g.part1: function to load and pre-process acceleration files

In PeteJWatson/ggircal: Raw Accelerometer Data Analysis

Description

Calls function g.getmeta and g.calibrate, and converts the output to .RData-format which will be the input for g.part2. Here, the function generates a folder structure to keep track of various output files. The reason why these g.part1 and g.part2 are not merged as one generic shell function is because g.part1 takes much longer to and involves only minor decisions of interest to the movement scientist. Function g.part2 on the other hand is relatively fast and comes with all the decisions that directly impact on the variables that are of interest to the movement scientist. Therefore, the user may want to run g.part1 overnight or on a computing cluster, while g.part2 can then be the main playing ground for the movement scientist. Function g.shell.GGIR provides the main shell that allows for operating g.part1 and g.part2.

Usage

g.part1(datadir=c(),outputdir=c(),f0=1,f1=c(),windowsizes = c(5,900,3600),
                   desiredtz = "Europe/London",chunksize=c(),studyname=c(),
                   do.enmo = TRUE,do.lfenmo = FALSE,do.en = FALSE,
                   do.bfen = FALSE,do.hfen=FALSE,do.hfenplus = FALSE,do.mad = FALSE,
                   do.anglex=FALSE,do.angley=FALSE,
                   do.anglez=FALSE,do.enmoa=FALSE,
                   do.roll_med_acc_x=FALSE,do.roll_med_acc_y=FALSE,
                   do.roll_med_acc_z=FALSE,do.dev_roll_med_acc_x=FALSE,
                   do.dev_roll_med_acc_y=FALSE,do.dev_roll_med_acc_z=FALSE,
                   do.cal = TRUE,lb = 0.2, hb = 15, n = 4,
                   use.temp=TRUE,spherecrit=0.3,minloadcrit=72,
                   printsummary=TRUE,print.filename=FALSE,overwrite=FALSE,
                   backup.cal.coef=c(),selectdaysfile=c(),dayborder=0,
                   dynrange=c())

Arguments

datadir	Directory where the accelerometer files are stored or list of accelerometer filenames and directories
outputdir	Directory where the output needs to be stored. Note that this function will attempt to create folders in this directory and uses those folder to organise output
f0	File index to start with (default = 1). Index refers to the filenames sorted in increasing order
f1	File index to finish with (defaults to number of files available)
windowsizes	see g.getmeta
desiredtz	see g.getmeta
chunksize	see g.getmeta
studyname	If the datadir is a folder then the study will be given the name of the data directory. If datadir is a list of filenames then the studyname will be used as name for the analysis
do.bfen	if TRUE, calculate metric BFEN with band-pass filter configuration set by lb and hb, see g.getmeta
do.enmo	if TRUE (default), calculate metric ENMO, see g.getmeta
do.lfenmo	if TRUE, calculate metric LFENMO with low-pass filter configuration set by hb,see g.getmeta
do.en	if TRUE, calculate metric EN, see g.getmeta
do.hfen	if TRUE, calculate metric HFEN with low-pass filter configuration set by hb, see g.getmeta
do.hfenplus	if TRUE, calculate metric HFENplus with band-pass filter configuration set by lb and hb, see g.getmeta
do.mad	if TRUE, calculate metric MAD (Mean Amplitude Deviation), see g.getmeta
do.anglex	if TRUE, calculate the angle of the x-axis relative to the horizontal plane (degrees) utilizing all three axes
do.angley	if TRUE, calculate the angle of the y-axis relative to the horizontal plane (degrees) utilizing all three axes
do.anglez	if TRUE, calculate the angle of the z-axis relative to the horizontal plane (degrees) utilizing all three axes
do.enmoa	if TRUE (default), calculate metric ENMOa which is equal to metric ENMO but with the absolute taken from the Euclidean norm minus one.
do.roll_med_acc_x	see g.getmeta
do.roll_med_acc_y	see g.getmeta
do.roll_med_acc_z	see g.getmeta
do.dev_roll_med_acc_x	see g.getmeta
do.dev_roll_med_acc_y	see g.getmeta
do.dev_roll_med_acc_z	see g.getmeta
do.cal	Whether to apply auto-calibration or not, see g.calibrate. Default and recommended setting is TRUE
lb	lower boundary of the frequency filter (in Hertz)
hb	upper boundary of the frequency filter (in Hertz), see g.getmeta
n	order of the frequency filter, see g.getmeta
use.temp	see g.calibrate use temperature sensor data if available (Geneactive only)
spherecrit	see g.calibrate 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	see g.calibrate 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 be reduced to under 0.01 g.
printsummary	see g.calibrate if TRUE will print a summary when done
print.filename	Whether to print the filename before before analysing it (default is FALSE). Printing the filename can be useful to investigate problems (e.g. to verify that which file is being read).
overwrite	Overwrite previously generated milestone data by this function for this particular dataset. If FALSE then it will skip the previously processed files (default = FALSE).
backup.cal.coef	If the auto-calibration fails then the user has the option to provide back-up calibration coefficients via this argument. The value of the argument needs to be the name and directory of a csv-spreadsheet with the following column names and subsequent values: 'filename' with the names of accelerometer files on which the calibration coefficients need to be applied in case auto-calibration fails; 'scale.x', 'scale.y', and 'scale.z' with the scaling coefficients; 'offset.x', 'offset.y', and 'offset.z' with the offset coefficients, and; 'temperature.offset.x', 'temperature.offset.y', and 'temperature.offset.z' with the temperature offset coefficients. The argument is intended for analysing short lasting laboratory experiments with insufficient sphere data, but for which calibration coefficients can be derived in an alternative way. It is the users responsibility to compile the csv-spreadsheet.
selectdaysfile	Optional functionality. Character pointing at a csv file holding the relationship between device serial numbers (first column) and measurement dates of interest (second and third column). The date format should be dd/mm/yyyy. And the first row if the csv file is assumed to have a character variable names, e.g. "serialnumber" "Day1" and "Day2" respectively. Raw data will be extracted and stored in the output directory in a new subfolder named 'raw'.
dayborder	Hour at which days start and end (default = 0), value = 4 would mean 4 am
dynrange	Optional, provide dynamic range for accelerometer data to overwrite hardcoded 6 g for GENEA and 8 g for other brands

Value

The function provides no values, it only ensures that the output from other functions is stored in .RData(one file per accelerometer file) in folder structure

Author(s)

Vincent T van Hees <[e-mail]>

References

• van Hees VT, Gorzelniak L, Dean Leon EC, Eder M, Pias M, et al. (2013) Separating Movement and Gravity Components in an Acceleration Signal and Implications for the Assessment of Human Daily Physical Activity. PLoS ONE 8(4): e61691. doi:10.1371/journal.pone.0061691

• 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

• Aittasalo M, Vaha-Ypya H, Vasankari T, Husu P, Jussila AM, and Sievanen H. Mean amplitude deviation calculated from raw acceleration data: a novel method for classifying the intensity of adolescents physical activity irrespective of accelerometer brand. BMC Sports Science, Medicine and Rehabilitation (2015).

Examples

## Not run: 
datafile = "C:/myfolder/mydata"
outputdir = "C:/myresults"
g.part1(datadir,outputdir)

## End(Not run)

PeteJWatson/ggircal documentation built on Nov. 24, 2021, 11:14 a.m.