track_harmonic: 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.

Author

Jerome Sueur, modified by Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)

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.

References