Speed up POSIX calls in part 6 that were recently revised to facilitate backward compatibility with older R versions

NEWS.md

@@ -5,7 +5,9 @@
 - Part 6 and new visual report: Fix bug related to determining the combination of thresholds to use for the 
   visual report and for part 6 analyses when there are several options and 
   part6_threshold_combi is NULL. #1260
-
+
+- Part 6: Revise fix to #1181 and #1245 in 3.1-11 as it slowed down part 6 substantially. #1263
+
 # CHANGES IN GGIR VERSION 3.1-11
 
 - Part 2:
@@ -40,7 +42,7 @@ with only 1 valid day, these were previously skipped. #1246
   - Change extraction of imputation code from sleep diary, which is now assumed to 
   correspond to preceding night. #1251
 
-- Part 1, 5 and 6: Update code to be backward compatible with R 4.2.0
+- Part 1, 5 and 6: Update code to be backward compatible with R 4.2.0 #1181 and #1245
 
 - Part 5: Default values for parameters `do.sibreport` and `save_ms5rawlevels` changed
 to TRUE, for `save_ms5raw_format` changed to "RData" in order to ease generating visual 

R/g.part6.R

@@ -169,9 +169,8 @@ 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"]],
-                                                  origin = "1970-01-01")
+          mdat$time = mdat$timestamp = .POSIXct(mdat$timenum,
+                                                tz =  params_general[["desiredtz"]])
           return(mdat)
         }
         mdat = imputeTimeGaps(mdat, epochSize)
@@ -240,8 +239,7 @@ g.part6 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
       summary[fi] = unlist(strsplit(fnames.ms5raw[i], "_"))[1]
       s_names[fi] = "ID"
       fi = fi + 1
-      starttime = as.POSIXlt(ts$time[1], tz = params_general[["desiredtz"]],
-                             origin = "1970-01-01")
+      starttime = .POSIXct(ts$time[1], tz = params_general[["desiredtz"]])
       summary[fi] = format(starttime)
       s_names[fi] = "starttime"
       fi = fi + 1
@@ -294,10 +292,10 @@ 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$time, tz = params_general[["desiredtz"]], origin = "1970-01-01"))
-        sec = tempp$sec
-        min = tempp$min
-        hour = tempp$hour
+        tempp = .POSIXct(acc4cos$time, tz = params_general[["desiredtz"]])
+        sec = data.table::second(tempp)
+        min = data.table::minute(tempp)
+        hour = data.table::hour(tempp)
         if (params_general[["dayborder"]] == 0) {
           nightsi = which(sec == 0 & min == 0 & hour == 0)
         } else {

tests/testthat/test_part6.R

@@ -1,7 +1,7 @@
 library(GGIR)
 context("g.part6")
 
-test_that("Part 6 with household co-analysis", {
+test_that("Part 6 can run household co-analysis and Circadian Rhythm analysis", {
 
   # Create test files for household co-analysis
   metadatadir = "./output_testpart6"