g.calibrate: function to estimate calibration error and make...

In ucl-cls/mcs-acc: Raw Accelerometer Data Analysis

Description

Function starts by identifying ten second windows of non-movement. Next, the average acceleration per axis per window is used to estimate calibration error (offset and scaling) per axis. The function provides recommended correction factors to address the calibration error and a summary of the callibration procedure.

Usage

g.calibrate(datafile, use.temp = TRUE, spherecrit = 0.3, minloadcrit = 72, 
printsummary = TRUE,chunksize=c(),windowsizes=c(5,900,3600),selectdaysfile=c(),
dayborder=0)

Arguments

datafile	name of accelerometer file
use.temp	use temperature sensor data if available (Geneactive only)
spherecrit	the minimum required acceleration value (in g) on both sides of 0 g for each axis. Used to judge whether the sphere is sufficiently populated
minloadcrit	the minimum number of hours the code needs to read for the autocalibration procedure to be effective (only sensitive to multitudes of 12 hrs, other values will be ceiled). After loading these hours only extra data is loaded if calibration error has not been reduced to under 0.01 g.
printsummary	if TRUE will print a summary when done
chunksize	number between 0.2 and 1 to specificy the size of chunks to be loaded as a fraction of a 12 hour period, e.g. 0.5 equals 6 hour chunks. The default is 1 (12 hrs). For machines with less than 4Gb of RAM memory a value below 1 is recommended.
windowsizes	see g.getmeta
selectdaysfile	see g.part1
dayborder	see g.part1

Value

scale	scaling correction values, e.g. c(1,1,1)
offset	offset correction values, e.g. c(0,0,0)
tempoffset	correction values related to temperature, e.g. c(0,0,0)
cal.error.start	absolute difference between Euclidean norm during all non-movement windows and 1 g before autocalibration
cal.error.end	absolute difference between Euclidean norm during all non-movement windows and 1 g after autocalibration
spheredata	average, standard deviation, Euclidean norm and temperature (if available) for all ten second non-movement windows as used for the autocalibration procedure
npoints	number of 10 second no-movement windows used to populate the sphere
nhoursused	number of hours of measurement data scanned to find the ten second time windows with no movement
meantempcal	mean temperature corresponding to the data as used for autocalibration. Only applies to data collected with GENEActiv monitor.

Author(s)

Vincent T van Hees <[e-mail]> Zhou Fang

References

• van Hees VT, Fang Z, Langford J, Assah F, Mohammad A, da Silva IC, Trenell MI, White T, Wareham NJ, Brage S. Auto-calibration of accelerometer data for free-living physical activity assessment using local gravity and temperature: an evaluation on four continents. J Appl Physiol (1985). 2014 Aug 7

Examples

## Not run: 
datafile = "C:/myfolder/testfile.bin"

#Apply autocalibration:
C = g.calibrate(datafile)
print(C$scale)
print(C$offset)

## End(Not run)

ucl-cls/mcs-acc documentation built on May 3, 2019, 2:22 p.m.