Package 'seewave'

Title: Sound Analysis and Synthesis
Description: Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses. See Sueur et al. (2008) <doi:10.1080/09524622.2008.9753600> and Sueur (2018) <doi:10.1007/978-3-319-77647-7>.
Authors: Jerome Sueur [aut, cre], Thierry Aubin [aut], Caroline Simonis [aut], Laurent Lellouch [ctr], Pierre Aumond [ctr], Adèle de Baudouin [ctr], Ethan C. Brown [ctr], Guillaume Corbeau [ctr], Marion Depraetere [ctr], Camille Desjonquères [ctr], François Fabianek [ctr], Amandine Gasc [ctr], Sylvain Haupert [ctr], Eric Kasten [ctr], Jonathan Lees [ctr], Jean Marchal [ctr], Andre Mikulec [ctr], Sandrine Pavoine [ctr], David Pinaud [ctr], Alicia Stotz [ctr], Luis J. Villanueva-Rivera [ctr], Zev Ross [ctr], Carl G. Witthoft [ctr], Hristo Zhivomirov [ctr]
Maintainer: Jerome Sueur <[email protected]>
License: GPL (>= 2)
Version: 2.2.3
Built: 2024-11-12 06:53:06 UTC
Source: CRAN

Help Index


Acoustic Complexity Index

Description

This function computes the Acoustic Complexity Index (ACI) as described in Pieretti et al. (2011)

Usage

ACI(wave, f, channel = 1, wl = 512, ovlp = 0,  wn = "hamming", flim = NULL, nbwindows = 1)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

window length for the analysis (even number of points) (by default = 512).

ovlp

overlap between two successive windows (in %).

wn

window name, see ftwindow (by default "hanning").

flim

a numeric vector of length 2 to select a frequency band (in kHz).

nbwindows

a numeric vector of length 1 specifying the number of windows (by default 1, ie a single window including the complete wave object.

Details

The function computes first a short-term Fourier transform and then the ACI index.
The function returns only the ACI total, ACI tot in Pieretti et al. (2010).
See the references for details on computation.

Value

A vector of length 1 returning the ACI total.

Note

Values returned were checked with the results provided by the add-on Soundscapemeter for the software Wavesurfer.

Author(s)

Laurent Lellouch, improved by Amandine Gasc and Morgane Papin

References

Pieretti N, Farina A, Morri FD (2011) A new methodology to infer the singing activity of an avian community: the Acoustic Complexity Index (ACI). Ecological Indicators, 11, 868-873.
Farina A, Pieretti N, Piccioli L (2011) The soundscape methodology for long-term bird monitoring: a Mediterranean Europe case-study. Ecological Informatics, 6, 354-363.

See Also

spectro, specflux

Examples

data(tico)
ACI(tico)
## dividing the sound sample into 4 windows of equal duration
ACI(tico, nbwindows=4)
## selection of a frequency band
ACI(tico, flim=c(2,6))

Statistics on time and frequency STFT contours

Description

This function returns statistics based on STFT time and frequency contours.

Usage

acoustat(wave, f, channel = 1, wl = 512, ovlp = 0, wn = "hanning",
tlim = NULL, flim = NULL,
aggregate = sum, fraction = 90,
plot = TRUE, type = "l", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

window length for the analysis (even number of points) (by default = 512).

ovlp

overlap between two successive windows (in %).

wn

window name, see ftwindow (by default "hanning").

tlim

modifications of the time limits of the analysis (in s).

flim

modifications of the frequency limits of the analysis (in kHz).

aggregate

a character vector of length 1 specifying the function to be applied on the rows (time) and columns (frequency) of the STFT matrix. By default set to sum.

fraction

a numeric vector of length 1, specifying a particular fraction of the contours amplitude to be captured by the initial and terminal percentile values (in %). See details.

plot

a logical, if TRUE a two-frame plot is returned with the time and frequency contours and percentiles displayed.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

...

other plot graphical parameters.

Details

The principle of acoustat is as follows:

  1. Compute the short-term Fourier transform (STFT) with usual parameters (wl for window length, ovlp for overlap of successive windows, and wn for the name of window shape).

  2. This results in a time * frequency matrix.

  3. Compute an aggregation function (specified with the argument aggregate set by default to sum) accross rows and columns of time * frequency matrix.)

  4. This results in two components: (i) the time contour, and (ii) the frequency contour.

  5. Each contour is considered as a probability mass function (PMF) and transformed into a cumulated distribution function (CDF).

  6. Measures are extracted from each CDF: median (M), initial percentile (P1) value, terminal percentile (P2) value, interpercentile range (IPR). P1, P2 and IPR are defined using a fraction parameter (fraction) that sets the percent of the contour amplitude to be captured by the initial and terminal percentile values. A fraction of 50% would result in the familiar quartiles and interquartile range. An energy fraction of 80% would return the 10th and 90th percentile values, and the width of the range in between.

