improve description method 1 set_reference and updated reference

R/internal_functions.R

@@ -1903,7 +1903,7 @@
 
     # method 1 compare to closest distance to source
     if (meth == 1) {
-      # if column transect is found select the lowest distance in that trasnect
+      # if column transect is found select the lowest distance in that transect
       if (!is.null(Z$transect)) {
         W <-
           Z[Z$transect == Z$transect[Z$.sgnl.temp == x] &

R/set_reference_sounds.R

@@ -5,11 +5,11 @@
 #' @param X 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 transects if more than 1) and 8) "distance": distance (numeric) at which each test sound was re-recorded. A 'transect' column labeling those sounds recorded in the same transect is required if 'method = 2'. 'X' can only have 1 copy for any given sound id in a distance or a transect-distance combination (if column 'transect' is supplied). In addition, 'selec' column values in 'X' cannot be duplicated within a sound file ('sound.files' column) as this combination is used to refer to specific rows in the output 'reference' column.
 #' @param method Integer vector of length 1 to indicate the 'experimental design' for measuring degradation. Two methods are available:
 #' \itemize{
-#' \item \code{1}: compare sounds (by 'sound.id') with their counterpart that was recorded at the closest distance to source (e.g. compare a sound recorded at 5m, 10m and 15m with its counterpart recorded at 1m). This is the default method. The function will try to use references from the same transect. However, if there is another test sound from the same 'sound.id' at a shorter distance in other transects, it will be used as reference instead.
+#' \item \code{1}: compare sounds (by 'sound.id') with their counterpart that was recorded at the closest distance to source (e.g. compare sounds recorded at 5m, 10m and 15m with its counterpart recorded at 1m). This is the default method. The function will try to use references from the same transect. However, if there is another test sound from the same 'sound.id' at a shorter distance in other transects, it will be used as reference instead. This behavior aims to account for the fact that in this type of experiments reference sounds are typically recorded at 1 m and at single transect.
 #' \item \code{2}: compare all sounds with their counterpart recorded at the distance immediately before within a transect (e.g. a sound recorded at 10m compared with the same sound recorded at 5m, then sound recorded at 15m compared with same sound recorded at 10m and so on). 'transect' column in 'X' is required.
 #' }
 #' Can be set globally for the current R session via the "method" option (see \code{\link[base]{options}}).
-#' @details This function adds a 'reference' column defining which sounds will be used by other functions as reference. Two methods are available (see 'methods' argument description). It will attempt to use re-recorded sounds from the shortest distance in the same transect as reference. However, if there is another re-recorded sound from the same 'sound.id' at a shorter distance in other transects, it will be used as reference instead. This behavior aims to account for the fact that in this type of experiments reference sounds are typically recorded at 1 m and at single transect. Note that if users want to define their own reference sound this can be set manually. If so, NAs must be used to indicate rows to be ignored. References must be indicated as a the combination of the 'sound.files' and 'selec' column. For instance, '10m.wav-1' indicates that the row in which the 'selec' column is '1' and the sound file is '10m.wav' should be used as reference. The function also checks that the information 'X' is in the right format so it wont produce errors in downstream analysis (see 'X' argument description for details on format). The function will ignore rows with 'sound.id' 'ambient', 'start_marker' and 'end_marker'
+#' @details This function adds a 'reference' column defining which sounds will be used by other functions as reference. Two methods are available (see 'methods' argument description). For method 1 the function will attempt to use re-recorded sounds from the shortest distance in the same transect as reference. However, if there is another re-recorded sound from the same 'sound.id' at a shorter distance in other transects, it will be used as reference instead. This behavior aims to account for the fact that in this type of experiments reference sounds are typically recorded at 1 m and at single transect. Note that if users want to define their own reference sound this can be set manually. If so, NAs must be used to indicate rows to be ignored. References must be indicated as a the combination of the 'sound.files' and 'selec' column. For instance, '10m.wav-1' indicates that the row in which the 'selec' column is '1' and the sound file is '10m.wav' should be used as reference. The function also checks that the information 'X' is in the right format so it wont produce errors in downstream analysis (see 'X' argument description for details on format). The function will ignore rows in which the column 'sound.id' is equals to 'ambient', 'start_marker' or 'end_marker'.
 #' @return An object similar to 'X' with one additional column, 'reference', with the ID of the sounds to be used as reference by degradation-quantifying functions in downstream analyses. The ID is created as \code{paste(X$sound.files, X$selec, sep = "-")}. 
 #' @export
 #' @family quantify degradation
@@ -24,7 +24,6 @@
 #' # save wav file examples
 #' X <- test_sounds_est[test_sounds_est$sound.files != "master.wav", ]
 #'
-#'
 #' # method 1
 #' Y <- set_reference_sounds(X = X)
 #'

README.Rmd

@@ -102,7 +102,7 @@ The packages [seewave](https://cran.r-project.org/package=seewave) and  [tuneR](
 
 Please cite [baRulho](https://docs.ropensci.org/baRulho//) as follows:
 
-Araya-Salas, M. (2020), *baRulho: quantifying degradation of (animal) acoustic signals in R*. R package version 1.0.0.
+Araya-Salas M., E. Grabarczyk, M. Quiroz-Oliva, A. Garcia-Rodriguez, A. Rico-Guevara. (2023), *baRulho: an R package to quantify degradation in animal acoustic signals*. bioRxiv 2023.11.22.568305.
 
 ## References