From c9d26af9ab43f940d092229001bdb2721fd58f28 Mon Sep 17 00:00:00 2001
From: Vincent van Hees <v.vanhees@accelting.com>
Date: Wed, 20 Nov 2024 11:56:12 +0100
Subject: [PATCH] #1218 improve extraction of timewindow from log and ignore
 column with the word impute

---
 R/filterNonwearNight.R | 17 ++++++++++++++---
 R/g.conv.actlog.R      |  1 +
 man/GGIR.Rd            |  2 +-
 3 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/R/filterNonwearNight.R b/R/filterNonwearNight.R
index d3dddddef..6b7524b31 100644
--- a/R/filterNonwearNight.R
+++ b/R/filterNonwearNight.R
@@ -53,10 +53,21 @@ filterNonwearNight = function(r1, metalong, qwindowImp, desiredtz,
       r1B$date = as.Date(metalong$time_POSIX)
       for (qi in 1:nrow(qwindowImp)) {
         qwindow_temp = qwindowImp$qwindow_values[[qi]]
+        # filter only SPT and time in bed reports
+        qwindow_temp = qwindow_temp[grep(pattern = "bed|wakeup|sleeponset", x = qwindowImp$qwindow_names[[qi]])]
+        qwindow_temp = sort(qwindow_temp)
         if (length(qwindow_temp) > 3) {
-          # if diary has at least two timestamps other than 0 and 24
-          start = rev(qwindow_temp)[2]
-          end = qwindow_temp[2]
+          # convert to continuous scale to ease finding start and end
+          below18 = which(qwindow_temp < 18)
+          if (length(below18) > 0) {
+            qwindow_temp = qwindow_temp[below18] + 24
+          }
+          start = min(qwindow_temp)
+          end = max(qwindow_temp)
+          if (length(below18) > 0) {
+            start = ifelse(start > 24, yes = start - 24, no = start)
+            end = ifelse(end > 24, yes = end - 24, no = end)
+          }
           if (start > end) {
             r1B$filterWindow[which(r1B$date == qwindowImp$date[qi] & 
                                      r1B$hr >= start |
diff --git a/R/g.conv.actlog.R b/R/g.conv.actlog.R
index b03255801..c25655ed2 100644
--- a/R/g.conv.actlog.R
+++ b/R/g.conv.actlog.R
@@ -4,6 +4,7 @@ g.conv.actlog = function(qwindow, qwindow_dateformat="%d-%m-%Y", epochSize = 5)
   # local functions:
   time2numeric = function(x) {
     x = unlist(x)
+    x = x[grep(pattern = "impute", x = names(x), invert = TRUE)]
     c2t = function(x2) {
       tmp = as.numeric(unlist(strsplit(as.character(x2),":")))
       if (length(tmp) == 2) hourinday = tmp[1] + (tmp[2]/60)
diff --git a/man/GGIR.Rd b/man/GGIR.Rd
index 1829c1bf6..e09b477d5 100644
--- a/man/GGIR.Rd
+++ b/man/GGIR.Rd
@@ -985,7 +985,7 @@ GGIR(mode = 1:5,
         defined by activity diary file and a diary entry is missing use midnight-6am
         as fall back setting. The main purpose of this functionality is to offer
         the option to ignore short lasting nonwear episodes during the night
-        when there is suspicious that these are falsely detect, e.g. in individuals
+        when there is suspicion that these are falsely detect, e.g. in individuals
         with extended motionless sleep periods caused by medication.}
       
       \item{nonwearFilterWindow}{