Function to extract meta-data (features) from data in accelerometer file

Reads a accelerometer file in blocks, extracts various features and stores average feature value per short or long epoch. Acceleration and angle metrics are stored at short epoch length. The non-wear indication score, the clipping score, temperature (if available), light (if available), and Euclidean norm are stored at long epoch length. The function has been designed and thoroughly tested with accelerometer files from GENEA and GENEActiv bin files. Further, the function should be able to cope with ActiGraph gt3x and csv files, Axivity cwa and csv files, Movisens bin files, and ad-hoc csv files read through the read.myacc.csv function.

Usage

g.getmeta(datafile, params_metrics = c(), params_rawdata = c(),
                     params_general = c(), params_cleaning = c(), daylimit = FALSE,
                     offset = c(0, 0, 0), scale = c(1, 1, 1), tempoffset = c(0, 0, 0),
                     meantempcal = c(), myfun = c(), verbose = TRUE, ...)

Arguments

datafile: name of accelerometer file
params_metrics: See details in GGIR.
params_rawdata: See details in GGIR.
params_general: See details in GGIR.
params_cleaning: See details in GGIR.
daylimit: number of days to limit (roughly), if set to FALSE no daylimit will be applied
offset: offset correction value per axis, usage: value = scale(value,center = -offset, scale = 1/scale)
scale: scaling correction value per axis, usage: value = scale(value,center = -offset, scale = 1/scale)
tempoffset: temperature offset correction value per axis, usage: value = scale(value,center = -offset, scale = 1/scale) + scale(temperature, center = rep(averagetemperate,3), scale = 1/tempoffset)
meantempcal: mean temperature corresponding to the data as used for autocalibration. If autocalibration is not done or if temperature was not available then leave blank (default)
myfun: External function object to be applied to raw data. See details applyExtFunction.
verbose: Boolean (default = TRUE). to indicate whether console message should be printed. Note that warnings and error are always printed and can be suppressed with suppressWarning() or suppressMessages().
...: Any argument used in the previous version of g.getmeta, which will now be used to overrule the arguments specified with the parameter objects.

Value

metalong: dataframe with long epoch meta-data: EN, non-wear score, clipping score, temperature
metashort: dataframe with short epoch meta-data: timestamp and metric
tooshort: indicator of whether file was too short for processing (TRUE or FALSE)
corrupt: indicator of whether file was considered corrupt (TRUE or FALSE)

Author

Vincent T van Hees <v.vanhees@accelting.com>

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
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

  if (FALSE) {
    datafile = "C:/myfolder/testfile.bin"

    #Extract meta-data:
    M = g.getmeta(datafile)

    #Inspect first couple of rows of long epoch length meta data:
    print(M$metalong[1:5,])

    #Inspect first couple of rows of short epoch length meta data:
    print(M$metalong[1:5,])
  }