spcc measures spectrographic cross-correlation as a measure of sound distortion in sounds referenced in an extended selection table.
Arguments
- X
The output of
set_reference_soundswhich is an object of class 'data.frame', 'selection_table' or 'extended_selection_table' (the last 2 classes are created by the functionselection_tablefrom the warbleR package) with the reference to the test sounds . Must contain the following columns: 1) "sound.files": name of the .wav files, 2) "selec": unique selection identifier (within a sound file), 3) "start": start time and 4) "end": end time of selections, 5) "bottom.freq": low frequency for bandpass, 6) "top.freq": high frequency for bandpass, 7) "sound.id": ID of sounds used to identify counterparts across distances and 8) "reference": identity of sounds to be used as reference for each test sound (row). Seeset_reference_soundsfor more details on the structure of 'X'.- cores
Numeric vector of length 1. Controls whether parallel computing is applied by specifying the number of cores to be used. Default is 1 (i.e. no parallel computing). Can be set globally for the current R session via the "mc.cores" option (see
options).- pb
Logical argument to control if progress bar is shown. Default is
TRUE. Can be set globally for the current R session via the "pb" option (seeoptions).- cor.method
Character string indicating the correlation coefficient to be applied ("pearson", "spearman", or "kendall", see
cor).- hop.size
A numeric vector of length 1 specifying the time window duration (in ms). Default is 11.6 ms, which is equivalent to 512 wl for a 44.1 kHz sampling rate. Ignored if 'wl' is supplied. Can be set globally for the current R session via the "hop.size" option (see
options).- wl
a vector with a single even integer number specifying the window length of the spectrogram, default is
NULL. If supplied, 'hop.size' is ignored. Odd integers will be rounded up to the nearest even number. Can be set globally for the current R session via the "wl" option (seeoptions).- ovlp
Numeric vector of length 1 specifying % of overlap between two consecutive windows, as in
spectro. Default is 90. High values of ovlp slow down the function but produce more accurate results. Can be set globally for the current R session via the "ovlp" option (seeoptions).- wn
A character vector of length 1 specifying the window name as in
ftwindow.- path
Character string containing the directory path where the sound files are found. Only needed when 'X' is not an extended selection table. If not supplied the current working directory is used. Can be set globally for the current R session via the "sound.files.path" option (see
options).
Value
Object 'X' with an additional column, 'cross.correlation', containing the computed spectrogram cross-correlation coefficients.
Details
Spectrographic cross-correlation measures frequency distortion of sounds as a similarity metric. Values close to 1 means very similar spectrograms (i.e. little sound distortion has occurred). Cross-correlation is measured of sounds in which a reference playback has been re-recorded at increasing distances. The 'sound.id' column must be used to indicate the function to only compare sounds belonging to the same category (e.g. song-types). The function compares each sound to the corresponding reference sound within the supplied frequency range (e.g. bandpass) of the reference sound ('bottom.freq' and 'top.freq' columns in 'X'). Two methods for computing cross-correlation are provided (see 'method' argument). The function is a wrapper on warbleR's cross_correlation function.
References
Araya-Salas M., E. Grabarczyk, M. Quiroz-Oliva, A. Garcia-Rodriguez, A. Rico-Guevara. (2023), baRulho: an R package to quantify degradation in animal acoustic signals .bioRxiv 2023.11.22.568305.Clark, C.W., Marler, P. & Beeman K. (1987). Quantitative analysis of animal vocal phonology: an application to Swamp Sparrow song. Ethology. 76:101-115.
See also
blur_ratio, manual_realign, cross_correlation
Other quantify degradation:
blur_ratio(),
detection_distance(),
envelope_correlation(),
plot_blur_ratio(),
plot_degradation(),
set_reference_sounds(),
signal_to_noise_ratio(),
spectrum_blur_ratio(),
spectrum_correlation(),
tail_to_signal_ratio()
Author
Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)
Examples
{
# load example data
data("test_sounds_est")
# add reference to X
X <- set_reference_sounds(X = test_sounds_est)
# get spcc
spcc(X = X)
}
#> Object of class 'extended_selection_table'
#> * The output of the following call:
#> selection_table(X = alg, path = "./testing/example_data/tailored_files_tlalpan/", extended = TRUE, confirm.extended = FALSE, mar = 10, by.song = "sound.files")
#>
#> Contains:
#> * A selection table data frame with 25 row(s) and 11 columns:
#> | |sound.files | selec| start| end| bottom.freq| top.freq|
#> |:--|:--------------|-----:|------:|------:|-----------:|--------:|
#> |8 |10m_closed.wav | 1| 0.0500| 0.2000| 1.3333| 2.6667|
#> |9 |10m_closed.wav | 2| 1.3000| 1.5000| 7.8750| 8.8050|
#> |10 |10m_closed.wav | 3| 1.5500| 1.7500| 3.2080| 4.0690|
#> |11 |10m_closed.wav | 4| 1.8000| 2.0001| 0.4220| 1.2230|
#> |12 |10m_closed.wav | 5| 2.0501| 2.2501| 6.9050| 7.9170|
#> |13 |10m_open.wav | 1| 0.0500| 0.2000| 1.3333| 2.6667|
#> ... 5 more column(s) (sound.id, transect, distance, reference, cross.correlation)
#> and 19 more row(s)
#>
#> * 5 wave object(s) (as attributes):
#> 10m_closed.wav, 10m_open.wav, 1m_open.wav, 30m_closed.wav, 30m_open.wav
#>
#> * A data frame (check.results) with 25 rows generated by check_sels() (as attribute)
#>
#> Additional information:
#> * The selection table was created by song (see 'class_extended_selection_table')
#> * 1 sampling rate(s) (in kHz): 22.05
#> * 1 bit depth(s): 16
#> * Created by warbleR 1.1.29