R/numPeaksByDay.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, generate the number of peaks
# Returns a data frame - the number of peaks in each day, and the average across all days overall.
numPeaksByDay <- function(validDays) {

	nps = c()

	# column names for each auc value we generate	
	cnames = c()

	count=1

	# for each valid day, calculate the auc
	for (vd in validDays) {
		
		# sequence of timepoints for this day
		raw = vd@glucose

		# auc of this day only
		npVD = numPeaks(raw)

		nps = append(nps, c(npVD))
		
		cnames = append(cnames, c(paste("numpeaks_day", count, sep="")))

                count=count+1
	}

	# set column names for auc values
	res = rbind(nps)
	colnames(res) = cnames

	npAv = meanAcrossDays("numpeaks_day", res)

	othervars = c(npAv)
  	othervars = rbind(othervars)
	colnames(othervars) = c("meannumpeaksperDay")

	res = cbind(res, othervars)

	return(res)

}