Find a segment of ambient noise to be used as reference
Source:R/spot_ambient_noise.R
spot_ambient_noise.Rdspot_ambient_noise finds a segment of ambient noise to be used as reference by other functions.
Arguments
- X
Object of class 'data.frame', or 'selection_table' (a class are created by the function
selection_tablefrom the warbleR package) with the test sound files' annotations ('extended_selection_table' are not supported). 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/transects. 'selec' column values in 'X' cannot be duplicated within a sound file ('sound.files' column) as this combination is used to refer to specific rows.- 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).- 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).- length
Numeric. Length (in s) of the segments to be used as ambient noise. Must be supplied. Default is
NULL.- ovlp
Numeric vector of length 1 specifying the percentage of overlap between two consecutive segments. Default is 0. Can be set globally for the current R session via the "ovlp" option (see
options).- fun
Function to be applied to select the segment to be used as ambient noise. It must be a function that takes a numeric vector (peak sound pressure level values for each candidate segment) and a single value with the index of the value to keep. Default is
function(x) which.min(abs(x - mean(x))).
Value
An object similar to 'X' with one additional row for each sound file, containing the selected 'ambient' reference.
Details
This function finds a segment of ambient noise to be used as reference by other functions. The function first finds candidate segments that do not overlap with annotated sounds in 'X'. Then, it calculates the peak sound pressure level (SPL) of each candidate segment and applies the function supplied by the argument 'fun' to select a single segment. By default 'fun' searches for the segment with the closest value to the mean peak SPL across all candidate segments. Ambient noise annotations are added as a new row in 'X'. Ambient noise annotations are used by the functions signal_to_noise_ratio and noise_profile to determine background noise levels. Note that this function does not work with annotations in 'extended_selection_table' format.
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 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.
See also
signal_to_noise_ratio, noise_profile
Other prepare acoustic data:
master_sound_file(),
synth_sounds()
Author
Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)
Examples
{
# set temporary directory
td <- tempdir()
# load example data
data("test_sounds_est")
########## save acoustic data (This doesn't have to be done
# with your own data as you will have them as sound files already.)
# save example files in working director
for (i in unique(test_sounds_est$sound.files)[1:2]) {
writeWave(object = attr(test_sounds_est, "wave.objects")[[i]],
file.path(tempdir(), i))
}
test_sounds_df <- as.data.frame(test_sounds_est)
test_sounds_df <- test_sounds_df[test_sounds_df$sound.id != "ambient", ]
test_sounds_df <-
test_sounds_df[test_sounds_df$sound.files %in%
unique(test_sounds_est$sound.files)[1:2], ]
####
# closest to mean (default)
spot_ambient_noise(X = test_sounds_df, path = td, length = 0.12, ovlp = 20)
# min peak
spot_ambient_noise(X = test_sounds_df, path = td, length = 0.12, ovlp = 20, fun = which.min)
}
#> sound.files selec start end bottom.freq top.freq sound.id
#> 1 10m_closed.wav 2 1.300000 1.500023 7.875 8.805 freq:9
#> 2 10m_closed.wav 3 1.550023 1.750045 3.208 4.069 freq:4
#> 3 10m_closed.wav 4 1.800045 2.000068 0.422 1.223 freq:1
#> 4 10m_closed.wav 5 2.050068 2.250091 6.905 7.917 freq:7
#> 5 10m_closed.wav 6 0.192000 0.312000 0.422 8.805 ambient
#> 6 10m_open.wav 2 1.300000 1.500023 7.875 8.805 freq:9
#> 7 10m_open.wav 3 1.550023 1.750045 3.208 4.069 freq:4
#> 8 10m_open.wav 4 1.800045 2.000068 0.422 1.223 freq:1
#> 9 10m_open.wav 5 2.050068 2.250091 6.905 7.917 freq:7
#> 10 10m_open.wav 6 0.096000 0.216000 0.422 8.805 ambient
#> transect distance
#> 1 closed 10
#> 2 closed 10
#> 3 closed 10
#> 4 closed 10
#> 5 <NA> NA
#> 6 open 10
#> 7 open 10
#> 8 open 10
#> 9 open 10
#> 10 <NA> NA