Pooled Sleep & PA GGIR shell

sleepIPD.R

g.shell.GGIR(
  mode=c(1,2,3,4,5),
  datadir=datadir,
  outputdir=outdir,
  do.report=c(2,4,5),
  overwrite = TRUE,
  do.enmo = TRUE,
  do.hfen = TRUE,
  do.enmoa = TRUE,
  #=====================
  # Part 2
  #=====================
  strategy = 2,
  maxdur = 0,
  includedaycrit = 16,
  qwindow=c(0,24),
  mvpathreshold = 100,
  bout.metric = 4,
  excludefirstlast = TRUE,
  includenightcrit = 16,
  MX.ig.min.dur = 10,
  iglevels = 50,
  epochvalues2csv = FALSE,
  winhr = 16,
  qlevels = c(
    960/1440, # 2/3rds of the day
    1320/1440, # Top 120min
    1380/1440, # Top 60min
    1410/1440, # Top 30min
    1425/1440, # Top 15min
    1435/1440 # Top 5min
  ),
  #=====================
  # Part 3 + 4
  #=====================
  def.noc.sleep = 1,
  outliers.only = TRUE,
  criterror = 4,
  do.visual = TRUE,
  #=====================
  # Part 5
  #=====================
  threshold.lig = c(
    44.8, # Adults - AG wrist
    47.4, # Adults - AG hip
    46.9, # Adults - GA hip
    45.8, # Adults - GA wrist
    63.3, # Child - AG hip
    64.1, # Child - GA hip
    56.3, # Child - GA wrist
    35.6 # Child - AG wrist
  ),
  threshold.mod = c(
    61.1, # Adults - AG hip
    68.7, # Adults - GA hip
    93.2, # Adults - GA wrist
    100.6, # Adults - AG wrist
    142.6, # Child - AG hip
    152.8, # Child - GA hip
    191.6, # Child - GA wrist
    201.4 # Child - AG wrist
  ),

  threshold.vig = c(
    258.7, # Adults - AG hip
    266.8, # Adults - GA hip
    418.3, # Adults - GA wrist
    428.8, # Adults - AG wrist
    464.6, # Child - AG hip
    514.3, # Child - GA hip
    695.8, # Child - GA wrist
    707.0 # Child - AG wrist
  ),
  boutcriter = 0.8,      boutcriter.in = 0.9,     boutcriter.lig = 0.8,
  boutcriter.mvpa = 0.8, boutdur.in = c(1,10,30), boutdur.lig = c(1,10),
  boutdur.mvpa = c(1),
  includedaycrit.part5 = 2/3,
  #=====================
  # Visual report
  #=====================
  timewindow = c("WW"),
  visualreport=FALSE)

Added winhr = 16, per Rowland's suggestion to do IG for most active 16 hours.