fix: handle errorneous measurements

umg-minai · Jun 10, 2024 · c73a3dd · c73a3dd
1 parent 710b7bf
commit c73a3dd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dltr
 Title: Draeger logbook and trend reader
-Version: 0.0.2.9000
+Version: 0.0.3
 Authors@R:
     person(
         given = "Sebastian", family = "Gibb",

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,10 @@
 
 ## Changes in development version
 
+## Changes in 0.0.3
+
+- Fix `.melt_measurements` for erroneous values ("ERR" or "+++").
+
 ## Changes in 0.0.2
 
 - Export `add_anesthesia_case_id`.

diff --git a/R/read_logbook.R b/R/read_logbook.R
@@ -303,7 +303,11 @@ add_anaesthesia_case_id <- function(x) {
     measure.vars <- colnames(x)[
         grepl("^etCO2|^MV|^Pmean|^PIP|^PP|^PEEP|^FiO|^prim.", colnames(x))
     ]
-    x[, (measure.vars) := lapply(.SD, as.double), .SDcols = measure.vars]
+    x[,
+        (measure.vars) :=
+            lapply(.SD, function(x)as.double(sub("ERR|\\+\\+\\+", "", x))),
+        .SDcols = measure.vars
+    ]
     m <- melt(
         x[Label == "Measurements", c("DateTime", measure.vars), with = FALSE],
         id.vars = "DateTime",

diff --git a/tests/testthat/test_read_logbook.R b/tests/testthat/test_read_logbook.R
@@ -176,8 +176,8 @@ test_that(".melt_measurements", {
             c(rep("2024-06-04 12:45", 3), "2024-06-04 13:00")
         ),
         Label = c("Measurements", "foo", "bar", "Measurements"),
-        `etCO2 [mmHg]` = c(35, NA, NA, 37),
-        `MV [l/min]` = c(5.0, NA, NA, 4.8)
+        `etCO2 [mmHg]` = c(35, "ERR", NA, 37),
+        `MV [l/min]` = c(5.0, NA, "+++", 4.8)
     )
     r <- data.table(
         DateTime = lubridate::ymd_hm(