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Measure full spectrum sound noise profiles

Source: R/noise_profile.R
noise_profile.Rd

noise_profile() measures full spectrum sound pressure levels (i.e. noise profiles) in sound files or extended selection tables.

Usage

noise_profile(
  X = NULL,
  files = NULL,
  mar = NULL,
  noise.ref = c("adjacent", "custom"),
  cores = getOption("mc.cores", 1),
  pb = getOption("pb", TRUE),
  path = getOption("sound.files.path", "."),
  bp = NULL,
  hop.size = getOption("hop.size", 1),
  wl = getOption("wl", NULL),
  PSD = FALSE,
  norm = TRUE,
  dB = c("A", "B", "C", "D", "ITU", "max0"),
  averaged = TRUE
)

Arguments

X

Object of class data.frame, selection_table, or extended_selection_table (the last 2 classes are created by warbleR::selection_table() from the warbleR package) with the test sound files' annotations. 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, and 7) sound.id: ID of sounds used to identify counterparts across distances (needed for "custom" noise reference, see the noise.ref argument). Default NULL.

files

Character vector with names of wave files to be analyzed. Files must be found in the supplied path (or in the working directory if path is not supplied). Default NULL.

mar

Numeric vector of length 1. Specifies the margins adjacent to the start and end points of a selection over which to measure ambient noise. Required if X is supplied, and ignored if X is not supplied. Default NULL.

noise.ref

Character vector of length 1 determining which noise segment must be used for measuring ambient noise. Ignored if X is not supplied. Two options are available:

  • adjacent: measure ambient noise right before the sound (using the mar argument to define duration of ambient noise segments).

  • custom: measure ambient noise segments referenced in the selection table (labeled as "ambient" in the sound.id column).

cores

Numeric vector of length 1. Controls whether parallel computing is applied by specifying the number of cores to be used. Default 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 TRUE. Can be set globally for the current R session via the "pb" option (see options()).

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()).

bp

Numeric vector of length 2 giving the lower and upper limits of a frequency bandpass filter (in kHz). Default NULL.

hop.size

Numeric vector of length 1 specifying the time window duration (in ms). Default 1 ms, which is equivalent to ~45 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

Numeric vector of length 1 specifying the window length of the spectrogram. Default NULL. Ignored if bp = NULL. If supplied, hop.size is ignored. Note that lower values will increase time resolution, which is more important for amplitude ratio calculations.

PSD

Logical to control whether the Probability Mass Function (the probability distribution of frequencies) is returned. See seewave::meanspec(). Default FALSE.

norm

Logical to control whether amplitude values are normalized (divided by the maximum) so the highest value is 1. See seewave::meanspec(). Default TRUE.

dB

Character string of length 1 specifying the type of dB to return: "max0" for a maximum dB value at 0, "A", "B", "C", "D", and "ITU" for common dB weights. See seewave::meanspec(). Default "A".

averaged

Logical to control if frequency spectra are averaged within a sound file. Default TRUE.

Value

A data.frame containing the frequency spectra for each sound file or wave object (if X is supplied and is of class extended_selection_table).

Details

The function estimates full spectrum sound pressure levels (i.e. noise profiles) of ambient noise. This can be done on data frames/(extended) selection tables (using the segments containing no target sound or the "ambient" sound ID) or over complete sound files in the working directory (or supplied path). The function uses seewave::meanspec() internally to calculate frequency spectra.

References

Araya-Salas, M., Grabarczyk, E. E., Quiroz-Oliva, M., Garcia-Rodriguez, A., & Rico-Guevara, A. (2025). Quantifying degradation in animal acoustic signals with the R package baRulho. Methods in Ecology and Evolution, 00, 1-12. https://doi.org/10.1111/2041-210X.14481.

See also

excess_attenuation

Other miscellaneous: add_noise(), attenuation()

Author

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

Examples

{
  # load example data
  data("test_sounds_est")

  # measure on custom noise reference
  noise_profile(X = test_sounds_est, mar = 0.01, pb = FALSE, noise.ref = "custom")

  # remove noise selections so noise is measured right before the signals
  pe <- test_sounds_est[test_sounds_est$sound.id != "ambient", ]

  noise_profile(X = pe, mar = 0.01, pb = FALSE, noise.ref = "adjacent")
}
#>       sound.files      freq           amp
#> 1  10m_closed.wav  1.002273  -1.478756370
#> 2  10m_closed.wav  2.004545  -8.554912560
#> 3  10m_closed.wav  3.006818 -15.653879395
#> 4  10m_closed.wav  4.009091 -20.594564397
#> 5  10m_closed.wav  5.011364 -24.596826317
#> 6  10m_closed.wav  6.013636 -27.741536121
#> 7  10m_closed.wav  7.015909 -28.631141207
#> 8  10m_closed.wav  8.018182 -29.343274598
#> 9  10m_closed.wav  9.020455 -31.581649783
#> 10 10m_closed.wav 10.022727 -37.142756979
#> 11   10m_open.wav  1.002273  -1.470944432
#> 12   10m_open.wav  2.004545  -5.716210091
#> 13   10m_open.wav  3.006818 -14.060376878
#> 14   10m_open.wav  4.009091 -21.637019767
#> 15   10m_open.wav  5.011364 -28.007595476
#> 16   10m_open.wav  6.013636 -31.998254047
#> 17   10m_open.wav  7.015909 -33.040067144
#> 18   10m_open.wav  8.018182 -33.446761775
#> 19   10m_open.wav  9.020455 -36.054384166
#> 20   10m_open.wav 10.022727 -40.262096085
#> 21    1m_open.wav  1.002273   0.001384514
#> 22    1m_open.wav  2.004545  -4.328099010
#> 23    1m_open.wav  3.006818 -12.731830547
#> 24    1m_open.wav  4.009091 -20.519891620
#> 25    1m_open.wav  5.011364 -24.786032150
#> 26    1m_open.wav  6.013636 -27.331145913
#> 27    1m_open.wav  7.015909 -27.522403062
#> 28    1m_open.wav  8.018182 -27.601169568
#> 29    1m_open.wav  9.020455 -30.958903505
#> 30    1m_open.wav 10.022727 -36.213758740
#> 31 30m_closed.wav  1.002273  -5.018620398
#> 32 30m_closed.wav  2.004545 -19.660800804
#> 33 30m_closed.wav  3.006818 -26.467263845
#> 34 30m_closed.wav  4.009091 -29.190019017
#> 35 30m_closed.wav  5.011364 -33.368022266
#> 36 30m_closed.wav  6.013636 -37.485873353
#> 37 30m_closed.wav  7.015909 -39.725404754
#> 38 30m_closed.wav  8.018182 -42.088478865
#> 39 30m_closed.wav  9.020455 -44.455196777
#> 40 30m_closed.wav 10.022727 -47.253627732
#> 41   30m_open.wav  1.002273  -0.794205765
#> 42   30m_open.wav  2.004545  -5.394132145
#> 43   30m_open.wav  3.006818 -16.362837354
#> 44   30m_open.wav  4.009091 -21.711879855
#> 45   30m_open.wav  5.011364 -26.204882614
#> 46   30m_open.wav  6.013636 -26.312227870
#> 47   30m_open.wav  7.015909 -28.104324225
#> 48   30m_open.wav  8.018182 -28.673914281
#> 49   30m_open.wav  9.020455 -32.218532962
#> 50   30m_open.wav 10.022727 -34.076725570