R/madByDay.R

In MRCIEU/GLU: Derives Summary Variables from Continuous Glucose Monitoring (CGM) data

# The MIT License (MIT)
# Copyright (c) 2018 Louise AC Millard, MRC Integrative Epidemiology Unit, University of Bristol
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# For each valid day in validDays, derive the median absolute deviation (MAD).
# Returns the MAD for each day, and the average across all days overall.
madByDay <- function(validDays) {

	mads = c()

	cnames=c()
	count=1
	for (vd in validDays) {

		raw = getDayGlucoseValues(vd)

		# MAD of this valid day only
		madVD = mad(raw$sgReading, constant=1, na.rm=TRUE)

		# nighttime, daytime aucs
		raw = getDayGlucoseValues(vd, night=TRUE)
		madVDn = mad(raw$sgReading, constant=1, na.rm=TRUE)

		raw = getDayGlucoseValues(vd, day=TRUE)
		madVDd = mad(raw$sgReading, constant=1, na.rm=TRUE)

		mads = append(mads, c(madVD, madVDn, madVDd))
		cnames = append(cnames, c(paste("mad_day", count, sep=""), paste("mad_nt_day", count, sep=""), paste("mad_dt_day", count, sep="")))


                count=count+1
	}


	res = rbind(mads)
        colnames(res) = cnames

	madAv = meanAcrossDays("mad_day", res)
	madAvN = meanAcrossDays("mad_nt_day", res)
	madAvD = meanAcrossDays("mad_dt_day", res)
	othervars = c(madAv, madAvN, madAvD)
  	othervars = rbind(othervars)
	colnames(othervars) = c("meanmadPerDay", "meanmadPerDay_nt","meanmadPerDay_dt")
	res = cbind(res, othervars)

	return(res)

}