getGENEAsegments: import and segment one or more bin files.

In GENEAclassify: Segmentation and Classification of Accelerometer Data

import and segment one or more bin files.

Description

Import and summarize GENEActiv bin data for manual classification.

Usage

getGENEAsegments(
  testfile,
  start = NULL,
  end = NULL,
  Use.Timestamps = FALSE,
  radians = FALSE,
  keep_raw_data = TRUE,
  mmap.load = (.Machine$sizeof.pointer >= 8),
  outputtoken = "_segmented",
  outputdir = "GENEAclassification",
  datacols = "default",
  decimalplaces = "default",
  filterWave = FALSE,
  filtername = "haar",
  j = 8,
  changepoint = c("UpDownDegrees", "TempFreq", "UpDownFreq", "UpDownMean", "UpDownVar",
    "UpDownMeanVar", "DegreesMean", "DegreesVar", "DegreesMeanVar",
    "UpDownMeanVarDegreesMeanVar", "UpDownMeanVarMagMeanVar"),
  penalty = "Manual",
  pen.value1 = 40,
  pen.value2 = 400,
  intervalseconds = 30,
  mininterval = 5,
  samplefreq = 100,
  filterorder = 2,
  boundaries = c(0.5, 5),
  Rp = 3,
  plot.it = FALSE,
  hysteresis = 0.1,
  stft_win = 10,
  plot_changepoints = FALSE,
  plot_changepoints_outputfile = "Changepoint",
  verbose = FALSE,
  ...
)

Arguments

testfile	character vector stating path to a GENEActiv bin file, or a folder containing GENEActiv bin files.
start	Where to start reading observations.
end	Where to end reading observations.
Use.Timestamps	To use timestamps as the start and end time values this has to be set to TRUE. (Default FALSE)
radians	calculate degrees rotation in radians.
keep_raw_data	Keep the raw data for calculating steps using stepcounter.
mmap.load	Default is (.Machine$sizeof.pointer >= 8). see mmap for more details
outputtoken	single character string to be appended to the file name for saving the segmenation output (default '_segmentated').
outputdir	The absolute or relative path to directory in which artifacts (plot and changes files) should be created, or NULL (default "GENEAclassification").
datacols	a vector constructed 'column.summary' or 'default'. See segmentation for details.
decimalplaces	named numeric vector of decimal places with which to round summary columns. NULL returns unrounded values. The length 1 character vector 'default' applies default roundings: Start.Time = 0, Degrees.mean = 3, Degrees.median = 3, Degrees.var = 3, Degrees.sd = 3, Degrees.mad = 3, Magnitude.mean = 3, UpDown.mean = 3, UpDown.median = 3, UpDown.var = 3 UpDown.sd = 3, UpDown.mad = 3, Principal.Frequency.median = 3, Principal.Frequency.mad = 3, Principal.Frequency.ratio = 3, Principal.Frequency.sumdiff = 3, Principal.Frequency.meandiff = 3, Principal.Frequency.abssumdiff = 3, Principal.Frequency.sddiff = 3, Light.mean = 0, Light.max = 0, Temp.mean = 1, Temp.sumdiff = 3 Temp.meandiff = 3 Temp.abssumdiff = 3 Temp.sddiff = 3 Step.count = 0 Step.sd = 1 Step.mean = 0 Step.GENEAamplitude = 3 Step.GENEAwavelength = 3 Step.GENEAdistance = 3 This can be changed by using a named list. e.g decimalplaces = c(Start.Time = 2, Degrees.mean = 4).
filterWave	single logical, should a smoothing filter from wave.filter be applied? (default FALSE).
filtername	single character, the name of the wavelet to use for smoothing when filter is TRUE. (default "haar") Passed to link[waveslim]{wave.filter}.
j	single numeric, the level to which to smooth. Passed to link[waveslim]{wave.filter} (default 8).
changepoint	defines the change point analysis to use. UpDownDegrees performs the change point analysis on the variance of arm elevation and wrist rotation. TempFreq performs a change point on the variance in the temperature and frequency (Typically better for sleep behaviours).
penalty	single character, the penalty to use for changepoint detection. default ("SIC").
pen.value1	Value of the type 1 error required when penalty is "Asymptotic".
pen.value2	Default set as NULL and so equals pen.value1 if no input.
intervalseconds	An integer number of seconds between 5 and 30 during which at most one changepoint may occur.
mininterval	single numeric that defines the smallest changepoint initially found. Passed to cpt.var as the variable minseglen
samplefreq	The sampling frequency of the data, in hertz, when calculating the step number. (default 100).
filterorder	The order of the filter applied with respect to the butter or cheby options. See cheby1 or butter.
boundaries	to pass to the filter in the step counting algorithm.
Rp	the decibel level that the cheby filter takes. See cheby1.
plot.it	single logical, Creates a plot showing the zero crossings counted by the step counting algorithm#' @param Centre Centres the xz signal about 0 when set to True.
hysteresis	The hysteresis applied after zero crossing. (default 100mg)
stft_win	numeric for the window to calculate the frequency of an event using the stft function.
plot_changepoints	single logical, Creates a plot displaying the changepoint locations.
plot_changepoints_outputfile	The name of the png file created that shows the change points on a positionals plots.
verbose	single logical should additional progress reporting be printed at the console? (default TRUE).
...	other arguments to be passed to dataImport, segmentation and other functions with these functions.

Value

segmented data are returned

See Also

The returned object can be interrogated with head.

Examples

## testfile = file.path(system.file(package = "GENEAread"),
##                                  "binfile",
##                                  "TESTfile.bin")
## 
## segData <- getGENEAsegments(testfile = testfile,
##                             outputdir = file.path(tempdir(), "GENEAclassification"),    
##                             changepoint = "UpDownDegrees",
##                             pen.value1 = 1,
##                             pen.value2 = 1)
## head(segData)
## list.files(file.path(tempdir(), "GENEAclassification"))

GENEAclassify documentation built on March 31, 2023, 9:01 p.m.