update version number and minor fixes on warnings and checks for sleep detection

Author: jhmigueles

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: actimetric
 Type: Package
 Title: Classifies Accelerometer Data Into Physical Activity Types
-Version: 0.1.4.9000
+Version: 0.1.4.9002
 Authors@R: c(person("Jairo H","Migueles", role = c("aut","cre"),
                     email = "[email protected]",
                     comment = c(ORCID = "0000-0003-0366-6935")),

R/aggregate_per_date.R

@@ -88,7 +88,6 @@ aggregate_per_date = function(tsDir, epoch, classifier, classes,
       dsnames[ci] = paste("dur", "total", "nighttime", "min", sep = "_")
       ci = ci + 1
     }
-
     # total minutes in classes
     ci2 = ci + length(classes) - 1
     time_in_classes = aggregate(activity ~ date, data = ts, FUN = min_in_class, epoch = epoch)
@@ -105,32 +104,40 @@ aggregate_per_date = function(tsDir, epoch, classifier, classes,
     }
     if ("nighttime.awake" %in% classes) {
       noons = which(ts$time == "12:00:00")
-      start_end_nighttime = find_start_end(ts, column = "activity",
-                                           class = c("nighttime.awake", "nighttime.sleep"))
-      start_end_nighttime_dates = NULL
-      for (ni in 1:length(start_end_nighttime$ends)) {
-        next_noon = which(noons > start_end_nighttime$ends[ni])[1]
-        if (is.na(next_noon)) {
-          # if there is not a next_noon, meaning that recording finished before 12pm
-          # following the last wake up
-          prev_noon = max(which(noons < start_end_nighttime$ends[ni]))
-          start_end_nighttime_dates[ni] = as.character(as.Date(ts$date[noons[prev_noon]]) + 1)
-        } else {
-          start_end_nighttime_dates[ni] = ts$date[noons[next_noon]]
+      if (sum(grepl("nighttime", ts$activity)) > 0) {
+        # if sleep periods have been detected...
+        start_end_nighttime = find_start_end(ts, column = "activity",
+                                             class = c("nighttime.awake", "nighttime.sleep"))
+        start_end_nighttime_dates = NULL
+        for (ni in 1:length(start_end_nighttime$ends)) {
+          next_noon = which(noons > start_end_nighttime$ends[ni])[1]
+          if (is.na(next_noon)) {
+            # if there is not a next_noon, meaning that recording finished before 12pm
+            # following the last wake up
+            prev_noon = max(which(noons < start_end_nighttime$ends[ni]))
+            start_end_nighttime_dates[ni] = as.character(as.Date(ts$date[noons[prev_noon]]) + 1)
+          } else {
+            start_end_nighttime_dates[ni] = ts$date[noons[next_noon]]
+          }
         }
+        # start_end_nighttime_dates = ts$date[start_end_nighttime$ends] # dates based on wakeup
+        rows2fill = which(availableDates %in% start_end_nighttime_dates)
+        ds[rows2fill, ci] = as.character(ts$timestamp[start_end_nighttime$starts])
+        ds[rows2fill, ci + 1] = as.character(ts$timestamp[start_end_nighttime$ends])
+        dsnames[ci:(ci + 1)] = paste("timestamp", c("sleepOnset", "wakeup"), sep = "_")
+        ci = ci + 2
+      } else {
+        # sleep periods have not been detected (e.g., participant removed devices all nights)
+        # only store names to be consistent in columns in the full dataset,
+        # but leave all data as NA
+        dsnames[ci:(ci + 1)] = paste("timestamp", c("sleepOnset", "wakeup"), sep = "_")
+        ci = ci + 2
       }
-      # start_end_nighttime_dates = ts$date[start_end_nighttime$ends] # dates based on wakeup
-      rows2fill = which(availableDates %in% start_end_nighttime_dates)
-      ds[rows2fill, ci] = as.character(ts$timestamp[start_end_nighttime$starts])
-      ds[rows2fill, ci + 1] = as.character(ts$timestamp[start_end_nighttime$ends])
-      dsnames[ci:(ci + 1)] = paste("timestamp", c("sleepOnset", "wakeup"), sep = "_")
-      ci = ci + 2
     }
-
     # bouts of behaviors
     boutdur = sort(boutdur, decreasing = TRUE)
     for (classi in classes) {
-      if (grepl("^nighttime|^nonwear", classes[classi])) break
+      if (grepl("^nighttime|^nonwear", classi)) break
       for (boutduri in 1:length(boutdur)) {
         look4bouts = ifelse(ts$activity == classi, 1, 0)
         # getBout is a copy of GGIR::g.getbout with which we are experimenting

R/runActimetric.R

@@ -133,29 +133,8 @@ runActimetric = function(input_directory = NULL, output_directory = NULL, studyn
   if (grepl("thigh", classifier)) body_attachment_site = "thigh"
   # check on do.sleep and body attachment site
   if (do.sleep == TRUE & body_attachment_site != "wrist") {
-    warning("Sleep detection only available for wrist attachment site for now.\n
-            Setting do.sleep to FALSE and n_valid_hours_nighttime = 0")
-    do.sleep = FALSE
-    n_valid_hours_nighttime = 0
-  }
-  # redefine classes
-  if (do.sleep == TRUE) {
-    classes = c(classes, "nighttime", "sleep")
-  }
-  if (do.nonwear == TRUE) {
-    classes = c(classes, "nonwear")
-  }
-  # Welcome message
-  if (verbose) {
-    cat('\n')
-    cat(paste0(rep('_', options()$width), collapse = ''))
-    cat(paste0("\n\nWelcome to the actimetric R package!\n",
-               "\nIf you experiment any technical issue or wish to contribute to actimetric,",
-               "\nplease contact Jairo at [email protected] or Matthew at [email protected]\n\n"))
-    cat(paste0(rep('_', options()$width), collapse = ''))
-    cat(paste0("\n\nClassifier: ", classifier, "\n\n"))
-    cat(paste0(rep('_', options()$width), collapse = ''))
-    cat("\n")
+    warning(paste("The sleep detection method was developed and validated for wrist-worn devices.",
+                  "Accuracy may be compromised when used with other attachment sites."))
   }
   # -------------------------------------------------------------------------
   # Check directories and list files
@@ -202,6 +181,28 @@ runActimetric = function(input_directory = NULL, output_directory = NULL, studyn
   data.table::fwrite(config, file = file.path(output_directory, "configuration.csv"),
                      na = "", row.names = FALSE)
   # -------------------------------------------------------------------------
+  # redefine classes
+  if (do.sleep == TRUE) {
+    classes = c(classes, "nighttime", "sleep")
+  }
+  if (do.nonwear == TRUE) {
+    classes = c(classes, "nonwear")
+  }
+  # Welcome message
+  if (verbose) {
+    cat('\n')
+    cat(paste0(rep('_', options()$width), collapse = ''))
+    cat(paste0("\n\nWelcome to the actimetric R package!",
+               "\nactimetric version ", actimetricversion,
+               "\nactimetricModels version ", actimetricModelsversion, "\n",
+               "\nIf you experiment any technical issue or wish to contribute to actimetric,",
+               "\nplease contact Jairo at [email protected] or Matthew at [email protected]\n\n"))
+    cat(paste0(rep('_', options()$width), collapse = ''))
+    cat(paste0("\n\nClassifier: ", classifier, "\n\n"))
+    cat(paste0(rep('_', options()$width), collapse = ''))
+    cat("\n")
+  }
+  # -------------------------------------------------------------------------
   # Load files...
   for (file in files) {
     # file format and ID