raven.list {SoundShape}

Sample of tables containing selection boxes from Raven Pro software

Description

This sample file features a list of three data.frame objects containing the selection boxes for the acoustic units of centralis, cuvieri and kroyeri. The selection was performed manually using Raven Pro software, which is commonplace in bioacoustic analysis.

Usage

data(raven.list)

Format

An object of the class "list" (base package).

Details

This sample list was built to illustrate the usage of raven.to.wave function. Each data.frame in the list represent selection boxes from Raven Pro software featuring either centralis, cuvieri or kroyeri samples. These, in turn, are acoustic recordings containing three stereotyped calls emitted by a male frog Physalaemus cuvieri, P. centralis or P. kroyeri (Amphibia, Anura, Leptodactylidae), respectively.

Source

Sample data of "Wave" objects:

• centralis: Advertisement call of Physalaemus centralis; original recording housed at Fonoteca Neotropical Jacques Vielliard (FNJV-0031188). Recorded by Adão José Cardoso.

• cuvieri: Advertisement call of Physalaemus cuvieri; original recording housed at Coleção Bioacústica da Universidade Federal de Minas Gerais (CBUFMG-00196). Recorded by Pedro Rocha.

• kroyeri: Advertisement call of Physalaemus kroyeri; Original recording housed at Fonoteca Neotropical Jacques Vielliard (FNJV-0032047). Recorded by Werner Bokermann.

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

raven.to.wave

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.wave 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 the process with new settings