cgmvariables {cgmanalysis}

Calculate CGM Variables

Description

This function takes cleaned CGM data and returns clinically relevant measures (e.g. percent time spent over 140, MAGE, MODD, etc.).

Usage

cgmvariables(inputdirectory,
outputdirectory = tempdir(),
outputname = "REDCap Upload",
customintervals = list(c(180,250),c(250,400)),
aboveexcursionlength = 35,
belowexcursionlength = 10,
magedef = "1sd",
congan = 1,
daystart = 6,
dayend = 22,
id_filename = F,
format = "rows",
printname = F,
unit = "mg/dL")

Arguments

inputdirectory

The directory containing cleaned CSV files for analysis.

outputdirectory

The directory where you would like the results spreadsheet to be written.

outputname

The name of the file containing final CGM variables (without the file extension).

customintervals

A list of custom blood glucose intervals. Minutes and percent time below the lower bound, in the specified range, and above the upper bound are calculated for each interval in the list. Number of excursions below the lower bound and above the upper bound are also calculated for each interval.

aboveexcursionlength

The number of minutes blood sugar must be above threshold to count an excursion.

belowexcursionlength

The number of minutes blood sugar must be below threshold to count an excursion.

magedef

How large an excursion needs to be in order to count in the MAGE calculation (e.g. greater than 1 standard deviation).

congan

CONGA interval in hours.

daystart

The numeric hour at which daytime should start (e.g. to start counting day time at 6:00am, set daystart = 6).

dayend

The numeric hour at which daytime should end (this parameter uses military time, so to stop counting day time at 10:00pm, set dayend = 22).

id_filename

If true, the file name will be used for subject ID rather than the ID contained in the data.

format

Whether observations are in rows or columns.

printname

Whether or not to print each file name (for troubleshooting).

unit

Default unit is mg/dL. Any other value will multiply the "sensorglucose" column by 18 (i.e. the package assumes that unit != "mg/dL" implies that the units are mmol/L). All relevant results are output in mg/dL.

Details

All files must be saved as a csv, and must have three columns, the first of which contains the subject ID in the first cell and date of CGM placement in the second (see example files). The names of the columns must be "subjectid" "timestamp" and "sensorglucose" (without quotes) respectively. Files can be cleaned and formatted using this package's cleandata() function.

Value

A data frame containing calculated CGM variables, with each column representing one CGM file.

Examples

cgmvariables(system.file("extdata","Cleaned",package = "cgmanalysis"))