track_harmonic: Track harmonic frequency contour

In maRce10/warbleR: Streamline Bioacoustic Analysis

Track harmonic frequency contour

Description

track_harmonic tracks the frequency contour of the dominant harmonic.

Usage

track_harmonic(wave, f, wl = 512, wn = "hanning", ovlp = 0, fftw = FALSE, at = NULL,
tlim = NULL, threshold = 10, bandpass = NULL, clip = NULL, plot = TRUE,
xlab = "Times (s)", ylab = "Frequency (kHz)",  ylim = c(0, f/2000),
adjust.wl = FALSE, dfrq = FALSE, ...)

track_harmonic(
  wave,
  f,
  wl = 512,
  wn = "hanning",
  ovlp = 0,
  fftw = FALSE,
  at = NULL,
  tlim = NULL,
  threshold = 10,
  bandpass = NULL,
  clip = NULL,
  plot = TRUE,
  xlab = "Times (s)",
  ylab = "Frequency (kHz)",
  ylim = c(0, f/2000),
  adjust.wl = FALSE,
  dfrq = FALSE,
  ...
)

Arguments

wave	A 'wave' object produced by readWave or similar functions.
f	Sampling frequency of the wave object (in Hz). Does not need to be specified if embedded in wave.
wl	A numeric vector of length 1 specifying the window length for the FFT, default is 512.
wn	Character vector of length 1 specifying window name. Default is "hanning". See function ftwindow for more options. This is used for calculating the frequency spectrum (using meanspec) and producing the spectrogram (using spectro, if plot = TRUE).
ovlp	Numeric vector of length 1 specifying % of overlap between two consecutive time windows, as in spectro. Default is 0.
fftw	if TRUE calls the function FFT of the library fftw. See Notes of the spectro function. Default is FALSE.
at	Time position where the harmonic frequency contour has to be computed (in seconds). Default is NULL.
tlim	time range in which to measure frequency contours. Default is NULL (which means it will measure across the entire wave object).
threshold	Amplitude threshold (%) for dominant frequency and detection. Default is 10.
bandpass	A numeric vector of length 2 for the lower and upper limits of a frequency bandpass filter (in kHz).
clip	A numeric value to select dominant frequency values according to their amplitude in reference to a maximal value of 1 for the whole signal (has to be >0 & < 1).
plot	Logical, if TRUE plots the dominant frequency against time. Default is TRUE.
xlab	Label of the time axis.
ylab	Label of the frequency axis.
ylim	A numeric vector of length 2 for the frequency limit of the spectrogram (in kHz), as in spectro. Default is c(0, f/2000).
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 FALSE.
dfrq	Logical. If TRUE seewave's dfreq is used instead. Default is FALSE.
...	Additional arguments to be passed to the plotting function.

Details

This is a modified version of seewave's dfreq function that allows to track the frequency contour of a dominant harmonic even when the highest amplitude jumps between harmonics. The arguments and default values of the original dfreq function have been kept unchanged to facilitate switching between the 2 functions.

see track_harmonic for documentation. track_harmonic will be deprecated in future versions.

Author(s)

Jerome Sueur, modified by 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

track_freq_contour for tracking frequencies iteratively on selections tables.

maRce10/warbleR documentation built on April 8, 2024, 11:08 p.m.