Spectrograms with frequency measurements

track_freq_contour creates spectrograms to visualize dominant and fundamental frequency measurements (contours)

Usage

track_freq_contour(X, wl = 512, wl.freq = 512, flim = NULL, wn = "hanning", pal =
  reverse.gray.colors.2, ovlp = 70, inner.mar = c(5, 4, 4, 2), outer.mar =
  c(0, 0, 0, 0), picsize = 1, res = 100, cexlab = 1, title = TRUE, propwidth = FALSE,
  xl = 1, osci = FALSE, gr = FALSE, sc = FALSE, bp = NULL, cex = c(0.6, 1),
  threshold = 15, threshold.time = NULL, threshold.freq = NULL, contour = "both",
  col = c("#E37222B3", "#07889BB3"), pch = c(21, 24),  mar = 0.05, lpos = "topright",
  it = "jpeg", parallel = 1, path = NULL, img.suffix = NULL, custom.contour = NULL,
  pb = TRUE, type = "p", leglab = c("Ffreq", "Dfreq"), col.alpha = 0.6, line = TRUE,
   fast.spec = FALSE, ff.method = "seewave", frange.detec = FALSE, fsmooth = 0.1,
   widths = c(2, 1), freq.continuity = NULL, clip.edges = 2, track.harm = FALSE, ...)

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). The output auto_detec can also be used as the input data frame.
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.
flim: A numeric vector of length 2 for the frequency limit of the spectrogram (in kHz), as in spectro. Default is NULL.
wn: Character vector of length 1 specifying window name. Default is "hanning". See function ftwindow for more options.
pal: A color palette function to be used to assign colors in the plot, as in spectro. Default is reverse.gray.colors.2.
ovlp: Numeric vector of length 1 specifying % of overlap between two consecutive windows, as in spectro. Default is 70.
inner.mar: Numeric vector with 4 elements, default is c(5,4,4,2). Specifies number of lines in inner plot margins where axis labels fall, with form c(bottom, left, top, right). See par.
outer.mar: Numeric vector with 4 elements, default is c(0,0,0,0). Specifies number of lines in outer plot margins beyond axis labels, with form c(bottom, left, top, right). See par.
picsize: Numeric argument of length 1. Controls relative size of spectrogram. Default is 1.
res: Numeric argument of length 1. Controls image resolution. Default is 100 (faster) although 300 - 400 is recommended for publication/ presentation quality.
cexlab: Numeric vector of length 1 specifying the relative size of axis labels. See spectro.
title: Logical argument to add a title to individual spectrograms. Default is TRUE.
propwidth: Logical argument to scale the width of spectrogram proportionally to duration of the selected call. Default is FALSE.
xl: Numeric vector of length 1. A constant by which to scale spectrogram width. Default is 1.
osci: Logical argument to add an oscillogram underneath spectrogram, as in spectro. Default is FALSE.
gr: Logical argument to add grid to spectrogram. Default is FALSE.
sc: Logical argument to add amplitude scale to spectrogram, default is FALSE.
bp: A numeric vector of length 2 for the lower and upper limits of a frequency bandpass filter (in kHz) or "frange" to indicate that values in bottom.freq and top.freq columns will be used as bandpass limits. Default is NULL.
cex: Numeric vector of length 2, specifies relative size of points plotted for frequency measurements and legend font/points, respectively. See spectro.
threshold: amplitude threshold (%) for fundamental and dominant frequency detection as well as frequency range from the spectrum (see 'frange.detec'). Default is 15. WILL BE DEPRECATED. Use 'threshold.time' and 'threshold.time' instead.
threshold.time: amplitude threshold (%) for the time domain. Use for fundamental and dominant 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.
contour: Character vector, one of "df", "ff" or "both", specifying whether the dominant or fundamental frequencies or both should be plotted. Default is "both".
col: Vector of length 1 or 2 specifying colors of points plotted to mark fundamental and dominant frequency measurements respectively (if both are plotted). Default is c("#E37222B3", "#07889BB3"). Extreme values (lowest and highest) are highlighted in yellow.
pch: Numeric vector of length 1 or 2 specifying plotting characters for the frequency measurements. Default is c(21, 24).
mar: Numeric vector of length 1. Specifies the margins adjacent to the selections to set spectrogram limits. Default is 0.05.
lpos: Character vector of length 1 or numeric vector of length 2, specifying position of legend. If the former, any keyword accepted by xy.coords can be used (see below). If the latter, the first value will be the x coordinate and the second value the y coordinate for the legend's position. Default is "topright".
it: A character vector of length 1 giving the image type to be used. Currently only "tiff" and "jpeg" are admitted. Default is "jpeg".
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).
path: Character string containing the directory path where the sound files are located. If NULL (default) then the current working directory is used.
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.
custom.contour: A data frame with frequency contours for exactly the same sound files and selection as in X. The frequency values are assumed to be equally spaced in between the start and end of the signal. The first 2 columns of the data frame should contain the 'sound.files' and 'selec' columns and should be identical to the corresponding columns in X (same order).
pb: Logical argument to control progress bar. Default is TRUE.
type: A character vector of length 1 indicating the type of frequency contour plot to be drawn. Possible types are "p" for points, "l" for lines and "b" for both.
leglab: A character vector of length 1 or 2 containing the label(s) of the frequency contour legend in the output image.
col.alpha: A numeric vector of length 1 within [0,1] indicating how transparent the lines/points should be.
line: Logical argument to add red lines (or box if bottom.freq and top.freq columns are provided) at start and end times of selection. Default is TRUE.
fast.spec: Logical. If TRUE then image function is used internally to create spectrograms, which substantially increases performance (much faster), although some options become unavailable, as collevels, and sc (amplitude scale). This option is indicated for signals with high background noise levels. Palette colors gray.1, gray.2, gray.3, topo.1 and rainbow.1 (which should be imported from the package monitoR) seem to work better with 'fast' spectrograms. Palette colors gray.1, gray.2, gray.3 offer decreasing darkness levels.
ff.method: Character. Selects the method used to calculate the fundamental frequency. Either 'tuneR' (using FF) or 'seewave' (using fund). Default is 'seewave'. 'tuneR' performs faster (and seems to be more accurate) than 'seewave'.
frange.detec: Logical. Controls whether frequency range of signal is automatically detected using the freq_range_detec function. If so, the range is used as the bandpass filter (overwriting 'bp' argument). Default is FALSE.
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.
widths: Numeric vector of length 2 to control the relative widths of the spectro (first element) and spectrum (second element, (when frange.detec = TRUE)).
freq.continuity: Numeric vector of length 1 to control whether dominant frequency detections outliers(i.e that differ from the frequency of the detections right before and after) would be removed. Should be given in kHz. Default is NULL.
clip.edges: Integer vector of length 1 to control if how many 'frequency-wise discontinuous' detection would be remove at the start and end of signals (see 'freq.continuity' argument). Default is 2. Ignored if freq.continuity = NULL.
track.harm: Logical to control if track_harmonic or a modified version of dfreq is used for dominant frequency detection. Default is FALSE (use dfreq).
...: Additional arguments to be passed to the internal spectrogram creating function for customizing graphical output. The function is a modified version of spectro, so it takes the same arguments.

