fix: value_at for multiple cases

umg-minai · Jun 9, 2024 · b1bf478 · b1bf478
1 parent a507998
commit b1bf478
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Showing 4 changed files with 50 additions and 25 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(add_anaesthesia_case_id)
 export(case_duration)
 export(case_end)
 export(case_start)

diff --git a/R/read_logbook.R b/R/read_logbook.R
@@ -36,7 +36,7 @@
         )
     )[order(DateTime),]
     lb[, Current := as.double(Current)]
-    .add_anaesthesia_case_id(lb)
+    add_anaesthesia_case_id(lb)
     lb[!is.na(CaseId) & CaseId > 0,]
 }
 
@@ -61,12 +61,11 @@ value_at <- function(x, label, time,
                         "mechanical-ventilation"
                     )) {
     reference <- match.arg(reference)
-    x[,
-        .SD[
-            Label == label &
-            DateTime <= .reference_time(x, reference) + minutes(time),
-            Current[.N]
-        ],
+    r <- .reference_time(x, reference)
+    r[, ReferenceTime := ReferenceTime + minutes(time)]
+    m <- merge(x, r)
+    m[,
+        .SD[Label == label & DateTime <= ReferenceTime, Current[.N]],
         by = CaseId
     ]
 }
@@ -84,8 +83,9 @@ value_at <- function(x, label, time,
         "mechanical-ventilation" = "Ventilation settings"
     )
     x[,
-      .SD[Label == ref_label & !Current %in% c(0, 9), DateTime[1]],
-      by = CaseId][,V1]
+      .(ReferenceTime =
+        .SD[Label == ref_label & !Current %in% c(0, 9), DateTime[1]]),
+      by = CaseId]
 }
 
 #' Filter cases
@@ -132,7 +132,7 @@ case_start  <- function(x, reference = c(
                    "start", "vaporizer-opening",
                    "mechanical-ventilation"
                    )) {
-    .reference_time(x, reference)
+    .reference_time(x, reference)[, ReferenceTime]
 }
 
 #' @return `POSIXct`, end times
@@ -166,10 +166,14 @@ is_volatile_anesthesia <- function(x) {
     ][, V1]
 }
 
+#' Case Id
+#'
+#' Add an additional column with a corresponding case id.
+#'
 #' @param x `data.table`, logbook data
-#' @return `integer`, row indices
-#' @noRd
-.add_anaesthesia_case_id <- function(x) {
+#' @return `data.table`, with additional CaseId column.
+#' @export
+add_anaesthesia_case_id <- function(x) {
     setorder(x, DateTime)
     x[, CaseId := cumsum(Label == "Start of therapy")]
     x[, CaseId := fifelse(

diff --git a/man/add_anaesthesia_case_id.Rd b/man/add_anaesthesia_case_id.Rd
diff --git a/tests/testthat/test_read_logbook.R b/tests/testthat/test_read_logbook.R
@@ -12,16 +12,17 @@ test_that(".read_logbook", {
 
 test_that("value_at", {
    lb <- data.table(
-        DateTime = 1:8 * 60,
+        DateTime = lubridate::ymd_hms("2024-06-09 20:00:00") +
+            lubridate::minutes(c(1:9, 12)),
         Label = c("Start of therapy", "Ventilation settings",
                   "Vaporizer setting", "Ventilation settings",
-                  "PEEP", "FGF", "FGF", "FGF"),
-        Current = c(2, 0, 0.5, 2, 5, 0.5, 0.6, 0.7),
-        CaseId = 1
+                  "PEEP", "FGF", "FGF", "FGF", "Start of therapy", "FGF"),
+        Current = c(2, 0, 0.5, 2, 5, 0.5, 0.6, 0.7, 2, 1.5),
+        CaseId = c(rep(1, 8), 2, 2)
     )
-    expect_equal(value_at(lb, "FGF", 5, "start")[,V1], 0.5)
-    expect_equal(value_at(lb, "FGF", 6, "start")[,V1], 0.6)
-    expect_equal(value_at(lb, "FGF", 7, "start")[,V1], 0.7)
+    expect_equal(value_at(lb, "FGF", 5, "start")[,V1], c(0.5, 1.5))
+    expect_equal(value_at(lb, "FGF", 6, "start")[,V1], c(0.6, 1.5))
+    expect_equal(value_at(lb, "FGF", 7, "start")[,V1], c(0.7, 1.5))
     expect_equal(value_at(lb, "FGF", 3, "vaporizer-opening")[,V1], 0.5)
     expect_equal(value_at(lb, "FGF", 2, "mechanical-ventilation")[,V1], 0.5)
     expect_equal(value_at(lb, "PEEP", 15, "start")[,V1], 5)
@@ -36,9 +37,11 @@ test_that(".reference_time", {
         Current = c(2, 0, 0.5, 2),
         CaseId = 1
     )
-    expect_equal(.reference_time(lb, "start"), 1)
-    expect_equal(.reference_time(lb, "vaporizer-opening"), 3)
-    expect_equal(.reference_time(lb, "mechanical-ventilation"), 4)
+    expect_equal(.reference_time(lb, "start")[, ReferenceTime], 1)
+    expect_equal(.reference_time(lb, "vaporizer-opening")[, ReferenceTime], 3)
+    expect_equal(
+        .reference_time(lb, "mechanical-ventilation")[, ReferenceTime], 4
+    )
 })
 
 test_that("filter_short_cases", {
@@ -102,15 +105,15 @@ test_that("is_volatile_anesthesia", {
     expect_equal(is_volatile_anesthesia(lb), c(FALSE, FALSE, TRUE, FALSE))
 })
 
-test_that(".add_anaesthesia_case_id", {
+test_that("add_anaesthesia_case_id", {
    lb <- data.table(
         DateTime = 1:6,
         Label = c(
             "Start of therapy", "Case duration", "bar",
             "Start of therapy", "Case duration", "foo"
         )
     )
-    expect_equal(.add_anaesthesia_case_id(lb)$CaseId, c(1, 1, NA, 2, 2, NA))
+    expect_equal(add_anaesthesia_case_id(lb)$CaseId, c(1, 1, NA, 2, 2, NA))
 })
 
 test_that(".fgf_index", {