Helper function to assist in reading data directly from sensor outputs. Should return a dataframe in correct format
for use with the rest of the iglu package. Assumes all data will be readable with base R read.csv() function.
Usage
read_raw_data(
filename,
sensor = c("dexcom", "libre", "librepro", "asc", "ipro"),
id = "filename",
tz = ""
)Arguments
- filename
String matching the name of the data to be read. Assumed to be .csv
- sensor
Default: "dexcom". String naming the type of sensor the data was exported from. Must be one of "dexcom", "libre", "librepro", "asc", or "ipro".
- id
Default: "filename". String indicating subject id. A value of "read" will cause the program to attempt to read the subject id from the file. A value of "filename" will cause the program to use the basename of the filename (i.e. filename without any directory information) with .csv removed, as subject id. A value of "default" will cause the program to use whichever of "read" or "filename" that is default for that specific sensor. Any other string will be treated as the unique id for the entire file.
Note the asc reader currently does not support id="read"
- tz
A character string specifying the time zone to be used. System-specific (see
as.POSIXct), but " " is the current time zone, and "GMT" is UTC (Universal Time, Coordinated). Invalid values are most commonly treated as UTC, on some platforms with a warning.
Details
A DataFrame object with the columns "id", "time" and "gl" and one row per reading will be returned. For the libre reader, if the phrase "mmol/l" is found in the column names, the glucose values will be multiplied by 18.
Assumes .csv format for all data.
Sensor formats change with ongoing development, so these functions may become deprecated. If any issues are encountered, contact the package maintainer: this is currently Irina Gaynanova, who can be reached at irinagn@umich.edu.
Note: this function is heavily derived from the readers avaiable in the cgmanalysis package's cleandata function.
References
Vigers et al. (2019) cgmanalysis: An R package for descriptive analysis of continuous glucose monitor data PLoS ONE 14(10): e0216851, doi:10.1371/journal.pone.0216851