warbleR_options: Setting warbleR options

In warbleR: Streamline Bioacoustic Analysis

Setting warbleR options

Description

warbleR_options sets global parameters for warbleR functions

Usage

warbleR_options(reset = FALSE, ...)

Arguments

reset	Logical. If TRUE then all global parameters are removed. Default is FALSE.
...	Arguments in 'parameter = value' form, or a list of tagged values. The tags (i.e. parameters) must come from the list of parameters described below.

Details

The function aims to simplify the use of parameters that apply to many warbleR functions (i.e. global parameters) by setting a default value that will be used to any function in downstream analyses. Tags that are set with warbleR_options will be used iby the functions that share those arguments. However, if an argument is set within a function call it will overwrite the values set by warbleR_options. Hence, the functions remain 'flexible' as their parameters can also be modified 'on the fly'. The following tags are available:

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

• collevels: A numeric vector of length 3. Specifies levels to partition the amplitude range of the spectrogram (in dB) as in spectro. The more levels the higher the resolution of the spectrogram. The lower the first value the darker the spectrograms.

• flim: A numeric vector of length 2 for the frequency limit in kHz of the spectrogram, as in spectro.

• it: A character vector of length 1 giving the image type to be used. Currently only "tiff" and "jpeg" are admitted.

• osci: Logical argument to add an oscillogram underneath spectrogram, as in spectro.

• pal: A color palette function to be used to assign colors in the plot, as in spectro.

• parallel: Numeric. Controls whether parallel computing is applied. It specifies the number of cores to be used in iterative functions.

• pb: Logical argument to control whether progress bar is used.

• res: Numeric argument of length 1. Controls image resolution in all image creating functions.

• wav.path: Character string containing the directory path where the sound files are located. Used as 'path' in all functions in which sound files are read.

• wl: A numeric vector of length 1 specifying the window length for creating spectrogram (either for plotting or for measuring spectrogram parameters).

• wn: Character vector of length 1 specifying the window name for creating spectrogram (either for plotting or for measuring spectrogram parameters). See function ftwindow for options.

Value

When parameters are set by warbleR_options, their former values are returned in an invisible named list. Such a list can be passed as an argument to pboptions to restore the parameter values. If the function is called with no arguments the current option values are printed.

Author(s)

Marcelo Araya-Salas ([e-mail])

Examples

{
  # load data and save in temporary working directory
  data(list = c("Phae.long1", "Phae.long2", "Phae.long3", "Phae.long4", "lbh_selec_table"))
  writeWave(Phae.long1, file.path(tempdir(), "Phae.long1.wav"))
  writeWave(Phae.long2, file.path(tempdir(), "Phae.long2.wav"))
  writeWave(Phae.long3, file.path(tempdir(), "Phae.long3.wav"))
  writeWave(Phae.long4, file.path(tempdir(), "Phae.long4.wav"))

  # sig2noise with progress bar (by default is TRUE)
  a <- sig2noise(X = lbh_selec_table, mar = 0.1, path = tempdir())

  # set progress bar to FALSE with warbleR_options
  warbleR_options(pb = FALSE, path = tempdir())

  # sig2noise without progress bar
  a <- sig2noise(X = lbh_selec_table, mar = 0.1)

  # sig2noise with progress bar by setting it within the function call (overwritting options)
  a <- sig2noise(X = lbh_selec_table, pb = TRUE, mar = 0.1)

  # sig2noise without progress bar using warbleR_options setting again
  a <- sig2noise(X = lbh_selec_table, mar = 0.1)
}

warbleR documentation built on Sept. 8, 2023, 5:15 p.m.