Value

The function returns a list with 10 items:

time.contour

the time contour as a two-column matrix, the first colum being time (s) and the second colum being the amplitude probability mass function (no scale).

freq.contour

the frequency contour as a two-column matrix, the first colum being frequency (kHz) and the second colum being the amplitude probability mass function (no scale).

time.P1

the time initial percentile

time.M

the time median

time.P2

the time terminal percentile

time.IPR

the time interpercentile range

freq.P1

the frequency initial percentile

freq.M

the frequency median

freq.P2

the frequency terminal percentile

freq.IPR

the frequency interpercentile range

Note

acoustat was originally developped in Matlab language by Kurt Fristrup and XXXX Watkins (1992) .
The R function was kindly checked by Kurt Fristrup.

Author(s)

Jerome Sueur

References

Fristrup, K. M. and Watkins, W. A. 1992. Characterizing acoustic features of marine animal sounds. Woods Hole Oceanographic Institution Technical Report WHOI-92-04.

See Also

meanspec, specprop

Examples

data(tico)
note <- cutw(tico, from=0.5, to=0.9, output="Wave")
## default setting
acoustat(note)
## change the percentile fraction
acoustat(note, fraction=50)
## change the STFT parameters
acoustat(note, wl=1024, ovlp=80)
## change the function to compute the aggregate contours
## standard deviation instead of sum   
acoustat(note, aggregate=sd)
## direct time and frequency selection     
acoustat(tico, tlim=c(0.5,0.9), flim=c(3,6))
## some useless graphical changes
acoustat(note, type="o", col="blue")

Add or insert a silence section

Description

Add or insert a silence section to a time wave.

Usage

addsilw(wave, f, channel = 1, at = "end", choose = FALSE, d = NULL,
plot = FALSE, output = "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

at

position where to add the silence section (in s). Can be also specified as "start", "middle" or "end".

choose

logical, if TRUE the point where silence will be added into wave2 (=at) can be graphically chosen with a cursor.

d

duration of the silence section to add (in s).

plot

logical, if TRUE returns an oscillographic plot of wave with the new silence section (by default TRUE).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected]

See Also

oscillo, cutw,deletew, fadew,pastew, mutew,revw, zapsilw


Amplitude filter

Description

This function deletes all signal which amplitude is below a selected threshold.

Usage

afilter(wave, f, channel = 1, threshold = 5, plot = TRUE,
listen = FALSE, output = "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

threshold

amplitude threshold (in %).

plot

logical, if TRUE plots the new oscillogram (by default TRUE).

listen

if TRUE the new sound is played back.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Details

The threshold value is in % relative to the maximal value of wave. Signal inferior to this value is clipped.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Note

This function is used as an argument (threshold) in the following functions: autoc, csh, dfreq, timer and zc.

Author(s)

Jerome Sueur [email protected]

See Also

oscillo

Examples

data(orni)
op<-par(mfrow=c(2,1))
afilter(orni,f=22050)
title(main = "threshold level = 5")
afilter(orni,f=22050,threshold=0.5,colwave="blue")
title(main = "threshold level = 0.5")
par(op)

Water tank minimum resonant and cutoff frequencies

Description

This function computes the resonant and cutoff frequencies when recording in a given aquarium according to the criteria explained in Akamatsu et al. (2002)

Usage

akamatsu(Lx, Ly, Lz, mode = c(1,1,1),
         c = 148000,  plot = FALSE, xlab = "Frequency (kHz)",
         ylab = "Attenuation distance (cm)", ...)

Arguments

Lx

watertank length (in cm).

Ly

watertank width (in cm).

Lz

watertank height (in cm).

mode

mode, see details.

c

sound velocity in cm/s (by default 148000 cm/s in water).

plot

logical, if TRUE plots the attenuation distance in function of frequency.

xlab

title of the x axis if plot is TRUE.

ylab

title of the y axis if plot is TRUE.

...

other plot graphical parameters.

Details

From Akamatsu et al. (2002):

1. Resonant frequency

The calculated resonant frequencies of a rectangular glass tank with the dimension of Lx , Ly , and Lz (in centimeters) can be described by the following equation:

flmnrectangular=c2×(lLx)2+(mLy)2+(nLz)2f^{rectangular}_{lmn} = \frac{c}{2} \times \sqrt{\left(\frac{l}{L_{x}}\right)^2 + \left(\frac{m}{L_{y}}\right)^2 + \left(\frac{n}{L_{z}}\right)^2}

where c is the sound velocity (cm/s) and each l, m, n reprents an integer, and the combination of these paramameters designates the 'mode number'. The mode (1, 1, 1) represents the resonance wave of minimum frequency. The mode (2, 1, 1) represents one of the higher order of resonant component and has additional node of the soundpressure level at the middle of the X axis, i.e., Lx/2.


