autodetec automatically detects the start and end of vocalizations in sound files based
on amplitude, duration, and frequency range attributes.
autodetec(X = NULL, threshold = 15, envt = "abs", ssmooth = NULL, msmooth = NULL,
power = 1, bp = NULL, osci = FALSE, wl = 512, xl = 1, picsize = 1, res = 100,
flim = c(0,22), ls = FALSE, sxrow = 10, rows = 10, mindur = NULL, maxdur =
NULL, redo = FALSE, img = TRUE, it = "jpeg", set = FALSE, flist = NULL, smadj = NULL,
parallel = 1, path = NULL, pb = TRUE, pal = reverse.gray.colors.2,
fast.spec = FALSE, ...)'selection_table' object or a data frame with columns for sound file name (sound.files), selection number (selec), and start and end time of signal (start and end). If provided the detection will be conducted only within the selections in 'X'.
A numeric vector of length 1 specifying the amplitude threshold for detecting signals (in %).
Character vector of length 1 specifying the type of envelope to be used: "abs" for absolute amplitude envelope or "hil" for Hilbert amplitude envelope. Default is "abs".
A numeric vector of length 1 to smooth the amplitude envelope with a sum smooth function. Default is NULL.
A numeric vector of length 2 to smooth the amplitude envelope with a mean sliding window. The first component is the window length and the second is the overlap between successive windows (in %). Faster than ssmooth but time detection is much less accurate. Will be deprecated in future versions. Default is NULL.
A numeric vector of length 1 indicating a power factor applied to the amplitude envelope. Increasing power will reduce low amplitude modulations and increase high amplide modulations, in order to reduce background noise. Default is 1 (no change).
Numeric vector of length 2 giving the lower and upper limits of a frequency bandpass filter (in kHz). Default is c(0, 22).
Logical argument to add an oscillogram underneath spectrogram, as
in spectro. Default is FALSE. Not applied if ls is
TRUE.
A numeric vector of length 1 specifying the window length of the spectrogram, default is 512.
Numeric vector of length 1, a constant by which to scale spectrogram width. Default is 1.
Numeric argument of length 1. Controls the relative size of the spectrogram. Default is 1.
Numeric argument of length 1 controling resolution of images. Default is 100 (faster) although 300 - 400 is recommended for publication/ presentation quality.
A numeric vector of length 2 for the frequency limit in kHz of
the spectrogram, as in spectro. Default is c(0, 22).
Logical argument. If TRUE, long spectrograms as in lspec
are produced.
A numeric vector of length 1. Specifies seconds of spectrogram
per row when creating long spectrograms. Default is 10. Applied when ls =
TRUE and/or when X is not provided.
A numeric vector of length 1. Specifies number of rows per
image file when creating long spectrograms. Default is 10. Applied when ls =
TRUE and/or when X is not provided.
Numeric vector of length 1 giving the shortest duration (in seconds) of the signals to be detected. It removes signals below that threshold.
Numeric vector of length 1 giving the longest duration (in seconds) of the signals to be detected. It removes signals above that threshold.
Logical argument. If TRUE all selections will be analyzed again
when code is rerun. If FALSE only the selections that do not have an 'autodetec' generated image
file in the working directory will be analyzed. Default is FALSE.
Logical argument. If FALSE, image files are not produced. Default is TRUE.
A character vector of length 1 giving the image type to be used. Currently only "tiff" and "jpeg" are admitted. Default is "jpeg".
A logical argument indicating wheter the settings of the autodetection
process should be included in the image file name. If TRUE, threshold (th), envelope (envt), bandpass (bp),
power (pw), smooth (smo, either mmsooth[1] or ssmooth), maxdur (mxdu), and mindur (midu) are included.
character vector or factor indicating the subset of files that will be analyzed. Ignored if X is provided.
adjustment for amplitude smoothing. Character vector of length one indicating whether start end
values should be adjusted. "start", "end" or "both" are the inputs admitted by this argument. Amplitude
smoothing through ssmooth generates a predictable deviation from the actual start and end positions of the signals,
determined by the threshold and ssmooth values. This deviation is more obvious (and problematic) when the
increase and decrease in amplitude at the start and end of the signal (respectively) is not gradual. Ignored if ssmooth is NULL.
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 argument to control progress bar. Default is TRUE.
Logical. If TRUE then image function is used internally to create spectrograms, which substantially
increases performance (much faster), although some options become unavailable, as collevels, and sc (amplitude scale).
This option is indicated for signals with high background noise levels. Palette colors gray.1, gray.2,
gray.3, topo.1 and rainbow.1 (which should be imported from the package monitoR) seem
to work better with 'fast.spec' spectograms. Palette colors gray.1, gray.2,
gray.3 offer
decreasing darkness levels.
Additional arguments to be passed internally specreator for customizing
graphical output.
Image files with spectrograms showing the start and end of the detected signals. It also returns a data frame containing the start and end of each signal by sound file and selection number.
This function determines the start and end of signals in the sound file selections listed
in the input data frame ('X'). Alternatively, if no data frame is provided, the function detects signals across
each entire sound file. It can also create long spectrograms highlighting the start and of the detected
signals for all sound files in the working directory (if img = TRUE). Sound files should be located in the
working directory or the path to the sound files should be provided using the 'path' argument. The input
data frame should have the following columns: c("sound.files","selec","start","end"). The ouptut of
manualoc can be used as the input data frame. This function uses a modified version of the
timer function from seewave package to detect signals.
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 to temporary working directory
data(list = c("Phae.long1", "Phae.long2", "Phae.long3", "Phae.long4"))
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"))
writeWave(Phae.long4, file.path(tempdir(), "Phae.long4.wav"))
ad <- autodetec(threshold = 5, env = "hil", ssmooth = 300, power=1,
bp=c(2,9), xl = 2, picsize = 2, res = 200, flim= c(1,11), osci = TRUE,
wl = 300, ls = FALSE, sxrow = 2, rows = 4, mindur = 0.1, maxdur = 1, set = TRUE, path = tempdir())
#run it with different settings
ad <- autodetec(threshold = 90, env = "abs", ssmooth = 300, power = 1, redo = TRUE,
bp=c(2,9), xl = 2, picsize = 2, res = 200, flim= c(1,11), osci = TRUE,
wl = 300, ls = FALSE, sxrow = 2, rows = 4, mindur=0.1, maxdur=1, set = TRUE, path = tempdir())
#check this folder!!
tempdir()
# }
# NOT RUN {
# }
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