fix bug when ndayswindow is higher than the days recorded in part 5 a…

…nd minor change to g.plot to facilitate visualization of the study protocol

R/g.impute.R

@@ -187,13 +187,16 @@ g.impute = function(M, I, params_cleaning = c(), desiredtz = "",
         if (p1 > length(atest)) break
         atestlist[ati] = mean(atest[p0:p1], na.rm = TRUE)
       }
-      atik = which(atestlist == max(atestlist))[1]
+      atik = 1 # intitialise atik as 1, which will be used in case ndayswindow is longer than recording days
+      if (!is.null(atestlist)) atik = which(atestlist == max(atestlist))[1]
       if (firstmidnighti != 1) { #ignore everything before the first midnight plus hrs.del.start
         ignore_until = (midnightsi[atik] - 1) + (params_cleaning[["hrs.del.start"]]*(3600/ws2))
         r4[1:ignore_until] = 1 #-1 because first midnight 00:00 itself contributes to the first full day
       }
       #ignore everything after the last midnight plus hrs.del.end
       ignore_from = midnightsi[atik + params_cleaning[["ndayswindow"]]] - (params_cleaning[["hrs.del.end"]]*(3600/ws2))
+      # if ndayswindow is higher than number of midnights, use last midnight
+      if (is.na(ignore_from)) ignore_from = midnightsi[length(midnightsi)] - (params_cleaning[["hrs.del.end"]]*(3600/ws2))
       r4[ignore_from:length(r4)] = 1
     }
     starttimei = 1

R/g.plot.R

@@ -127,9 +127,16 @@ g.plot = function(IMP, M, I, durplot) {
   }
 
   MEND = length(timeline)
-  ticks = seq(0, nrow(M$metalong) + n_ws2_perday, by = n_ws2_perday)
+  mnights = grep("T00:00:00", M$metalong$timestamp)
+  noons = grep("T12:00:00", M$metalong$timestamp)
+  ticks = sort(c(mnights, noons))
+  if (mnights[1] < noons[1]) {
+    tick_labels = rep(c("00", "12"), length.out = length(ticks))
+  } else if (noons[1] < mnights[1]) {
+    tick_labels = rep(c("12", "00"), length.out = length(ticks))
+  }
   # creating plot functions to avoid duplicated code
-  plot_acc = function(timeline, Acceleration, durplot, ticks, metricName) {
+  plot_acc = function(timeline, Acceleration, durplot, ticks, metricName, tick_labels) {
     if (metricName %in% c("ZCX", "ZCY", "ZCX") == TRUE | 
         length(grep(pattern = "count", x = metricName, ignore.case = TRUE)) > 0) {
       # Metric is not on a G scale
@@ -153,11 +160,11 @@ g.plot = function(IMP, M, I, durplot) {
       YLIM = c(0, 0.6)
       YTICKS = c(0, 0.2, 0.4, 0.6)
     }
-    plot(timeline, Acceleration, type = "l", xlab = "Day (24 hour blocks relative to start of recording)",
+    plot(timeline, Acceleration, type = "l", xlab = "Time (Hours)",
          ylab = ylabel,
          bty = "l", lwd = 0.1, xlim = c(0, durplot), ylim = YLIM, axes = FALSE, cex.lab = 0.8)
     axis(side = 2, at = YTICKS)
-    axis(side = 1, at = ticks, labels = 0:(length(ticks) - 1))
+    axis(side = 1, at = ticks, labels = tick_labels)
   }
 
   plot_nonwear = function(timeline, M, durplot, ticks) {
@@ -171,7 +178,7 @@ g.plot = function(IMP, M, I, durplot) {
   if (mon == MONITOR$GENEACTIV || (mon == MONITOR$AXIVITY && dformat == FORMAT$CWA)) {
     # Recordings with temperature
     par(fig = c(0,1,0,0.65), new = T)
-    plot_acc(timeline, Acceleration, durplot, ticks, metricName)
+    plot_acc(timeline, Acceleration, durplot, ticks, metricName, tick_labels)
 
     par(fig = c(0, 1, 0.45, 0.80), new = T)
     plot_nonwear(timeline, M, durplot, ticks)
@@ -187,7 +194,7 @@ g.plot = function(IMP, M, I, durplot) {
   } else {
     # Recordings without temperature
     par(fig = c(0, 1, 0, 0.80), new = T)
-    plot_acc(timeline, Acceleration, durplot, ticks, metricName)
+    plot_acc(timeline, Acceleration, durplot, ticks, metricName, tick_labels)
 
     par(fig = c(0, 1, 0.60, 0.95), new = T)
     plot_nonwear(timeline, M, durplot, ticks)