more group fixes

Author: miloswrath

code/core/acc_new.R

@@ -84,6 +84,7 @@ main <- function() {
 
       try({
         GGIR(
+          # ==== Initialization ====
           mode = 1:6,
           datadir = datadir,
           outputdir = outputdir,
@@ -92,24 +93,29 @@ main <- function() {
           desiredtz = "America/Chicago",
           print.filename = TRUE,
           idloc = 2,
-          save_ms5rawlevels = "csv"
+          save_ms5rawlevels = "csv",
 
+          # ==== Part 1: Data loading and basic signal processing ====
           do.report = c(2, 4, 5, 6),
           epochvalues2csv = TRUE,
           do.ENMO = TRUE,
           acc.metric = "ENMO",
           windowsizes = c(5, 900, 3600),
 
+          # ==== Part 2: Non-wear detection ====
           ignorenonwear = TRUE,
 
+          # ==== Part 3: Sleep detection (optional if using external file) ====
           # Uncomment the below if using external sleep log:
           # loglocation = "/Shared/vosslabhpc/Projects/BOOST/InterventionStudy/3-experiment/data/act-int-test/sleep.csv",
           # colid = 1,
           # coln1 = 2,
           # sleepwindowType = "SPT",
 
+          # ==== Part 4: Physical activity summaries ====
           timewindow = c("WW", "MM", "OO"),
 
+          # ==== Part 5: Day-level summaries ====
           hrs.del.start = 4,
           hrs.del.end = 3,
           maxdur = 9,