align_test_files {baRulho}R Documentation

Align test sound files


align_test_files aligns test (re-recorded) sound files.


align_test_files(X, Y, output = "est", path = NULL, = TRUE, marker = "start", ...)



object of class 'data.frame', 'selection_table' or 'extended_selection_table' (the last 2 classes are created by the function selection_table from the warbleR package). This should be the same data than that used for aligning signals in search_templates.


object of class 'data.frame' with the output of search_templates.


Character vector of length 1 to determine if an extended selection table ('est', default) or a data.frame ("data.frame").


Character string containing the directory path where test (re-recorded) sound files are found.

Logical argument to indicate if the extended selection table should be created by song (see '' selection_table argument). Default is TRUE.


Character string to define whether a "start" or "end" marker would be used for aligning re-recorded sound files. Default is "start".


Additional arguments to be passed to selection_table for customizing extended selection table.


The function takes the output of find_peaks ('Y') and aligns signals found in re-recorded sound files according to a master sound file referenced in 'X'. The function outputs a 'extended selection table'.


An extended selection table with the aligned signals from test (re-recorded) sound files.


Marcelo Araya-Salas (


Araya-Salas, M. (2020). baRulho: baRulho: quantifying habitat-induced degradation of (animal) acoustic signals in R. R package version 1.0.2

See Also

spcc_align; search_templates


## Not run: 
# set temporary directory
td <- tempdir()  

# load example data from warbleR
data(list = c("Phae.long1", "Phae.long2", "Phae.long3", "Phae.long4", "lbh_selec_table"))

# save sound files to temporary folder
writeWave(Phae.long1, file.path(td, "Phae.long1.wav"))
writeWave(Phae.long2, file.path(td, "Phae.long2.wav"))
writeWave(Phae.long3, file.path(td, "Phae.long3.wav"))
writeWave(Phae.long4, file.path(td, "Phae.long4.wav"))

# make an extended selection table
est <- warbleR::selection_table(X = lbh_selec_table, extended = TRUE, 
confirm.extended = FALSE, path = td, pb = FALSE)

# create master sound file
master.sf <- master_sound_file(X = est, = "example_master", 
dest.path = td, gap.duration = 0.3)

# read master
exmp.master <- readWave(file.path(td, "example_master.wav"))

# add 1 s silence
exmp.test1 <- addsilw(wave = exmp.master, at = "start", d = 1, output = "Wave", 
f = exmp.master@samp.rate)

exmp.test2 <- addsilw(wave = exmp.master, at = "start", d = 2, output = "Wave", 
f = exmp.master@samp.rate)

# create noise
ns <- noisew(f = exmp.master@samp.rate, d = duration(exmp.test2) + 1, 
output = "Wave")

# make noise exactly the same length and add noise to 2 examples
exmp.test1@left <- exmp.test1@left + (ns@left[1:length(exmp.test1@left)] * 500)
exmp.test2@left <- exmp.test2@left + (ns@left[1:length(exmp.test2@left)] * 500)

# normalize before saving
exmp.test1 <- normalize(exmp.test1, unit = "16")
exmp.test2 <- normalize(exmp.test2, unit = "16")

# save examples
writeWave(object = exmp.test1, filename = file.path(td, "example_test1.wav"), 
extensible = FALSE)

writeWave(object = exmp.test2, filename = file.path(td, "example_test2.wav"), 
extensible = FALSE)

# find  tempaltes
found.templts <- search_templates(X = master.sf, 
template.rows = which(master.sf$orig.sound.file == "start_marker"), 
test.files = c("example_test1.wav", "example_test2.wav"), path = td, pb = FALSE)

# align signals and output extended selection table
alg.tests <- align_test_files(X =  master.sf, Y = found.templts, path = td, pb = FALSE)

## End(Not run)

[Package baRulho version 1.0.5 Index]