Measure blur ratio in the time domain

blur_ratio() measures blur ratio of sounds referenced in an extended selection table, as described by Dabelsteen et al. (1993). Low values indicate low degradation of sounds.

Usage

blur_ratio(
  X,
  cores = getOption("mc.cores", 1),
  pb = getOption("pb", TRUE),
  env.smooth = getOption("env.smooth", 200),
  envelopes = FALSE,
  hop.size = getOption("hop.size", 11.6),
  wl = getOption("wl", NULL),
  ovlp = getOption("ovlp", 70),
  n.samples = 100,
  path = getOption("sound.files.path", ".")
)

Arguments

X: The output of set_reference_sounds(), an 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, 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). See set_reference_sounds() for 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 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()).
env.smooth: Numeric vector of length 1 determining the length of the sliding window (in amplitude samples) used for a sum smooth for amplitude envelope calculation (used internally by seewave::env()). Default 200. Can be set globally for the current R session via the "env.smooth" option (see options()).
envelopes: Logical to control if envelopes are returned (as attributes, attributes(X)$envelopes). Default FALSE.
hop.size: Numeric vector of length 1 specifying the time window duration (in ms). Default 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 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 (see options()).
ovlp: Numeric vector of length 1 specifying the percentage of overlap between two consecutive windows, as in seewave::spectro(). Default 70. Used for applying bandpass filtering. Can be set globally for the current R session via the "ovlp" option (see options()).
n.samples: Numeric vector of length 1 specifying the number of amplitude samples to use for representing amplitude envelopes. Default 100. If NULL the raw amplitude envelope is used (note that this can result in high RAM memory usage for large data sets). Amplitude envelope values are interpolated using stats::approx().
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, blur.ratio, containing the computed blur ratio values. If envelopes = TRUE the output would also include amplitude envelopes for all sounds as attributes (attributes(X)$envelopes).

Details

The function measures the blur ratio on sounds in which a reference playback has been re-recorded at different distances. Blur ratio is measured as the mismatch between amplitude envelopes (expressed as probability mass functions) of the reference sound and the re-recorded sound. By converting envelopes to probability mass functions, the effect of energy attenuation is removed, focusing the analysis on the modification of the envelope shape. 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). The sound.id column must be used to tell the function to only compare sounds belonging to the same category (e.g. song-types). Two methods for setting the experimental design are provided. All wave objects in the extended selection table must have the same sampling rate so the length of envelopes is comparable.

References

Dabelsteen, T., Larsen, O. N., & Pedersen, S. B. (1993). Habitat-induced degradation of sound signals: Quantifying the effects of communication sounds and bird location on blur ratio, excess attenuation, and signal-to-noise ratio in blackbird song. The Journal of the Acoustical Society of America, 93(4), 2206.

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

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)
  blur_ratio(X = X)

  # using method 2
X <- set_reference_sounds(X = test_sounds_est, method = 2)
  blur_ratio(X = X)

  # get envelopes
  br <- blur_ratio(X = X, envelopes = TRUE)
  envs <- attributes(br)$envelopes

  # make distance a factor for plotting
  envs$distance <- as.factor(envs$distance)

  
  # plot
  rlang::check_installed("ggplot2")
  library(ggplot2)
  
  ggplot(envs, aes(x= time, y = amp, col = distance)) +
  geom_line() + facet_wrap(~ sound.id) +
  scale_color_viridis_d() +
  labs(x = "Time (s)", y = "Amplitude (PMF)") +
  theme_classic()
  
}