soundMat: Soundscape Saturation Matrix

In Ruido: Soundscape Background Noise, Power, and Saturation

Soundscape Saturation Matrix

Description

Get the Soundscape Saturation matrix with all threshold combinations instead of the combination with the most normal distribution.

Usage

soundMat(
  soundpath,
  channel = "stereo",
  timeBin = 60,
  dbThreshold = -90,
  targetSampRate = NULL,
  wl = 512,
  window = signal::hamming(wl),
  overlap = ceiling(length(window)/2),
  histbreaks = "FD",
  DCfix = TRUE,
  powthr = c(5, 20, 1),
  bgnthr = c(0.5, 0.9, 0.05),
  beta = TRUE,
  backup = NULL
)

Arguments

soundpath	single or multiple directories to your audio files
channel	channel where the saturation values will be extract from. Available channels are: "stereo", "mono", "left" or "right". Defaults to "stereo".
timeBin	size (in seconds) of the time bin. Set to NULL to use the entire audio as a single bin. Defaults to 60
dbThreshold	minimum allowed value of dB for the spectrograms. Set to NULL to leave db values unrestricted Defaults to -90, as set by Towsey 2017
targetSampRate	desired sample rate of the audios. This argument is only used to down sample the audio. If NULL, then audio's sample rate remains the same. Defaults to NULL
wl	window length of the spectrogram. Defaults to 512
window	window used to smooth the spectrogram. Switch to signal::hanning(wl) to use hanning instead. Defaults to signal::hammning(wl)
overlap	overlap between the spectrogram windows. Defaults to wl/2 (half the window length)
histbreaks	breaks used to calculate Background Noise. Available breaks are: "FD", ⁠"Sturges⁠", "scott" and 100. Defaults to "FD". Can also be set to any numerical value to limit or increase the amount of breaks.
DCfix	if the DC offset should be removed before the metrics are calculated. Defaults to TRUE
powthr	numeric vector of length three containing the the range of thresholds used to evaluate the Soundscape Power of the Activity Matrix (in dB). The values correspond to the minimum threshold, maximum threshold and step size respectively. Defaults to c(5, 20, 1), which evaluates thresholds from 5 dB to 20 dB in increments of 1 dB
bgnthr	numeric vector of length three containing the the range of thresholds used to evaluate the Background Noise of the Activity Matrix (in %). The values correspond to the minimum threshold, maximum threshold and step size respectively. Defaults to c(0.5, 0.9, 0.05), which evaluates thresholds from 50% to 90% in increments of 5%
beta	how BGN thresholds are calculated. If TRUE, BGN thresholds are calculated using all recordings combined. If FALSE, BGN thresholds are calculated separately for each recording. Defaults to TRUE
backup	path to save the backup. Defaults to NULL

Details

Check soundSat() to see how the indices are calculated.

If backup is set to a valid directory, a file named "SATBACKUP.RData" is saved after every batch of five processed files. If the function execution is interrupted (e.g., manual termination, an R session crash, or a system shutdown), this backup file can be passed to satBackup() (e.g., as ~path/SATBACKUP.RData) to resume the original process. Once a backup is created, all arguments and file paths must remain unchanged, unless they are manually modified within the .RData object.

Value

A list containing three objects. The first (info) contains the following variables from every audio file: PATH, AUDIO, CHANNEL, DURATION, BIN, SAMPRATE. The second (values) contains saturation values from all possible threshold combinations. The third (errors) contains the error messages and the paths to the files that returned an error during processing.

References

Burivalova, Z., Towsey, M., Boucher, T., Truskinger, A., Apelis, C., Roe, P., & Game, E. T. (2018). Using soundscapes to detect variable degrees of human influence on tropical forests in Papua New Guinea. Conservation Biology, 32(1), 205-215. https://doi.org/10.1111/cobi.12968

See Also

soundSat() to get only the threshold with the most normal distribution and multActivity() to generate only activity matrices. Also, check satBackup() if you are working with larger datasets and want some safety.

Examples

oldpar <- par(no.readonly = TRUE)
### Downloading audiofiles from public Zenodo library
dir <- paste(tempdir(), "forExample", sep = "/")
dir.create(dir)
recName <- paste0("GAL24576_20250401_", sprintf("%06d", seq(0, 200000, by = 50000)), ".wav")
recDir <- paste(dir, recName, sep = "/")

for (rec in recName) {
  print(rec)
  url <- paste0("https://zenodo.org/records/17575795/files/",
                rec,
                "?download=1")
  download.file(url, destfile = paste(dir, rec, sep = "/"), mode = "wb")
}

### Running the function
sat <- soundMat(dir)

### Plotting results
sides <- sat$info$CHANNEL

thresholds <- colnames(sat$values)
split <- strsplit(thresholds, "/")

shapNorm <- apply(sat$values, 2, function(x)

  if (var(x) == 0) {
    0
  } else {
    shapiro.test(x)$statistic
  })

shapPos <- which.max(shapNorm)

par(mfrow = c(3, 2))

plot(
  sat$values[sides == "left", 1],
  main = paste0("POW = ", split[[1]][1], "dB | BGN = ", split[[1]][2], "%"),
  type = "b",
  ylim = c(0,1),
  xlab = "Time Index", ylab = "Soundsacpe Saturation (%)", col = "goldenrod"
)
points(sat$values[sides == "right", 1], col = "maroon", type = "b")

hist(sat$values[,1], main = paste("Histogram of POW = ", split[[1]][1],
"dB | BGN = ", split[[1]][2], "%"), xlab = "Soundscape Saturation (%)")

plot(
sat$values[sides == "left", 144],
main = paste0("POW = ", split[[144]][1], "dB | BGN = ", split[[144]][2], "%"),
type = "b",
ylim = c(0,1),
xlab = "Time Index", ylab = "Soundsacpe Saturation (%)", col = "goldenrod"
)
points(sat$values[sides == "right", 144], col = "maroon", type = "b")

hist(sat$values[,144], main = paste("Histogram of POW = ", split[[144]][1],
"dB | BGN = ", split[[144]][2], "%"), xlab = "Soundscape Saturation (%)")

plot(
  sat$values[sides == "left", shapPos],
  main = paste0(
    "POW = ",
    split[[shapPos]][1],
    "dB | BGN = ",
    split[[shapPos]][2],
    "%",
    "\nshapiro.test. statistic (W): ",
    which.max(shapNorm)
  ),
  type = "b",
  ylim = c(0,1),
  xlab = "Time Index", ylab = "Soundsacpe Saturation (%)", col = "goldenrod"
)
points(sat$values[sides == "right", shapPos], col = "maroon", type = "b")
hist(sat$values[,shapPos], main = paste("Histogram of POW = ",
split[[shapPos]][1], "dB | BGN = ", split[[shapPos]][2], "%"),
xlab = "Soundscape Saturation (%)")

unlink(dir, recursive = TRUE)
par(oldpar)

Ruido documentation built on April 18, 2026, 5:07 p.m.