Extract the dominant frequency values as a time series

dfts extracts the dominant frequency values as a time series. of signals selected by manualoc or autodetec.

dfts(X, wl = 512, wl.freq = 512, length.out = 20, wn = "hanning", ovlp = 70,
bp = c(0, 22), threshold = 0, threshold.time = NULL, threshold.freq = NULL,
img = TRUE, parallel = 1, path = NULL, img.suffix = "dfts", pb = TRUE,
clip.edges = FALSE, leglab = "dfts", frange.detec = FALSE, fsmooth = 0.1,
 raw.contour = FALSE, track.harm = FALSE, adjust.wl = TRUE, ...)

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 of `manualoc` or `autodetec` can 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.
length.out	A numeric vector of length 1 giving the number of measurements of dominant 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 c(0, 22). If 'frange' then the 'bottom.freq' and 'top.freq' columns are used bandpass limits.
threshold	amplitude threshold (%) for dominant frequency detection. Default is 0. Note that amplitude threshold for time and frequency domains can be defined independently. See "threshold.time" and "threshold.freq" arguments.
threshold.time	amplitude threshold (%) for the time domain. Use for 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.
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).
path	Character string containing the directory path where the sound files are located.
img.suffix	A character vector of length 1 with a sufix (label) to add at the end of the names of image files.
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` this edges will be excluded and signal contour will be calculated on the remaining values. Default is `FALSE`.
leglab	A character vector of length 1 or 2 containing the label(s) of the frequency contour legend in the output image.
frange.detec	Logical. Controls whether frequency range of signal is automatically detected using the `frange.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.
raw.contour	Logical. If `TRUE` then a list with the original contours (i.e. without interpolating values to make all contours of equal length) is returned (and no images are produced).
track.harm	Logical. If true warbleR's `track_harm` function is used to track frequency contours. Otherwise seewave's `dfreq` is used by default.
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`.
...	Additional arguments to be passed to `trackfreqs`.

Value

The function returns a data frame with the dominant frequency values measured across the signals. If raw.contour = TRUE a list with the raw frequency detections (i.e. without interpolating values to make all contours of equal length) is returned. If img is TRUE it also produces image files with the spectrograms of the signals listed in the input data frame showing the location of the dominant frequencies (see trackfreqs description for more details).

Details

This function extracts the dominant frequency values as a time series. The function uses the approx function to interpolate values between dominant frequency measures. If there are no frequencies above the amplitude threshold at the beginning or end of the signals then NAs will be generated. On the other hand, if there are no frequencies above the amplitude threshold in time windows in between the signal in which amplitude was detected then the values of the adjacent will be interpolated to fill out the missing values (e.g. no NAs in between detected amplitude segments).

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.

Examples