Merge pull request #1255 from wadpac/test_with_R42

Make backward compatible with R 4.2.0

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: GGIR
 Type: Package
 Title: Raw Accelerometer Data Analysis
-Version: 3.1-10
-Date: 2025-01-10
+Version: 3.1-11
+Date: 2025-01-23
 Authors@R: c(person("Vincent T","van Hees",role=c("aut","cre"),
                     email="v.vanhees@accelting.com"),
              person("Jairo H","Migueles",role="aut",

NEWS.md

@@ -1,4 +1,4 @@
-# CHANGES IN GGIR VERSION 3.1-??
+# CHANGES IN GGIR VERSION 3.1-11
 
 - Part 2:
 
@@ -21,6 +21,10 @@
   - Added warning when there are two accelerometer recordings with the same ID.
 
   - Change extraction of imputation code from sleep diary, which is now assumed to correspond to preceding night. This is now also documented. #1251
+
+- Part 1, 5 and 6:
+
+  - Update code to be backward compatible with R 4.2.0
 
 # CHANGES IN GGIR VERSION 3.1-10
 

R/g.imputeTimegaps.R

@@ -124,14 +124,28 @@ g.imputeTimegaps = function(x, sf, k=0.25, impute = TRUE,
           x$next_epoch_delay = 0
           longEpochDayCut = seq(0, 24 * 60^2, by = longEpochSize)
           x$imputation = 0; imp = 0 # keep track of the imputation to organize data later on
+          Rversion_lt_420 = as.numeric(R.Version()$major) >= 4 && as.numeric(R.Version()$minor) > 2
           for (i in gap90i) { 
             imp = imp + 1
+            if (Rversion_lt_420) {
+              time_i = x$time[i]
+              time_ip1 = x$time[i + 1]
+            } else {
+              # Further down data.table is used to extract hour and minute from time stamps
+              # In R 4.2.0 and earlier numeric time cannot be provided to data.table
+              # For those older version of R convert timestamp format
+              # Tz is set to GMT because at this point we do not care about the specific time
+              # as time is removed at the end of the function, we only use it
+              # to identify time gaps and their size.
+              time_i = as.POSIXct(x$time[i], origin = "1970-01-01", tz = "GMT")
+              time_ip1 = as.POSIXct(x$time[i + 1], origin = "1970-01-01", tz = "GMT")
+            }
             # short epochs to add to fill up to next long epoch cut
-            seconds = data.table::hour(x$time[i]) * 60^2 + data.table::minute(x$time[i]) * 60 + data.table::second(x$time[i]) + 1 
+            seconds = data.table::hour(time_i) * 60^2 + data.table::minute(time_i) * 60 + data.table::second(time_i) + 1 
             seconds_from_prevCut = seconds - max(longEpochDayCut[which(longEpochDayCut <= seconds)])
             shortEpochs2add_1 = (longEpochSize - seconds_from_prevCut) / shortEpochSize
             # short epochs to add after time gap
-            seconds = data.table::hour(x$time[i + 1]) * 60^2 + data.table::minute(x$time[i + 1]) * 60 + data.table::second(x$time[i + 1]) + 1 
+            seconds = data.table::hour(time_ip1) * 60^2 + data.table::minute(time_ip1) * 60 + data.table::second(time_ip1) + 1 
             seconds_from_prevCut = seconds - max(longEpochDayCut[which(longEpochDayCut <= seconds)])
             shortEpochs2add_2 = (seconds_from_prevCut - 1) / shortEpochSize
             # short epochs to add - total

R/g.part5.wakesleepwindows.R

@@ -23,8 +23,9 @@ g.part5.wakesleepwindows = function(ts, part4_output, desiredtz, nightsi,
   # Round seconds to integer number of epoch lengths (needed if cleaningcode = 5).
   round_seconds_to_epochSize = function(x, epochSize) {
     if (length(as.numeric(unlist(strsplit(x,":")))) == 3) {
-      xPOSIX = as.POSIXct(x, format = "%H:%M:%S")
-      xPOSIX_rounded = as.POSIXct(round(as.numeric(xPOSIX) / epochSize) * epochSize)
+      xPOSIX = as.POSIXct(x, format = "%H:%M:%S", origin = "1970-01-01")
+      xPOSIX_rounded = as.POSIXct(round(as.numeric(xPOSIX) / epochSize) * epochSize,
+                                  origin = "1970-01-01")
       x = format(xPOSIX_rounded, format = "%H:%M:%S")
     } else {
       x = ""
@@ -67,7 +68,8 @@ g.part5.wakesleepwindows = function(ts, part4_output, desiredtz, nightsi,
     w1[k] = paste(tt[3],"-", tt[2], "-", tt[1], " ", as.character(defWA_ts), sep = "")
     # if time is beyond 24 then change the date
     if (defSO >= 24) { 
-      w0[k] = as.character(as.POSIXlt(w0[k],tz = desiredtz) + (24*3600))
+      tmp_w0 = as.POSIXlt(w0[k],tz = desiredtz, origin = "1970-01-01")
+      w0[k] = as.character(tmp_w0 + (24*3600))
     }
     if (defWA >= 24 |
         (part4_output$daysleeper[k] == 1 & defWA < 18)) {

