baRulho: Quantifying (Animal) Sound Degradation

#' @param X The output of \code{\link{set_reference_sounds}} which is an object of class 'data.frame', 'selection_table' or 'extended_selection_table' (the last 2 classes are created by the function \code{\link[warbleR]{selection_table}} from the warbleR package) with the reference to the test sounds . 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 \code{\link{set_reference_sounds}} for more details on the structure of 'X'.
#' @param 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).
#' @param pb Logical argument to control if progress bar is shown. Default is \code{TRUE}.
#' @param 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.
#' @param wl a vector with a single even integer number specifying the window length of the spectrogram, default is \code{NULL}. If supplied, 'hop.size' is ignored. Odd integers will be rounded up to the nearest even number.
#' @param hop.size A numeric vector of length 1 specifying the time window duration (in ms). Default is 11.6 ms, which is equivalent to 512 wl for a 44.1 kHz sampling rate. Ignored if 'wl' is supplied.
#' @param bp Numeric vector of length 2 giving the lower and upper limits of a frequency bandpass filter (in kHz). Alternatively, when set to 'freq.range' (default), the function will use the 'bottom.freq' and 'top.freq' for each sound as the bandpass range.
#' @param dest.path Character string containing the directory path where the image files will be saved. If not supplied the current working directory will be used instead.
#' @param wn A character vector of length 1 specifying the window name as in \code{\link[seewave]{ftwindow}}.
#' @param noise.ref Character vector of length 1 to determined which noise segment must be used for measuring ambient noise. Two options are available:
#' \itemize{
#' \item \code{adjacent}: measure ambient noise right before test sounds (using argument 'mar' to define duration of ambient noise segments).
#' \item \code{custom}: measure ambient noise segments referenced in the selection table (labeled as 'ambient' in the 'sound.id' column). Those segments will be used to apply the same ambient noise reference to all sounds in a sound file. Therefore, at least one 'ambient' selection for each sound file must be provided. If several 'ambient' selections by sound file are supplied, then the root mean square of the amplitude envelope will be averaged across those selections.
#' }
#' @param cor.method Character string indicating the correlation coefficient to be applied ("pearson", "spearman", or "kendall", see \code{\link[stats]{cor}}).
#' 
#' @name template_params
NULL