add option to only use qwindow for filtering and not for other purposes

#1218

R/g.part2.R

@@ -18,9 +18,13 @@ g.part2 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
   params_output = params$params_output
   params_general = params$params_general
   #-----------------------------
+  use_qwindow_as_diary = TRUE # If there is a diary specified via qwindow use it
   if (is.numeric(params_247[["qwindow"]])) {
     params_247[["qwindow"]] = params_247[["qwindow"]][order(params_247[["qwindow"]])]
   } else if (is.character(params_247[["qwindow"]])) {
+    if (length(grep(pattern = "onlyfilter", x = params_247[["qwindow"]])) > 0) {
+      use_qwindow_as_diary = FALSE # Do not use it if it has the word onlyfilter
+    }
     params_247[["qwindow"]] = g.conv.actlog(params_247[["qwindow"]],
                                             params_247[["qwindow_dateformat"]],
                                             epochSize = params_general[["windowsizes"]][1])
@@ -83,7 +87,7 @@ g.part2 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
                         myfun=c(), params_cleaning = c(), params_247 = c(),
                         params_phyact = c(), params_output = c(), params_general = c(),
                         path, ms2.out, foldername, fullfilenames, folderstructure, referencefnames,
-                        daySUMMARY, pdffilenumb, pdfpagecount, csvfolder, cnt78, verbose) {
+                        daySUMMARY, pdffilenumb, pdfpagecount, csvfolder, cnt78, verbose, use_qwindow_as_diary) {
     Nappended = I_list = tail_expansion_log =  NULL
     if (length(ffdone) > 0) {
       if (length(which(ffdone == as.character(unlist(strsplit(fnames[i], "eta_"))[2]))) > 0) {
@@ -151,6 +155,10 @@ g.part2 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
           }
         }
         qwindowImp = params_247[["qwindow"]]
+        if (use_qwindow_as_diary == FALSE) {
+          # reset qwindow to default
+          params_247[["qwindow"]] = c(0, 24)
+        }
         if (inherits(qwindowImp, "data.frame")) {
           qwindowImp = qwindowImp[which(qwindowImp$ID == ID),]
           if (nrow(qwindowImp) == 0) {
@@ -324,7 +332,8 @@ g.part2 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
                                                   params_phyact, params_output, params_general,
                                                   path, ms2.out, foldername, fullfilenames,
                                                   folderstructure, referencefnames,
-                                                  daySUMMARY, pdffilenumb, pdfpagecount, csvfolder, cnt78, verbose)
+                                                  daySUMMARY, pdffilenumb, pdfpagecount, 
+                                                  csvfolder, cnt78, verbose, use_qwindow_as_diary)
 
                                      })
                                      return(tryCatchResult)
@@ -344,7 +353,8 @@ g.part2 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
                  params_phyact, params_output, params_general,
                  path, ms2.out, foldername, fullfilenames,
                  folderstructure, referencefnames,
-                 daySUMMARY, pdffilenumb, pdfpagecount, csvfolder, cnt78, verbose)
+                 daySUMMARY, pdffilenumb, pdfpagecount,
+                 csvfolder, cnt78, verbose, use_qwindow_as_diary)
     }
   }
 }

R/g.part5.R

@@ -448,10 +448,14 @@ g.part5 = function(datadir = c(), metadatadir = c(), f0=c(), f1=c(),
                     qqq_backup = c()
                     add_one_day_to_next_date = FALSE
                     if (is.character(params_247[["qwindow"]])) {
-                      params_247[["qwindow"]] = g.conv.actlog(params_247[["qwindow"]],
-                                                              params_247[["qwindow_dateformat"]],
-                                                              epochSize = ws3new)
-                      # This will be an object with numeric qwindow values for all individuals and days
+                      if (length(grep(pattern = "onlyfilter", x = params_247[["qwindow"]])) > 0) {
+                        params_247[["qwindow"]] = g.conv.actlog(params_247[["qwindow"]],
+                                                                params_247[["qwindow_dateformat"]],
+                                                                epochSize = ws3new)
+                        # This will be an object with numeric qwindow values for all individuals and days
+                      } else {
+                        params_247[["qwindow"]] = c(0, 24)
+                      }
                     }
                     lastDay = ifelse(Nwindows > 0, yes = FALSE, no = TRUE) # skip while loop if there are no days to analyses
                     wi = 1

man/GGIR.Rd

@@ -993,7 +993,12 @@ GGIR(mode = 1:5,
         as fall back setting. You may realise that these columns are the same as the
         advanced format for the sleelog accepted by GGIR part 4. So, if you already
         have an advanced format sleeplog for part 4 then you can provide this as value
-        for the qwindow parameter. The main purpose of this functionality is to offer
+        for the qwindow parameter.  If you want to
+        use \code{qwindow} to guide the nonwear filtering as described in here but 
+        do not want GGIR to use it for day segment analysis in part 2 or 5 then 
+        make sure the diary filename includes the word "onlyfilter" to tell GGIR to 
+        only use qwindow for nonwear filtering.
+        The main purpose of this functionality is to offer
         the option to ignore short lasting nonwear episodes during the night
         when there is suspicion that these are falsely detect, e.g. in individuals
         with extended motionless sleep periods caused by medication.}