View source: R/search_templates.R
search_templates | R Documentation |
search_templates
searches acoustic templates on test (re-recorded) sound files.
search_templates(X, template.rows, test.files, path = NULL, pb = TRUE, ...)
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 |
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.
A data frame with the time, start, end, test file names, template name, maximum cross-correlation score and the time where it was detected.
Marcelo Araya-Salas (marcelo.araya@ucr.ac.cr)
Araya-Salas, M. (2020). baRulho: baRulho: quantifying habitat-induced degradation of (animal) acoustic signals in R. R package version 1.0.2
spcc_align
; align_test_files
## 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)
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