R/auc.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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# Calculate AUC using trapezoid method.
# Returns AUC value for sequence raw.
auc <- function(raw) {

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

	# total time period of SG data in raw
	timeLengthPeriod = 0

	# for each timepoint, add auc between this timepoint and the previous timepoint
	aucValue = 0

	if (nrow(data)>1) {
		for (idx in 2:nrow(data)) {
			timeDiffMins = as.numeric(difftime(data$time[idx], data$time[idx-1], units="mins"))

			# only include if timepoint are 1 minute apart
			if (timeDiffMins == 1) {

				trapezoid = (data$sgReading[idx] + data$sgReading[idx-1]) * timeDiffMins * 0.5
				aucValue = aucValue + trapezoid

				timeLengthPeriod = timeLengthPeriod + timeDiffMins

			}
		}
	}

	# convert to auc per minute
	aucValue = aucValue/timeLengthPeriod

	return(aucValue)
}