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Find cross-correlation peaks

Source: R/find_peaks.R
find_peaks.Rd

find_peaks find peaks in cross-correlation scores from cross_correlation

Usage

find_peaks(xc.output, parallel = 1, cutoff = 0.4, path = NULL, pb = TRUE,
max.peak = FALSE, output = "data.frame")

Arguments

xc.output

output of cross_correlation after setting output = "list".

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).

cutoff

Numeric vector of length 1 with a value between 0 and 1 specifying the correlation cutoff for detecting peaks. Default is 0.4.

path

Character string containing the directory path where the sound files are located. If NULL (default) then the current working directory is used.

pb

Logical argument to control progress bar. Default is TRUE.

max.peak

Logical argument to control whether only the peak with the highest correlation value is returned (if TRUE; cutoff will be ignored). Default is FALSE.

output

Character vector of length 1 to determine if only the detected peaks are returned ('cormat') or a list ('list') containing 1) the peaks and 2) a data frame with correlation values at each sliding step for each comparison. The list, which is also of class 'peaks.output', can be used to graphically explore detections using full_spectrograms.

Value

The function returns a data frame with time and correlation score for the detected peaks.

Details

This function finds cross-correlation peaks along signals (analogous to findPeaks).

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.H. Khanna, S.L.L. Gaunt & D.A. McCallum (1997). Digital spectrographic cross-correlation: tests of sensitivity. Bioacoustics 7(3): 209-234

See also

auto_detec, findPeaks

Author

Marcelo Araya-Salas marcelo.araya@ucr.ac.cr)

Examples

{
  # load data
  data(list = c("Phae.long4", "Phae.long2", "lbh_selec_table2", "comp_matrix"))

  # save sound files
  writeWave(Phae.long4, file.path(tempdir(), "Phae.long4.wav"))
  writeWave(Phae.long2, file.path(tempdir(), "Phae.long2.wav"))

  # run cross-correlation
  xc.output <- cross_correlation(
    X = lbh_selec_table2, output = "list",
    compare.matrix = comp_matrix, path = tempdir()
  )

  # find peaks
  pks <- find_peaks(xc.output = xc.output, path = tempdir())
}
#> Warning: The use of this function for signal detection (with 'compare.matrix') 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)
#> running cross-correlation (step 1 of 1):
#> 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)