R/detectEventBouts.R

In GGIR: Raw Accelerometer Data Analysis

detectEventBouts = function(myfun, varnum_event, varnum, 
                            UnitReScale, daysummary, ds_names,
                            di, fi, ws3, boutnameEnding) {
  if ("ebout.dur" %in% names(myfun) == FALSE) myfun$ebout.dur = c(1, 5, 10)
  if ("ebout.th.cad" %in% names(myfun) == FALSE) myfun$ebout.th.cad = 30
  if ("ebout.th.acc" %in% names(myfun) == FALSE) myfun$ebout.th.acc = 50
  if ("ebout.criter" %in% names(myfun) == FALSE) myfun$ebout.criter = 0.8
  if ("ebout.condition" %in% names(myfun) == FALSE) myfun$ebout.condition = "AND"
  
  # varnum = metashort[anwindices, mi]
  cadence = varnum_event * (60/ws3)
  # Event bouts
  for (boutdur in myfun$ebout.dur) {
    boutduration = boutdur * (60/ws3) # per minute
    rr1 = matrix(0, length(varnum), 1)
    if (myfun$ebout.condition == "AND") {
      p = which(varnum * UnitReScale >= myfun$ebout.th.acc &
                  cadence >= myfun$ebout.th.cad); rr1[p] = 1
    } else if (myfun$ebout.condition == "OR") {
      p = which(varnum * UnitReScale >= myfun$ebout.th.acc |
                  cadence >= myfun$ebout.th.cad); rr1[p] = 1
    }
    getboutout = g.getbout(x = rr1, boutduration = boutduration,
                           boutcriter = myfun$ebout.criter,
                           ws3 = ws3)
    # time spent in bouts in minutes
    eventbout = length(which(getboutout == 1)) / (60/ws3)
    eboutname = paste0("ExtFunEvent_Bout_totdur_E", ws3, "S_B", boutdur,
                       "M", (myfun$ebout.criter  * 100),
                       "%_cadT",myfun$ebout.th.cad,"_",
                       myfun$ebout.condition,
                       "_accT", myfun$ebout.th.acc)
    ebout_varname = paste0(eboutname, "_", boutnameEnding)
    # fi = correct_fi(di, ds_names, fi, varname = ebout_varname)
    daysummary[di,fi] = eventbout # total time in ebouts
    ds_names[fi] = ebout_varname;
    fi = fi + 1
    # number of bouts
    rle_bout = rle(as.numeric(getboutout))
    rle_bout1 = which(rle_bout$values == 1)
    number_of_bouts = length(rle_bout1)
    
    eboutname = paste0("ExtFunEvent_Bout_number_E", ws3, "S_B", boutdur,
                       "M", (myfun$ebout.criter  * 100),
                       "%_cadT",myfun$ebout.th.cad,"_",
                       myfun$ebout.condition,
                       "_accT", myfun$ebout.th.acc)
    ebout_varname = paste0(eboutname, "_", boutnameEnding)
    daysummary[di,fi] = number_of_bouts
    ds_names[fi] = ebout_varname;
    fi = fi + 1
    # average bout duration in minutes
    if (number_of_bouts > 0) {
      mn_dur_bouts = mean(rle_bout$lengths[which(rle_bout$values == 1)]) / (60/ws3)
    } else {
      mn_dur_bouts = 0
    }
    eboutname = paste0("ExtFunEvent_Bout_meandur_E", ws3, "S_B", boutdur,
                       "M", (myfun$ebout.criter  * 100),
                       "%_cadT",myfun$ebout.th.cad,"_",
                       myfun$ebout.condition,
                       "_accT", myfun$ebout.th.acc)
    ebout_varname = paste0(eboutname, "_", boutnameEnding)
    daysummary[di,fi] = mn_dur_bouts
    ds_names[fi] = ebout_varname;
    fi = fi + 1
  }
  invisible(list(daysummary = daysummary, ds_names = ds_names,
                 fi = fi, di = di))
}