Value

Spectrograms of the signals listed in the input data frame showing the location of the dominant and fundamental frequencies.

Details

This function provides visualization of frequency measurements as the ones made by spectro_analysis, freq_ts and freq_DTW. Frequency measures can be made by the function or input by the user (see 'custom.contour' argument). If frange = TRUE the function uses freq_range_detec to detect the frequency range. In this case the graphical output includes a frequency spectrum showing the detection threshold. Extreme values (lowest and highest) are highlighted in yellow. Note that, unlike other warbleR functions that measure frequency contours, track_freq_contour do not interpolate frequency values.

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.

Author

Grace Smith Vidaurre and Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)

Examples

{
  # load data
  data("Cryp.soui")
  writeWave(Cryp.soui, file.path(tempdir(), "Cryp.soui.wav")) # save sound files

  # autodetec location of signals
  ad <- auto_detec(
    threshold = 6, bp = c(1, 3), mindur = 1.2, flim = c(0, 5),
    maxdur = 3, img = FALSE, ssmooth = 600, wl = 300, flist = "Cryp.soui.wav",
    path = tempdir()
  )

  # track dominant frequency graphs with freq range detection
  track_freq_contour(
    X = ad[!is.na(ad$start), ], flim = c(0, 5), ovlp = 90,
    it = "tiff", bp = c(1, 3), contour = "df", wl = 300, frange = TRUE,
    path = tempdir()
  )

  # using users frequency data (custom.contour argument)
  # first get contours using freq_ts
  df <- freq_ts(
    X = ad[!is.na(ad$start), ], flim = c(0, 5), ovlp = 90, img = FALSE,
    bp = c(1, 3), wl = 300, path = tempdir()
  )

  # now input the freq_ts output into track_freq_contour
  track_freq_contour(
    X = ad[!is.na(ad$start), ], custom.contour = df, flim = c(0, 5), ovlp = 90,
    it = "tiff", path = tempdir()
  )

  # Check this folder
  tempdir()

  # track both frequencies
  track_freq_contour(
    X = ad[!is.na(ad$start), ], flim = c(0, 5), ovlp = 90,
    it = "tiff", bp = c(1, 3), contour = "both", wl = 300, path = tempdir()
  )
}
#> Warning: This function will be deprecated in future warbleR versions, please look at the ohun package for automatic signal detection functions (https://marce10.github.io/ohun/index.html)
#> Warning: 'img' has been deprecated. Use full_spectrograms() to create images from auto_detec() output
#> Warning: 'flim' has been deprecated. Use full_spectrograms() to create images from auto_detec() output
#> NULL