list(x))))
+  for (c in hms) {
     highest_miss <-
-      if_else(is.na(partial[[c]]) & is.na(highest_miss), c, highest_miss)
+      if_else((is.na(partial[[c]]) & is.na(highest_miss)) |
+        (
+          !is.na(partial[[c]]) &
+            is.na(highest_miss) & as.numeric(partial[[c]]) != time_part[[c]]
+        ),
+      c,
+      highest_miss
+      )
   }
-  is_na <- is.na(dtm)
-  valid_dtc <- is_valid_dtc(dtc)
-  warn_if_invalid_dtc(dtc, valid_dtc)
 
   map <- c(
     hour = "H",

diff --git a/man/compute_tmf.Rd b/man/compute_tmf.Rd
diff --git a/tests/testthat/test-derive_date_vars.R b/tests/testthat/test-derive_date_vars.R
@@ -587,20 +587,26 @@ test_that("compute_tmf Test 30: compute TMF", {
     "2003-12-15T-:15:18",
     "2003-12-15T13:-:19",
     "2020-07--T00:00",
-    "2020-07--T00:00:00"
+    "2020-07--T00:00:00",
+    "2022-05--T00:00",
+    "2022-05--T23:00",
+    "2022-05--T23:59:00"
   )
   input_dtm <- c(
-    as.POSIXct("2019-07-18T15:25:52"),
-    as.POSIXct("2019-07-18T15:25:00"),
-    as.POSIXct("2019-07-18T15:00:00"),
+    ymd_hms("2019-07-18T15:25:52"),
+    ymd_hms("2019-07-18T15:25:00"),
+    ymd_hms("2019-07-18T15:00:00"),
     as.POSIXct("2019-07-18"),
     as.POSIXct("2019-02-01"),
     as.POSIXct(NA_character_),
     as.POSIXct(NA_character_),
-    as.POSIXct("2003-12-15T23:15:18"),
-    as.POSIXct("2003-12-15T13:59:19"),
-    as.POSIXct("2020-07-31T00:00:59"),
-    as.POSIXct("2020-07-31T00:00:59")
+    ymd_hms("2003-12-15T23:15:18"),
+    ymd_hms("2003-12-15T13:59:19"),
+    ymd_hms("2020-07-31T00:00:59"),
+    ymd_hms("2020-07-31T00:00:00"),
+    ymd_hms("2022-05-15T23:59:59"),
+    ymd_hms("2022-05-15T23:59:59"),
+    ymd_hms("2022-05-15T23:59:59")
   )
   expected_output <- c(
     NA_character_,
@@ -613,7 +619,10 @@ test_that("compute_tmf Test 30: compute TMF", {
     "H",
     "M",
     "S",
-    NA_character_
+    NA_character_,
+    "H",
+    "M",
+    "S"
   )
 
   expect_equal(