raven.to.wave {SoundShape}

Export sample ".wav" files using selections from Raven Pro software.

Description

Create one ".wav" file for each selection created using Raven Pro software, which is commonplace in bioacoustical analysis. Each selection (i.e. line in table) should represent an acoustic unit from the sample study.

Usage

raven.to.wave(
  orig.wav.folder = NULL,
  raven.at = orig.wav.folder,
  wav.samples = "wav samples"
)

Arguments

orig.wav.folder

filepath to the folder where original ".wav" files are stored. Should be presented between quotation marks. By default: orig.wav.folder = NULL (i.e. user must specify the filepath to ".wav" files)

raven.at

filepath to the folder where selection tables from Raven Pro software are stored. Should be presented between quotation marks. File name should end with "selections.txt". By default: raven.at = orig.wav.folder (i.e. raven tables stored in the same folder as original ".wav" files)

wav.samples

folder where new ".wav" files will be stored. Can be either a filepath to the intended folder, or the name of the folder i.e.(wav.samples = "wav samples"). In the later case, a new folder will be created within the one specified by orig.wav.folder. Should be presented between quotation marks. By default: wav.samples = "wav samples"

Author(s)

Pedro Rocha

References

Rocha, P. & Romano, P. (2021) The shape of sound: A new R package that crosses the bridge between Bioacoustics and Geometric Morphometrics. Methods in Ecology and Evolution, 12(6), 1115-1121.

See Also

align.wave, raven.list,

Useful links:

• https://github.com/p-rocha/SoundShape

• Report bugs at https://github.com/p-rocha/SoundShape/issues

• Raven Pro software https://ravensoundsoftware.com/software/raven-pro/

Examples

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
#  Create folders on your console  #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#

# Create temporary folder to store original ".wav" files containing multiple units
orig.wav <- file.path(base::tempdir(), "original wave")
if(!dir.exists(orig.wav)) dir.create(orig.wav)

# Create temporary folder to store sample ".wav" files from original recordings
wav.at <- file.path(base::tempdir(), "wav samples")
if(!dir.exists(wav.at)) dir.create(wav.at)

# Create temporary folder to store results
store.at <- file.path(base::tempdir(), "output")
if(!dir.exists(store.at)) dir.create(store.at)


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
#   Select acoustic units based on Raven Pro selections   #
#                                                         #
#              Using raven.to.wav function                #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#

# Export original sample ".wav" files from SoundShape examples
tuneR::writeWave(centralis, extensible = TRUE,
                filename = file.path(orig.wav, "centralis.wav"))
tuneR::writeWave(cuvieri, extensible = TRUE,
                filename = file.path(orig.wav, "cuvieri.wav"))
tuneR::writeWave(kroyeri, extensible = TRUE,
                filename = file.path(orig.wav, "kroyeri.wav"))

# Store Raven Pro selection tables at same folder from original ".wav" files
for(i in 1:length(raven.list)){
 write.table(raven.list[i], file=file.path(orig.wav, names(raven.list)[i]),
               quote=FALSE, sep="\t", row.names = FALSE,
               col.names = colnames(raven.list[[i]]))  } # end loop


# Verify if folder has both original ".wav" files and Raven's selections
dir(orig.wav)

###
## Start here when using your own recordings

# Export a ".wav" sample for each selection made in Raven Pro
raven.to.wave(orig.wav.folder = orig.wav, wav.samples = wav.at)

# Verify samples
dir(wav.at)


#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
#  Align acoustic units using align.wave  #
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#

# Place sounds at the beginning of a sound window
align.wave(wav.at=wav.at, wav.to="Aligned",
          time.length = 0.8, time.perc = 0.005, dBlevel = 25)

# Verify alignment using analysis.type = "twoDshape"
eigensound(analysis.type = "twoDshape", wav.at = file.path(wav.at, "Aligned"),
          dBlevel = 25, store.at=store.at, plot.exp=TRUE,
          flim=c(0, 4), tlim=c(0, 0.8), add.contour = TRUE)
# Go to folder specified by store.at and check jpeg files created
# If alignment/window dimensions are not ideal, repeat process with new settings