search_templates {baRulho} | R Documentation |
Search acoustic templates on test sound files
Description
search_templates
searches acoustic templates on test (re-recorded) sound files.
Usage
search_templates(X, template.rows, test.files, path = NULL, pb = TRUE, ...)
Arguments
X |
Object of class 'data.frame', 'selection_table' or 'extended_selection_table' (the last 2 classes are created by the function |
template.rows |
Numeric vector with the index of the rows from 'X' to be used as templates. If only 1 is supplied the same template will be run over all 'test.files'. Otherwise, 'template.rows' must be the same length as 'test.files'. Required. |
test.files |
Character vector of length 1 with the name(s) of the test (re-recorded) file(s) in which to search for the template(s) (see argument 'template.rows'). |
path |
Character string containing the directory path where test (re-recorded) sound files are found. |
pb |
Logical argument to control if progress bar is shown. Default is |
... |
Additional arguments to be passed to |
Details
The function takes a master sound file's reference data ('X') and finds the position of acoustics templates included as selections in 'X'. This is used to align signals found in re-recorded sound files according to a master sound file referenced in 'X'. Take a look at the package vignette for information on how to:: incorporate this into a sound degradation analysis workflow.
Value
A data frame with the time, start, end, test file names, template name, maximum cross-correlation score and the time where it was detected.
Author(s)
Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)
References
Araya-Salas, M. (2020). baRulho: baRulho: quantifying habitat-induced degradation of (animal) acoustic signals in R. R package version 1.0.2
See Also
Examples
## Not run:
# use a 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 <- 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, file.name = "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)
exmp.test1 <- tuneR::normalize(exmp.test1, unit = "16")
exmp.test2 <- tuneR::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)
# search using start marker as template
search_templates(X = master.sf,
template.rows = which(master.sf$orig.sound.file == "start_marker"),
test.files = c("example_test1.wav", "example_test2.wav"), path = td, pb = FALSE)
# search using end marker as template
search_templates(X = master.sf, template.rows = which(master.sf$orig.sound.file == "end_marker"),
test.files = c("example_test1.wav", "example_test2.wav"),
path = td, pb = FALSE)
# search using both start and end markers as template
search_templates(X = master.sf,
template.rows = which(master.sf$orig.sound.file == "start_marker" |
master.sf$orig.sound.file == "end_marker"),
test.files = c("example_test1.wav", "example_test2.wav"),
path = td, pb = FALSE)
## End(Not run)