Merge pull request #899 from wadpac/issue896_DQreport

data_quality_report when rerunning parts 1 and 2

NEWS.md

@@ -1,9 +1,12 @@
 # CHANGES IN GGIR VERSION 2.10-3
 
+- Part 1: Fixed minor bug to keep calibration data in the data quality report after re-running parts 1 and 2 with overwrite = TRUE and backup.cal.coef = "retrieve" #896
+
 - Part 5: Fix minor bug by which GGIR skipped the last day if measurement finishes before midnight and timewindow = MM #891
 
 - Part 4: Added parameter sleepefficiency.metric to decide if in-bed time (denominator) should be guider_spt or acc_spt + latency #811
 
+
 # CHANGES IN GGIR VERSION 2.10-2
 
 - Part 1: Revision to readability of code (credits: Lena Kushleyeva)

R/g.part1.R

@@ -215,9 +215,19 @@ g.part1 = function(datadir = c(), metadatadir = c(), f0 = 1, f1 = c(), myfun = c
         bcc.scalei = which(colnames(bcc.data) == "scale.x" | colnames(bcc.data) == "scale.y" | colnames(bcc.data) == "scale.z")
         bcc.offseti = which(colnames(bcc.data) == "offset.x" | colnames(bcc.data) == "offset.y" | colnames(bcc.data) == "offset.z")
         bcc.temp.offseti = which(colnames(bcc.data) == "temperature.offset.x" | colnames(bcc.data) == "temperature.offset.y" | colnames(bcc.data) == "temperature.offset.z")
+        bcc.QCmessagei = which(colnames(bcc.data) == "QCmessage")
+        bcc.npointsi = which(colnames(bcc.data) == "n.10sec.windows")
+        bcc.nhoursusedi = which(colnames(bcc.data) == "n.hours.considered")
+        bcc.use.tempi = which(colnames(bcc.data) == "use.temperature")
         C$scale = as.numeric(bcc.data[bcc.i[1],bcc.scalei])
         C$offset = as.numeric(bcc.data[bcc.i[1],bcc.offseti])
         C$tempoffset =  as.numeric(bcc.data[bcc.i[1],bcc.temp.offseti])
+        C$cal.error.start = as.numeric(bcc.data[bcc.i[1],bcc.cal.error.start])
+        C$cal.error.end = as.numeric(bcc.data[bcc.i[1],bcc.cal.error.end])
+        C$QCmessage = bcc.data[bcc.i[1],bcc.QCmessagei]
+        C$npoints = bcc.data[bcc.i[1], bcc.npointsi]
+        C$nhoursused = bcc.data[bcc.i[1], bcc.nhoursusedi]
+        C$use.temp = bcc.data[bcc.i[1], bcc.nhoursusedi]
         if (verbose == TRUE) {
           cat(paste0("\nRetrieved Calibration error (g) before: ",as.numeric(bcc.data[bcc.i[1],bcc.cal.error.start])))
           cat(paste0("\nRetrieved Callibration error (g) after: ",as.numeric(bcc.data[bcc.i[1],bcc.cal.error.end])))