R/classes.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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# of the Software.
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# called when day is created
# ensures day has 1441 glucose values (1 per minute plus the last minute of the next day for interpolation)
check_day <- function(object) {
	errors <- character()

	length_glucose <- nrow(object@glucose)

	if (length_glucose != 1441) {
		msg <- paste("Glucose is length ", length_glucose, ".  Should be 1441", sep = "")
		errors <- c(errors, msg)
	}

	if (length(errors) == 0) TRUE else errors

}


setClass("day", 
	slots = c(glucose = "data.frame",
			dayidx = "numeric",
			validday = "logical",
			events = "data.frame",
			bg = "data.frame")
	,validity = check_day
)




setClass("participantData",
	slots = c(nightstart = "POSIXlt",
			daystart = "POSIXlt",
			dayfirst = "logical",
			days = "list",
			numvaliddays = "numeric")
)

setClass("event",
	slots = c(events = "data.frame",
			meantimetopeak = "numeric",
			meanpp1 = "numeric",
			meanpp2 = "numeric")
)



setClass("runSettings",
	slots = c(indir = "character",
		outdir = "character", 
		device = "numeric",
		daystart = "POSIXlt",
		nightstart = "POSIXlt",
		dayPeriodStartTime = "POSIXlt",
		firstvalid = "logical",
		timeformat = "character",
		imputeApproximal = "logical", 
		imputeOther = "logical", 
		freq = "numeric",
		outlierthreshold = "numeric",
		hypothreshold = "numeric",
		hyperthreshold = "numeric",
		save = "logical",
		saveevents = "logical",
		pregnancy = "logical",
		diabetes = "logical",
		epochfrequency = "numeric",
		mgdl = "logical")
)