R/invalidDeviationsByDay.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 store in validDays arg, calculate the number of timepoints that have an 
# invalid SG reading deviation, defined as being >2SD away from the value of the previous timepoint.
# By the time this function is used, invalid deviations have been marked in the deviationLarge column
# Returns a data frame containing the number of deviations that occured on each day.
invalidDeviationsByDay <- function(validDays) {

	invalidDeviations = c()

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

	count=1

	hasInvalidDeviations = FALSE

	# for each valid day, calculate the number of invalid deviations
	for (vd in validDays) {

		# get number of invalid deviations in this day only

		raw = getDayGlucoseValues(vd)

		devs = length(which(raw$deviationLarge == TRUE))

		if (devs>0) {
			hasInvalidDeviations = TRUE
		}

                count=count+1
	}

	# add marker indicating if there are any abnormally large deviations
	invdevdf = c(hasInvalidDeviations)
        invdevdf = rbind(invdevdf)
        colnames(invdevdf) = c("hasInvalidDeviations")
	return(invdevdf)

}