R/g.part6.R

@@ -169,7 +169,9 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
           mdat$window[invalid] = 9999
           mdat$invalid_sleepperiod[invalid] = 100
           mdat$invalid_wakinghours[invalid] = 100
-          mdat$time = mdat$timestamp = as.POSIXct(mdat$timenum, tz =  params_general[["desiredtz"]])
+          mdat$time = mdat$timestamp = as.POSIXct(mdat$timenum,
+                                                  tz =  params_general[["desiredtz"]],
+                                                  origin = "1970-01-01")
           return(mdat)
         }
         mdat = imputeTimeGaps(mdat, epochSize)
@@ -238,7 +240,8 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
       summary[fi] = unlist(strsplit(fnames.ms5raw[i], "_"))[1]
       s_names[fi] = "ID"
       fi = fi + 1
-      starttime = as.POSIXlt(ts$time[1], tz = params_general[["desiredtz"]])
+      starttime = as.POSIXlt(ts$time[1], tz = params_general[["desiredtz"]],
+                             origin = "1970-01-01")
       summary[fi] = format(starttime)
       s_names[fi] = "starttime"
       fi = fi + 1
@@ -291,7 +294,7 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
         threshold = as.numeric(unlist(strsplit( params_phyact[["part6_threshold_combi"]], "_"))[1])
 
         # extract nightsi again
-        tempp = unclass(as.POSIXlt(acc4cos$time, tz = params_general[["desiredtz"]]))
+        tempp = unclass(as.POSIXlt(acc4cos$time, tz = params_general[["desiredtz"]], origin = "1970-01-01"))
         sec = tempp$sec
         min = tempp$min
         hour = tempp$hour

man/GGIR-package.Rd

@@ -21,8 +21,8 @@
   \tabular{ll}{
   Package: \tab GGIR\cr
   Type: \tab Package\cr
-  Version: \tab 3.1-10\cr
-  Date: \tab 2025-01-10\cr
+  Version: \tab 3.1-11\cr
+  Date: \tab 2025-01-23\cr
   License: \tab Apache License (== 2.0)\cr
   Discussion group: \tab https://groups.google.com/forum/#!forum/rpackageggir\cr
   }

tests/testthat/test_part6.R

@@ -39,15 +39,15 @@ test_that("Part 6 with household co-analysis", {
              "day_IN_bts_10_30", "day_LIG_bts_10")
 
   mdat$timenum = mdat$timenum - (5 * 60) 
-  mdat$timestamp = as.POSIXct(mdat$timenum, tz =  params_general[["desiredtz"]])
+  mdat$timestamp = as.POSIXct(mdat$timenum, tz =  params_general[["desiredtz"]], origin = "1970-01-01")
   filename = "800-900-001_left wrist.bin"
   save(mdat, filename, Lnames, file = paste0(dn, "/800-900-001_left wrist.RData"))
   mdat$timenum = mdat$timenum + (7 * 60)
-  mdat$timestamp = as.POSIXct(mdat$timenum, tz =  params_general[["desiredtz"]])
+  mdat$timestamp = as.POSIXct(mdat$timenum, tz =  params_general[["desiredtz"]], origin = "1970-01-01")
   filename = "800-900-002_left wrist.bin"
   save(mdat, filename, Lnames, file = paste0(dn, "/800-900-002_left wrist.RData"))
   mdat$timenum = mdat$timenum + (14 * 60)
-  mdat$timestamp = as.POSIXct(mdat$timenum, tz =  params_general[["desiredtz"]])
+  mdat$timestamp = as.POSIXct(mdat$timenum, tz =  params_general[["desiredtz"]], origin = "1970-01-01")
   filename = "800-900-003_left wrist.bin"
   save(mdat, filename, Lnames, file = paste0(dn, "/800-900-003_left wrist.RData"))
   mdat_file3 = mdat