R/runGLU.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
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
# documentation files (the "Software"), to deal in the Software without restriction, including without
# limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
# the Software, and to permit persons to whom the Software is furnished to do so, subject to the following
# conditions:
#
# The above copyright notice and this permission notice shall be included in all copies or substantial portions
# of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
# TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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# DEALINGS IN THE SOFTWARE.


#' Main function to run GLU from the command line
#'
#' @param opt List containing command line arguments.
#' @export
runGLU <- function(opt) {

# if user specifies a filename then process this, otherwise process all other files in indir
if (!is.null(opt$filename)) {

	fullfilename=paste0(opt$indir, opt$filename)

	if (!file.exists(fullfilename)) {
		stop(paste0('File ', fullfilename, ' does not exist'))
	}
	files=c(opt$filename)

} else {
	files = list.files(opt$indir, pattern=".*\\..*", full.names=FALSE)
}

runGLUForFiles(files=files, indir=opt$indir, outdir=opt$outdir, device=opt$device, daystart=opt$daystart, nightstart=opt$nightstart, dayPeriodStartTime=opt$dayPeriodStartTime, timeformat=opt$timeformat, imputeApproximal=opt$impute_approximal, imputeOther=opt$impute_other, freq=opt$freq, outlierthreshold=opt$outlierthreshold, hypothreshold=opt$hypothreshold, hyperthreshold=opt$hyperthreshold, save=opt$save, saveevents=opt$saveevents, pregnancy=opt$pregnancy, diabetes=opt$diabetes)

}