warbleR (version 1.0.2)

autodetec: Automatically detect vocalizations in sound files

Description

autodetec automatically detects the start and end of vocalizations in sound files based on amplitude, duration, and frequency range attributes.

Usage

autodetec(X= NULL, threshold=15, envt="abs", msmooth=c(300,90),
  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)

Arguments

X

Data frame with results from manualoc function or any data frame with columns for sound file name (sound.files), selection number (selec), and start and end time of signal (start and end).

threshold

A numeric vector of length 1 specifying the amplitude threshold for detecting signals (in %).

envt

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".

msmooth

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 %).

power

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).

bp

Numeric vector of length 2 giving the lower and upper limits of a frequency bandpass filter (in kHz). Default is c(0, 22).

osci

Logical argument to add an oscillogram underneath spectrogram, as in spectro. Default is FALSE. Not applied if ls is TRUE.

wl

A numeric vector of length 1 specifying the window length of the spectrogram, default is 512.

xl

Numeric vector of length 1, a constant by which to scale spectrogram width. Default is 1.

picsize

Numeric argument of length 1. Controls the relative size of the spectrogram. Default is 1.

res

Numeric argument of length 1 controling resolution of images. Default is 100 (faster) although 300 - 400 is recommended for publication/ presentation quality.

flim

A numeric vector of length 2 for the frequency limit in kHz of the spectrogram, as in spectro. Default is c(0, 22).

ls

Logical argument. If TRUE, long spectrograms as in lspec are produced.

sxrow

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.

rows

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.

mindur

Numeric vector of length 1 giving the shortest duration (in seconds) of the signals to be detected. It removes signals below that threshold.

maxdur

Numeric vector of length 1 giving the longest duration (in seconds) of the signals to be detected. It removes signals above that threshold.

redo

Logical argument. If TRUE all selections will be analyzed again when code is rerun. If FALSE only the selections that do not have a image file in the working directory will be analyzed. Default is FALSE.

img

Logical argument. If FALSE, image files are not produced. Default is TRUE.

it

A character vector of length 1 giving the image type to be used. Currently only "tiff" and "jpeg" are admitted. Default is "jpeg".

set

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), msmooth (msmo), maxdur (mxdu), and mindur (midu) ar

flist

character vector or factor indicating the subset of files that will be analyzed. Ignored if X is provided.

Value

• 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.

Details

This function determines the start and end of signals in the segments of the sound files listed in the input data frame. Alternatively, if no data frame is provided, the function detects signals across each entire sound file and creates long spectrograms for all sound files in the working directory. 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.

Examples

# First create empty folder
dir.create(file.path(getwd(),"temp"))
setwd(file.path(getwd(),"temp"))

data(list = c("Phae.long1", "Phae.long2", "Phae.long3", "Phae.long4"))
writeWave(Phae.long1,"Phae.long1.wav")
writeWave(Phae.long2,"Phae.long2.wav")
writeWave(Phae.long3,"Phae.long3.wav")
writeWave(Phae.long4,"Phae.long4.wav")

ad <- autodetec(threshold=5, env="hil", msmooth=c(900,90), 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)

#run it with different settings
ad <- autodetec(threshold=10, env="abs", msmooth=c(900,90), 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)

#check this folder!!
getwd()

#remove example directory
unlink(getwd(),recursive = TRUE)