Subset selection data frames based on manually filtered image files

filter_sels subsets selection data frames based on image files that have been manually filtered.

Usage

filter_sels(
  X,
  path = NULL,
  lspec = FALSE,
  img.suffix = NULL,
  it = "jpeg",
  incl.wav = TRUE,
  missing = FALSE,
  index = FALSE
)

Arguments

X

object of class 'selection_table', 'extended_selection_table' or data frame with the following columns: 1) "sound.files": name of the .wav files, 2) "sel": number of the selections.

path

Character string containing the directory path where the image files are located. If NULL (default) then the current working directory is used. warbleR_options 'wav.path' argument does not apply.

lspec

A logical argument indicating if the image files to be use for filtering were produced by the function full_spectrograms. All the image files that correspond to a sound file must be deleted in order to be filtered out.

img.suffix

A character vector of length 1 with the suffix (label) at the end of the names of the image files. Default is NULL (i.e. no suffix as in the images produced by spectrograms). Ignored if lspec = TRUE.

it

A character vector of length 1 giving the image type ("tiff", "jpeg" or "pdf") Default is "jpeg". Note that pdf files can only be generated by full_spectrogram2pdf.

incl.wav

Logical. To indicate if sound files extensions are included ( TRUE, default) or not in the image file names.

missing

Logical. Controls whether the output data frame (or row index if is index = TRUE) contains the selections with images in the working directory (Default, missing = FALSE) or the ones with no image.

index

Logical. If TRUE and missing = FALSE the row index for the selections with images in the working directory is returned. If missing = TRUE) then the row index of the ones with no image is returned instead. Default is FALSE.

Value

If all sound files are ok, returns message "All files are ok!". Otherwise returns "These file(s) cannot be read" message with names of the corrupted sound files.

Details

This function subsets selections (or sound files if lspec is TRUE) listed in a data frame based on the image files from spectrogram-creating functions (e.g. spectrograms) in the working directory. Only the selections/sound files with and image in the working directory will remain. This is useful for excluding selections from undesired signals. Note that the image files should be in the working directory (or the directory provided in 'path').

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

if (FALSE) { # \dontrun{
# save wav file examples
data(list = c("Phae.long1", "Phae.long2", "Phae.long3", "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"))

spectrograms(lbh_selec_table,
  flim = c(0, 11), inner.mar = c(4, 4.5, 2, 1), outer.mar = c(4, 2, 2, 1),
  picsize = 2, res = 300, cexlab = 2, mar = 0.05, wl = 300, path = tempdir()
)

# go to the working directory (tempdir()) and delete some images

# filter selection data frame
fmloc <- filter_sels(X = lbh_selec_table, path = tempdir())

# this data frame does not have the selections corresponding to the images that were deleted
fmloc

# now using lspec images
full_spectrograms(
  sxrow = 2, rows = 8, pal = reverse.heat.colors, wl = 300, ovlp = 10,
  path = tempdir()
)

# go to the working directory (tempdir()) and delete lspec
# images (the ones with several rows of spectrograms)

# filter selection data frame
fmloc2 <- filter_sels(
  X = lbh_selec_table, lspec = TRUE,
  path = tempdir()
)
} # }