freq_DTW: Acoustic dissimilarity using dynamic time warping on dominant...

In warbleR: Streamline Bioacoustic Analysis

Acoustic dissimilarity using dynamic time warping on dominant frequency contours

Description

freq_DTW calculates acoustic dissimilarity of frequency contours using dynamic time warping. Internally it applies the dtwDist function from the dtw package.

Usage

freq_DTW(
  X = NULL,
  type = "dominant",
  wl = 512,
  wl.freq = 512,
  length.out = 20,
  wn = "hanning",
  ovlp = 70,
  bp = NULL,
  threshold = 15,
  threshold.time = NULL,
  threshold.freq = NULL,
  img = TRUE,
  parallel = 1,
  path = NULL,
  ts.df = NULL,
  img.suffix = "dfDTW",
  pb = TRUE,
  clip.edges = TRUE,
  window.type = "none",
  open.end = FALSE,
  scale = FALSE,
  fsmooth = 0.1,
  adjust.wl = TRUE,
  max.obs.per.core = 20,
  ...
)

Arguments

X	object of class 'selection_table', 'extended_selection_table' or data frame containing columns for sound file name (sound.files), selection number (selec), and start and end time of signal (start and end).
type	Character string to determine the type of contour to be detected. Three options are available, "dominant" (default), "fundamental" and "entropy".
wl	A numeric vector of length 1 specifying the window length of the spectrogram, default is 512.
wl.freq	A numeric vector of length 1 specifying the window length of the spectrogram for measurements on the frequency spectrum. Default is 512. Higher values would provide more accurate measurements.
length.out	A numeric vector of length 1 giving the number of measurements of frequency desired (the length of the time series).
wn	Character vector of length 1 specifying window name. Default is "hanning". See function ftwindow for more options.
ovlp	Numeric vector of length 1 specifying % of overlap between two consecutive windows, as in spectro. Default is 70.
bp	A numeric vector of length 2 for the lower and upper limits of a frequency bandpass filter (in kHz). Default is NULL.
threshold	amplitude threshold (%) for frequency detection. Default is 15.
threshold.time	amplitude threshold (%) for the time domain. Use for frequency detection. If NULL (default) then the 'threshold' value is used.
threshold.freq	amplitude threshold (%) for the frequency domain. Use for frequency range detection from the spectrum (see 'frange.detec'). If NULL (default) then the 'threshold' value is used.
img	Logical argument. If FALSE, image files are not produced. Default is TRUE.
parallel	Numeric. Controls whether parallel computing is applied. It specifies the number of cores to be used. Default is 1 (i.e. no parallel computing). In this function parallelization improves performance only if the number of rows in 'X' is at least twice the number of cores to be used.
path	Character string containing the directory path where the sound files are located. If NULL (default) then the current working directory is used.
ts.df	Optional. Data frame with frequency contour time series of signals to be compared. If provided "X" is ignored.
img.suffix	A character vector of length 1 with a suffix (label) to add at the end of the names of image files. Default is NULL.
pb	Logical argument to control progress bar. Default is TRUE.
clip.edges	Logical argument to control whether edges (start or end of signal) in which amplitude values above the threshold were not detected will be removed. If TRUE (default) this edges will be excluded and contours will be calculated on the remaining values. Note that DTW cannot be applied if missing values (e.i. when amplitude is not detected).
window.type	dtw windowing control parameter. Character: "none", "itakura", or a function (see dtw).
open.end	dtw control parameter. Performs open-ended alignments (see dtw).
scale	Logical. If TRUE frequency values are z-transformed using the scale function, which "ignores" differences in absolute frequencies between the signals in order to focus the comparison in the frequency contour, regardless of the pitch of signals. Default is TRUE.
fsmooth	A numeric vector of length 1 to smooth the frequency spectrum with a mean sliding window (in kHz) used for frequency range detection (when frange.detec = TRUE). This help to average amplitude "hills" to minimize the effect of amplitude modulation. Default is 0.1.
adjust.wl	Logical. If TRUE 'wl' (window length) is reset to be lower than the number of samples in a selection if the number of samples is less than 'wl'. Default is TRUE.
max.obs.per.core	Numeric. Maximum number of observations per core to be used in parallel computing. Default is 100. Reduce this value if you have memory issues.
...	Additional arguments to be passed to track_freq_contour for customizing graphical output.

Details

This function extracts the dominant frequency values as a time series and then calculates the pairwise acoustic dissimilarity using dynamic time warping. The function uses the approx function to interpolate values between dominant frequency measures. If 'img' is TRUE the function also produces image files with the spectrograms of the signals listed in the input data frame showing the location of the dominant frequencies.

Value

A matrix with the pairwise dissimilarity values. If img is FALSE it also produces image files with the spectrograms of the signals listed in the input data frame showing the location of the dominant frequencies.

Author(s)

Marcelo Araya-Salas ([e-mail])

References

Araya-Salas, M., & Smith-Vidaurre, G. (2017). warbleR: An R package to streamline analysis of animal acoustic signals. Methods in Ecology and Evolution, 8(2), 184-191.

See Also

spectrograms for creating spectrograms from selections, snr_spectrograms for creating spectrograms to optimize noise margins used in sig2noise and freq_ts, freq_ts, for frequency contour overlaid spectrograms.

Other spectrogram creators: color_spectro(), multi_DTW(), phylo_spectro(), snr_spectrograms(), spectrograms(), track_freq_contour()

Examples

{
  # load data
  data(list = c("Phae.long1", "Phae.long2", "lbh_selec_table"))
  writeWave(Phae.long2, file.path(tempdir(), "Phae.long2.wav")) # save sound files
  writeWave(Phae.long1, file.path(tempdir(), "Phae.long1.wav"))

  # dominant frequency
  freq_DTW(lbh_selec_table,
    length.out = 30, flim = c(1, 12), bp = c(2, 9),
    wl = 300, path = tempdir()
  )

  # fundamental frequency
  freq_DTW(lbh_selec_table,
    type = "fundamental", length.out = 30, flim = c(1, 12),
    bp = c(2, 9), wl = 300, path = tempdir()
  )
}

warbleR documentation built on Sept. 11, 2024, 7:13 p.m.