R/runGLUForDirectory.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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#' Run GLU for all files in a directory
#'
#' @param indir Path of input directory containing input files.
#' @param outdir Path of output directory where derived data will be stored.
#' @param device Device type: 0 (medtronic ipro2); 1 (Dexcom G2); 2 (Abbott Freestyle Libre), default 0.
#' @param daystart Time of night to day transition in format HH:MM, default 06:30.
#' @param nightstart Time of day to night transition in format HH:MM, default 23:00.
#' @param dayPeriodStartTime Start time of day period, default is nightstart.
#' @param timeformat Time format in the CGM data, default \%d/\%m/\%y \%H:\%M:\%S.
#' @param imputeApproximal Logical. If TRUE then the 'approximal imputation' approach to dealing with missing data is used. If both imputeApproximal and imputeOther are FALSE then the 'complete days' approach is used. 
#' @param imputeOther Logical. If TRUE then the 'other day imputation' approach to dealing with missing data is used. If both imputeApproximal and imputeOther are FALSE then the 'complete days' approach is used.
#' @param freq Integer. CGM epoch data frequency (minutes).
#' @param outlierthreshold Numeric. The value k used for outlier detection threshold d=k*SD.
#' @param hypothreshold Numeric. Threshold between hypo- and normo- glycaemia.
#' @param hyperthreshold Numeric. Threshold between normo- and hyper- glycaemia.
#' @param save Logical. If TRUE then derived CGM sequence(s) are stored.
#' @param pregnancy Logical. If TRUE then data is for pregnancy study, so pregnancy specific statistics should be derived.
#' @param diabetes Logical. If TRUE then data is for diabetes study, so pregnancy specific statistics should be derived.
#' @export
runGLUForDirectory <- function(indir, outdir=NULL, device=0, daystart='06:30', nightstart='23:00', dayPeriodStartTime=NULL, firstvalid=FALSE, timeformat='%d/%m/%y %H:%M:%S', imputeApproximal=FALSE, imputeOther=FALSE, freq=5, outlierthreshold=5, hypothreshold=NULL, hyperthreshold=NULL, save=FALSE, saveevents=FALSE, pregnancy=FALSE, diabetes=FALSE, mgdl=FALSE) {


	files = list.files(indir, pattern=".*\\..*", full.names=FALSE)

	runGLUForFiles(files, indir, outdir, device=device, daystart=daystart, nightstart=nightstart, dayPeriodStartTime=dayPeriodStartTime, firstvalid=firstvalid, timeformat=timeformat, imputeApproximal=imputeApproximal, imputeOther=imputeOther, freq=freq, outlierthreshold=outlierthreshold, hypothreshold=hypothreshold, hyperthreshold=hyperthreshold, save=save, saveevents=saveevents, pregnancy=pregnancy, diabetes=diabetes, mgdl=mgdl)

}