R/fastingProxy.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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# Calculates a proxy measure of fasting SG - average of the 30 minute period with the lowest average.
# Returns fasting proxy value.
fastingProxy <- function(raw) {

	# get only rows with SG readings
	sgIdx = which(!is.na(raw$sgReading))
	raw = raw[sgIdx,]

	# get position 1-30, for the 30 consecutive values at each idx
	# each row has columns 1-30 for each index starting at the row (and some NAs if <30 after this index in sequence)
	raw$noct1 = raw$sgReading
	colnames=c("noct1")

	# create data frame with 30 columns so that each row corresponds to a particular 30 minute block in the night-time
	for (i in 2:30) {
		colname=paste("noct",i,sep='')

		# shift sgReadings up 1 each time
		colvals=raw$sgReading[i:nrow(raw)]
		colvalsna = rep(NA,i-1)
		colvals = c(colvals,colvalsna)

		raw[,colname] = colvals
		colnames=c(colnames, colname)
	}

	raw$noctMean = rowMeans(raw[,colnames])

	noctNotNA = raw$noctMean[which(!is.na(raw$noctMean))]

	# lowest of the 30 consecutive minutes
	fastProxy = min(noctNotNA)

	return(fastProxy)
}