checksels checks whether selections can be read by subsequent functions.
checksels(X, parallel = 1, path = NULL, check.header = FALSE, pb = TRUE,
wav.size = FALSE)'selection_table' object or data frame with the following columns: 1) "sound.files": name of the .wav
files, 2) "sel": number of the selections, 3) "start": start time of selections, 4) "end":
end time of selections. Alternatively, a 'selection_table' class object can be input to double check selections. The ouptut of manualoc or autodetec can
be used as the input data frame.
Numeric. Controls whether parallel computing is applied. It specifies the number of cores to be used. Default is 1 (i.e. no parallel computing).
Character string containing the directory path where the sound files are located.
If NULL (default) then the current working directory is used.
Logical. Controls whether sound file headers correspond to the actual file properties (i.e. if is corrupted). This could significantly affect the performance of the function (much slower) particularly with long sound files.
Logical argument to control progress bar. Default is TRUE.
Logical argument to control if the size of the wave object
when the selection is imported into R (as when using readWave
is calculated and added as a column. Size is return in MB. Default is FALSE.
A data frame including the columns in the input data frame (X) and the following additional columns:
check.res: diagnose for each selection
duration: duration of selection in seconds
min.n.samples number of samples in a selection. Note the number of samples available
in a selection limits the minimum window length (wl argument in other functions) that can be used in batch analyses.
sample.rate: sampling rate in kHz
channels: number of channels
bits: bit depth
sound.file.samples: number of samples in the sound file
This function checks the information in a selection data frame or selection table (i.e. data frame with annotations on sound files) to avoid problems in any warbleR analysis downstream. It specifically checks if:
'X' is an object of class 'data.frame' or 'selection_table' (see selection_table) and contains
the required columns to be used on any warbleR function ('sound.files', 'selec', 'start', 'end', if not returns an error)
'sound.files' in 'X' correspond to .wav files in the working directory or in the provided 'path' (if no file is found returns an error, if some files are not found returns error info in the ouput data frame)
time ('start', 'end') and frequency ('bottom.freq', 'top.freq', if provided) limit parameters are numeric and don't contain NAs (if not returns an error)
there are no duplicated selection labels ('selec') within a sound file (if not returns an error)
sound files can be read (error info in the ouput data frame)
the start and end time of the selections are found within the duration of the sound files (error info in the ouput data frame)
sound files can be read (error info in the ouput data frame)
sound files header is not corrupted (only if header = TRUE, error info in the ouput data frame)
selection time position (start and end) doesn't exceeds sound file length (error info in the ouput data frame)
'top.freq' is lower than half the sample rate (nyquist frequency, error info in the ouput data frame)
negative values aren't found in time or frequency limit parameters (error info in the ouput data frame)
'start' higher than 'end' or 'bottom.freq' higher than 'top.freq' (error info in the ouput data frame)
'channel' value is not higher than number of channels in sound files (error info in the ouput data frame)
The function returns a data frame that includes the information in 'X' plus additional columns about the format of sound
files (see 'Value') as well as the result of the checks ('check.res' column, value is 'OK' if everything is fine).
Sound files should be in the working directory (or the directory provided in 'path'). Corrupt files can be fixed using
fixwavs.
Araya-Salas, M., & Smith-Vidaurre, G. (2017). warbleR: An R package to streamline analysis of animal acoustic signals. Methods in Ecology and Evolution, 8(2), 184-191.
# NOT RUN {
{
# save wav file examples
data(list = c("Phae.long1", "Phae.long2", "Phae.long3", "lbh_selec_table"))
writeWave(Phae.long1, file.path(tempdir(), "Phae.long1.wav"))
writeWave(Phae.long2, file.path(tempdir(), "Phae.long2.wav"))
writeWave(Phae.long3, file.path(tempdir(), "Phae.long3.wav"))
checksels(X = lbh_selec_table, path = tempdir())
}
# }
Run the code above in your browser using DataLab