Find overlapping selections

overlapping_sels finds which selections overlap in time within a given sound file.

Usage

overlapping_sels(X, index = FALSE, pb = TRUE, max.ovlp = 0, relabel = FALSE,
drop = FALSE, priority = NULL, priority.col = NULL, unique.labs = NULL,
indx.row = FALSE, parallel = 1, verbose = TRUE)

Arguments

X: 'selection_table' object or data frame with the following columns: 1) "sound.files": name of the sound files, 2) "selec": number of the selections, 3) "start": start time of selections, 4) "end": end time of selections.
index: Logical. Indicates if only the index of the overlapping selections would be returned. Default is FALSE.
pb: Logical argument to control progress bar and messages. Default is TRUE.
max.ovlp: Numeric vector of length 1 specifying the maximum overlap allowed (in seconds) . Default is 0.
relabel: Logical. If TRUE then selection names ('selec' column) are reset within each sound files. Default is FALSE.
drop: Logical. If TRUE, when 2 or more selections overlap the function will remove all but one of the overlapping selection. Default is FALSE.
priority: Character vector. Controls the priority criteria used for removing overlapped selections. It must list the levels of the column used to determine priority (argument priority.col) in the desired priority order. Default is NULL.
priority.col: Character vector of length 1 with the name of the column use to determine the priority of overlapped selections. Default is NULL.
unique.labs: DEPRECATED.
indx.row: Logical. If TRUE then a character column with the indices of all selections that overlapped with each selection is added to the ouput data frame (if index = TRUE). For instance, if the selections in rows 1,2 and 3 all overlapped with each other, the 'indx.row' value would be "1/2/3" for all. However, if selection 3 only overlaps with 2 but not with 1, then it returns, "1/2" for row 1, "1/2/3" for row 2, and "2/3" for row 3. Default is FALSE.
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).
verbose: Logical to control if messages are printed to the console.

Value

A data frame with the columns in X plus an additional column ('ovlp.sels') indicating which selections overlap. For instance, if the selections in rows 1,2 overlap and 2 and 3 also overlap, the 'ovlp.sels' label would be the same for all 3 selections. If drop = TRUE only the non-overlapping selections are returned.and if 2 or more selections overlap only the first one is kept. The arguments 'priority' and 'priority.col' can be used to modified the criterium for droping overlapping selections.

Details

This function detects selections within a selection table that overlap in time. Selections must be listed in a data frame similar to lbh_selec_table. Note that row names are set to 1:nrow(X).

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.

Author

Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)

Examples

{
  # no overlap
  overlapping_sels(X = lbh_selec_table)

  # modified lbh_selec_table to make the first and second selection overlap
  Y <- lbh_selec_table
  Y$end[4] <- 1.5

  overlapping_sels(X = Y)

  # drop overlapping
  overlapping_sels(X = Y, drop = TRUE)

  # get index instead
  overlapping_sels(X = Y, index = TRUE)
}
#> No overlapping selections were found
#> 2 selections overlapped
#> 2 selections overlapped, 1 were removed
#> [1] 4 5