View source: R/envelope_correlation.R
envelope_correlation | R Documentation |
envelope_correlation
measures amplitude envelope correlation of sounds referenced in an extended selection table.
envelope_correlation(
X,
cores = getOption("mc.cores", 1),
pb = getOption("pb", TRUE),
cor.method = c("pearson", "spearman", "kendall"),
env.smooth = getOption("env.smooth", 200),
hop.size = getOption("hop.size", 11.6),
wl = getOption("wl", NULL),
ovlp = getOption("ovlp", 70),
path = getOption("sound.files.path", ".")
)
X |
The output of |
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 |
pb |
Logical argument to control if progress bar is shown. Default is |
cor.method |
Character string indicating the correlation coefficient to be applied ("pearson", "spearman", or "kendall", see |
env.smooth |
Numeric vector of length 1 to determine the length of the sliding window used for a sum smooth for amplitude envelope calculation (used internally by |
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 |
wl |
a vector with a single even integer number specifying the window length of the spectrogram, default is |
ovlp |
Numeric vector of length 1 specifying the percentage of overlap between two
consecutive windows, as in |
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 |
Amplitude envelope correlation measures the similarity of two sounds in the time domain. The function measures the envelope correlation coefficients of sounds in which a reference playback has been re-recorded at increasing distances. Values close to 1 means very similar amplitude envelopes (i.e. little degradation has occurred). If envelopes have different lengths (which means sounds have different lengths) cross-correlation is used and the maximum correlation coefficient is returned. Cross-correlation is achieved by sliding the shortest sound along the largest one and computing the correlation at each step. 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 envelope correlation are provided (see 'method' argument). Use blur_ratio
to create envelopes graphs.
Object 'X' with an additional column, 'envelope.correlation', containing the computed envelope correlation coefficients.
Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)
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.
Apol, C.A., Sturdy, C.B. & Proppe, D.S. (2017). Seasonal variability in habitat structure may have shaped acoustic signals and repertoires in the black-capped and boreal chickadees. Evol Ecol. 32:57-74.
blur_ratio
, spectrum_blur_ratio
Other quantify degradation:
blur_ratio()
,
detection_distance()
,
plot_blur_ratio()
,
plot_degradation()
,
set_reference_sounds()
,
signal_to_noise_ratio()
,
spcc()
,
spectrum_blur_ratio()
,
spectrum_correlation()
,
tail_to_signal_ratio()
{
# load example data
data("test_sounds_est")
# add reference to X
X <- set_reference_sounds(X = test_sounds_est)
envelope_correlation(X = X)
# method 2
# add reference to X
X <- set_reference_sounds(X = test_sounds_est, method = 2)
envelope_correlation(X = X)
}
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