Merge branch 'master' into issue839_add_DFA_to_part6

NEWS.md

@@ -4,15 +4,15 @@
 
 - Part 2 + 6: Revised and simplified IV and IS calculation which now ignores invalid timestamps and also comes with phi statistic (credits: Ian Meneghel Danilevicz). In part 2 we used to have 2 calculation, which is now replaced by just one and applied to all valid data points in the recordings. In part 6 this is repeated by for the time window as specified with parameter part6Window. Further, IVIS now uses argument threshold.lig as threshold to distinguish inactivity from active.
 
-Part 1:
+- Part 1:
 
-- Improved readability and maintainability of the code #1027
+  - Improved readability and maintainability of the code #1027
 
-- Improved processing speed for Axivity .cwa, GENEActiv .bin, and Movisens files
+  - Improved processing speed for Axivity .cwa, GENEActiv .bin, and Movisens files
 
-- Made sure that g.readaccfile() reads timestamps in the correct timezone, configtz, for all monitor types
+  - Made sure that g.readaccfile() reads timestamps in the correct timezone, configtz, for all monitor types
 
-- Note: there will be small differences in both metalong and metashort metrics calculated by this GGIR version, compared to prior versions. This is due to small improvements in the management of timestamps, calibration coefficients, and input data block boundaries.
+  - Note: there will be small differences in both metalong and metashort metrics calculated by this GGIR version, compared to prior versions. This is due to small improvements in the management of timestamps, calibration coefficients, and input data block boundaries.
 
 # CHANGES IN GGIR VERSION 3.0-5
 

R/g.analyse.perfile.R

@@ -20,6 +20,12 @@ g.analyse.perfile = function(I, C, metrics_nav,
     ds_names = ds_names[-cut]
     daysummary = daysummary[,-cut]
   }
+  # for a very small file, there could be just one row in daysummary[-cut,], so it gets coerced to a vector.
+  # But what we actually need is a 1-row matrix. So we need to transpose it. 
+  if(is.vector(daysummary)) { 
+    daysummary = t(daysummary)
+  }
+
   # Person identification number
   filesummary[vi] = file_summary$ID
   # Identify which of the metrics are in g-units to aid deciding whether to multiply by 1000

R/g.plot5.R

@@ -454,7 +454,7 @@ g.plot5 = function(metadatadir = c(), dofirstpage = FALSE, viewingwindow = 1,
           xaxislabels = c("noon","2pm", "4pm", "6pm", "8pm", "10pm", "midnight",
                           "2am", "4am", "6am", "8am", "10am", "noon")
         }
-        if (length(nightsi) > 0 & nrow(summarysleep_tmp) > 0) {
+        if (length(nightsi) > 0 && nrow(summarysleep_tmp) > 0 && nrow(P2daysummary_tmp)) {
           # Do not attempt to create a plot when there is no midnight in the data,
           # because calculation of t1 will be complicated.
           nplots = length(nightsi) + 1