Merge branch 'master' into issue1212_modify_nonwear_window

NEWS.md

@@ -1,9 +1,14 @@
-# CHANGES IN GGIR VERSION 3.1-?
+# CHANGES IN GGIR VERSION 3.1-5
 
-- Part 5: Fixed minor bug in g.part5.addfirstwake causing the first wake is not correctly added when
-no SIBs are detected from the beginning of the recording until the first detected night. #1198
+- Part 5: 
 
-- Part 5: Add parameters require_complete_lastnight_part5 to control whether last window is included if last night is incomplete. #1196
+  - Add parameters require_complete_lastnight_part5 to control whether last window is included if last night is incomplete. #1196
+
+  - Adjust sleeplog times to recording length in part 5 when classifying a night that was not detected in part 4. #1206
+
+  - Fixed minor bug in g.part5.addfirstwake causing the first wake is not correctly added when no SIBs are detected from the beginning of the recording until the first detected night. #1198
+
+  - Revise MM window definition in daylight saving time days, as it assumed fixed day duration of 24 hours #1211 
 
 - General: GGIR version look-up in .onattach() no longer crashes when computer is offline, fixes #1203.
 

R/g.part5.definedays.R

@@ -41,25 +41,14 @@ g.part5.definedays = function(nightsi, wi, indjump, nightsi_bu,
   # Check that it is possible to find both windows (WW and MM)
   # in the data for this day.
   if (timewindowi == "MM") {
-    NepochPerDay = ((24*3600) / epochSize)
-    # offset from prev midnight
-    t0 = format(ts$time[1], "%H:%M:%S")
-    hms = as.numeric(unlist(strsplit(t0, ":")))
-    NepochFromPrevMidnight = (hms[1]*60*60 + hms[2]*60 + hms[3]) / epochSize
-    NepochFromDayborder2Midnight = (-dayborder*60*60) / epochSize
-    NepochFromPrevNight = NepochFromPrevMidnight + NepochFromDayborder2Midnight
-    if (NepochFromPrevNight < 0) {
-      NepochFromPrevNight = NepochPerDay + NepochFromPrevNight
-    }
-    if (wi == 1) {
-      qqq[1] = 1
-      qqq[2] = NepochPerDay - NepochFromPrevNight
-    } else {
-      qqq[1] = ((wi - 1) * NepochPerDay) - NepochFromPrevNight + 1
-      qqq[2] = (wi * NepochPerDay) - NepochFromPrevNight
-    }
+    # include first and last partial days in MM
+    if (nightsi[1] > 1) nightsi = c(1, nightsi)
+    if (nightsi[length(nightsi)] < nrow(ts)) nightsi = c(nightsi, nrow(ts))
+    # define window
+    qqq[1] = nightsi[wi]
+    qqq[2] = nightsi[wi + 1] - 1
     # is this the last day?
-    if (qqq[2] >= Nts) {
+    if (qqq[2] >= Nts - 1) {
       qqq[2] = Nts
       lastDay = TRUE
     }
@@ -88,7 +77,10 @@ g.part5.definedays = function(nightsi, wi, indjump, nightsi_bu,
       breaks = qwindow2timestamp(qwindow, epochSize)
       if (24 %in% qwindow) {
         # 24:00:00: probably does not exist, replace by last timestamp in a day
-        latest_time_in_day = max(format(ts$time[1:pmin(Nts, NepochPerDay)], format = "%H:%M:%S"))
+        # here, we consider N epochs per day plus 1 hour just in case we are deriving this in 
+        # a 25-hour daylight saving time day
+        NepochPerDayPlusOneHr = ((25*3600) / epochSize)
+        latest_time_in_day = max(format(ts$time[1:pmin(Nts, NepochPerDayPlusOneHr)], format = "%H:%M:%S"))
         breaks = gsub(pattern = "24:00:00", replacement = latest_time_in_day, x = breaks)
       }
       breaks_i = c()

R/g.part5.wakesleepwindows.R

@@ -77,12 +77,24 @@ g.part5.wakesleepwindows = function(ts, part4_output, desiredtz, nightsi,
     s1 = findIndex(timeChar, wc = format(as.POSIXlt(w1[k], tz = desiredtz)))
 
     if (is.na(s0) == TRUE) {
-      s0 = 1
+      if (format(as.POSIXlt(w0[k], tz = desiredtz)) < timeChar[1]) {
+        # safe check, only turn s0 to 1 when the part4 wake up is before the first
+        # timestamp. Otherwise, if wake up is after the last timestamp, then the 
+        # whole time series is set to sleep period time (only occurs in nights with
+        # cleaningcode = 5 in part 4 (no accelerometer data available, but spt extracted from sleeplog))
+        s0 = 1
+      }
     }
     if (is.na(s1) == TRUE) {
       # might still be NA if the timestamps is not in ts (expanded time from expand_tail)
       # if so, we assume the participant is sleeping at the end of the recording, this night will be disregarded later on
-      s1 = nrow(ts)
+      if (format(as.POSIXlt(w1[k], tz = desiredtz)) > timeChar[length(timeChar)]) {
+        # safe check, only turn s1 to nrow(ts) when the part4 wake up is after the last
+        # timestamp. Otherwise, if sleep onset is before the first timestamp, then the 
+        # whole time series is set to sleep period time (only occurs in nights with
+        # cleaningcode = 5 in part 4 (no accelerometer data available, but spt extracted from sleeplog))
+        s1 = nrow(ts)
+      }
     }
 
     if (length(s1) != 0 & length(s0) != 0 & is.na(s0) == FALSE & is.na(s1) == FALSE && length(nightsi) > 0) {
@@ -95,7 +107,6 @@ g.part5.wakesleepwindows = function(ts, part4_output, desiredtz, nightsi,
       if (noon1 > Nts) noon1 = Nts
       nonwearpercentage = mean(ts$nonwear[noon0:noon1])
       if ((length(sleeplog) > 0 & (nonwearpercentage > 0.33) | part4_output$sleeponset_ts[k] == "")) { # added condition to detect nights that are not detected in part 4
-
         # If non-wear is high for this day and if sleeplog is available
         sleeplogonset = sleeplog$sleeponset[which(sleeplog$ID == ID & sleeplog$night == part4_output$night[k])]
         sleeplogwake = sleeplog$sleepwake[which(sleeplog$ID == ID & sleeplog$night == part4_output$night[k])]
@@ -124,10 +135,19 @@ g.part5.wakesleepwindows = function(ts, part4_output, desiredtz, nightsi,
               s0 = 1
             }
             s1 = closestmidnight + round(sleeplogwake_hr * Nepochsinhour)
+            # if sleeplog indicates a time after the ending of the recording, 
+            # then set the nrow(ts) + 1, so that the next line will set as 
+            # SPT all the time from sleep onset until the end of the recording.
+            if (s1 > nrow(ts) + 1) s1 = nrow(ts) + 1
           }
         }
       }
-      ts$diur[s0:(s1 - 1)] = 1
+      # it might also be that both the sleeplog reported sleeponset and
+      # wakeup goes beyond recording length, in that case, s1 < s0,
+      # so only assign SPT if s0 < s1
+      if (s0 < s1) {
+        ts$diur[s0:(s1 - 1)] = 1
+      }
     }
   }
   return(ts)