warbleR (version 1.1.17)

sig2noise: Measure signal-to-noise ratio

Description

sig2noise measures signal-to-noise ratio across multiple files.

Usage

sig2noise(X, mar, parallel = 1, path = NULL, pb = TRUE, type = 1, eq.dur = FALSE,
in.dB = TRUE, before = FALSE, lim.dB = TRUE, bp = NULL, wl = 10)

Arguments

X

object of class 'selection_table', 'extended_selection_table' or any data frame with columns for sound file name (sound.files), selection number (selec), and start and end time of signal (start and end). The ouptut of manual_loc can also be used as the input data frame.

mar

numeric vector of length 1. Specifies the margins adjacent to the start and end points of selection over which to measure noise.

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). It can also be set globally using the 'parallel' option (see warbleR_options).

path

Character string containing the directory path where the sound files are located. If NULL (default) then the current working directory is used. It can also be set globally using the 'wav.path' option (see warbleR_options).

pb

Logical argument to control if progress bar is shown. Default is TRUE. It can also be set globally using the 'pb' option (see warbleR_options).

type

Numeric. Determine the formula to be used to calculate the signal-to-noise ratio (S = signal , N = background noise):

• 1: ratio of S mean amplitude envelope to N mean amplitude envelope (mean(env(S))/mean(env(N)))

• 2: ratio of S amplitude envelope quadratic mean to N amplitude envelope quadratic mean (rms(env(S))/rms(env(N)))

• 3: ratio of the difference between S amplitude envelope quadratic mean and N amplitude envelope quadratic mean to N amplitude envelope quadratic mean ((rms(env(S)) - rms(env(N)))/rms(env(N)))

eq.dur

Logical. Controls whether the noise segment that is measured has the same duration than the signal (if TRUE, default FALSE). If TRUE then 'mar' argument is ignored.

in.dB

Logical. Controls whether the signal-to-noise ratio is returned in decibels (20*log10(SNR)). Default is TRUE.

before

Logical. If TRUE noise is only measured right before the signal (instead of before and after). Default is FALSE.

lim.dB

Logical. If TRUE the lowest signal-to-noise would be limited to -40 dB (if in.dB = TRUE). This would remove NA's that can be produced when noise segments have a higher amplitude than the signal itself. Default is TRUE.

bp

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

wl

A numeric vector of length 1 specifying the window length of the spectrogram for applying bandpass. Default is 10. Ignored if bp = NULL. It can also be set globally using the 'wl' option (see warbleR_options). Note that lower values will increase time resolution, which is more important for signal-to-noise ratio calculations.

Value

Data frame similar to autodetec output, but also includes a new variable with the signal-to-noise values.

Details

Signal-to-noise ratio (SNR) is a measure of the level of a desired signal compared to background noise. The function divides the mean amplitude of the signal by the mean amplitude of the background noise adjacent to the signal. A general margin to apply before and after the acoustic signal must be specified. Setting margins for individual signals that have been previously clipped from larger files may take some optimization, as for calls within a larger file that are irregularly separated. When margins overlap with another acoustic signal nearby, the signal-to-noise ratio (SNR) will be inaccurate. Any SNR less than or equal to one suggests background noise is equal to or overpowering the acoustic signal. snrspecs can be used to troubleshoot different noise margins.

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. Wikipedia: Signal-to-noise ratio

Examples

# NOT RUN {
{
data(list = c("Phae.long1","lbh_selec_table"))
writeWave(Phae.long1, file.path(tempdir(), "Phae.long1.wav")) #save sound files 

# specifying the correct margin is important
# use snrspecs to troubleshoot margins for sound files
sig2noise(lbh_selec_table[grep("Phae.long1", lbh_selec_table$sound.files), ], mar = 0.2, 
path = tempdir())

# this smaller margin doesn't overlap neighboring signals
sig2noise(lbh_selec_table[grep("Phae.long1", lbh_selec_table$sound.files), ], mar = 0.1, 
path = tempdir())
}

# }