2. Cutoff frequency

The cutoff frequency can be calculated as follows:

fcutoffrectangular=c2×(1Ly)2+(1Lz)2f^{rectangular}_{cutoff} = \frac{c}{2} \times \sqrt{ \left(\frac{1}{L_{y}}\right)^2 + \left(\frac{1}{L_{z}}\right)^2}



3. Attenuation distance

The theoretical attenuation distance D can be expressed in function of the cutoff frequency and the projected frequency following:

Drectangular(f)=2×log10×c4πfcutoffrectangular×11(ffcutoffrectangular)2D^{rectangular}(f) = 2 \times log_{10} \times \frac{c}{4 \pi f^{rectangular}_{cutoff}} \times \frac{1}{\sqrt{1-\left(\frac{f}{f^{rectangular}_{cutoff}}\right)^2}}

Value

A list of two items:

res

Resonant frequency (in Hz). See Details

cut

Cut frequency (in Hz). See Details

Author(s)

Camille Desjonqueres

References

Akamatsu T, Okumura T, Novarini N, Yan HY (2002) Emprical refinements applicable to the recording of fish sounds in small tanks. Journal of the Acoustical Society of America, 112, 3073-3082.

Examples

akamatsu(60, 30, 40)

Amplitude modulation analysis of a time wave

Description

This function computes the Fourier analysis of a time wave envelope. This allows to detect periodicity, in particular those generated by amplitude modulations.

Usage

ama(wave, f, channel = 1, envt = "hil", wl = 512, plot = TRUE, type = "l", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

envt

the type of envelope to be used: either "abs" for absolute amplitude envelope or "hil" for Hilbert amplitude envelope.

wl

length of the window for the analysis (even number of points, by default = 512).

plot

logical, if TRUE the spectrum of the envelope (by default TRUE).

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

...

other meanspec parameters.

Details

This function is based on env and meanspec.
The envelope of wave is first computed and the spectrum of this envelope is then processed. All env and meanspec arguments can be set up. Be sure to set up wl large enough if you want to detect low amplitude modulation periodicity.

Value

If plot is FALSE, ama returns a numeric vector corresponding to the computed spectrum. If peaks is not NULL, ama returns a list with two elements:

spec

the spectrum computed

peaks

the peaks values (in kHz).

Author(s)

Jerome Sueur [email protected]

See Also

env, fma, meanspec

Examples

data(orni)
# detection of the main amplitude modulation in a cicada song:
# one with a 0.258 kHz frequency (due to pulses in the echemes)
# one with a 2.369 kHz frequency (fundamental frequency)
ama(orni,f=22050,wl=1024)
# these amplitude modulations can be identify with a cursor:
ama(orni,f=22050,wl=1024,identify=TRUE)

Acoustic Richness index

Description

This function computes the Acoustic Richness index based on M and Ht indices

Usage

AR(..., datatype = "objects", envt = "hil",
msmooth = NULL, ksmooth = NULL, ssmooth = NULL,
pattern = "[wav]$|[WAV]$|[mp3]$")

Arguments

...

Wave, WaveMC, audioSample objects if datatype="objects", or a path as a character string to a directory including .wav and/or .mp3 files if datatype="files".

datatype

A character string to specify if inputs are either R objects (datatype="objects", default) or files (datatype="files").

envt

the type of envelope to be returned: either "abs" for absolute amplitude envelope or "hil" for Hilbert (default) amplitude envelope. See env.

msmooth

mean smooth. See env.

ksmooth

kernel smooth via kernel. See env.

ssmooth

sum smooth. See env.

pattern

an optional regular expression. Only file names which match the regular expression will be returned when datatype="files". By default .wav or .mp3 files. See dir.

Details

AR is ranked index based on the rank of the M and Ht indices obtained with the functions M and th respectively following:

AR=rank(M)×rank(Ht)n2AR = \frac{rank(M) \times rank(H_{t})}{n^2}

with

0AR10 \leq AR \leq 1

Value

A data.frame with three columns (M, Ht, AR) and n columns, with n the number of objects (respectively files) used as input.

Note

As a ranked index, the results returned by AR strongly depends with the set of objects (respectively files) used as input. Comparaison between different data sets may be spurious. Computing AR on a set of a single object does not make any sense but is allowed.

Author(s)

Jerome Sueur and Marion Depraetere

References

Depraetere M, Pavoine S, Jiguet F, Gasc A, Duvail S, Sueur J (2012) Monitoring animal diversity using acoustic indices: implementation in a temperate woodland. Ecological Indicators, 13, 46-54.

See Also

M, th, env

Examples

## input as R objects
data(orni)
data(tico)
AR(orni, tico)
## give names to objects if you wish to have them as row names of the returned data.frame
AR(orni=orni, tico=tico)
## input as files stored in the working directory
## file names will be used as row names of the returned data.frame
## Not run: 
require(tuneR)
AR(getwd(), datatype="files")

## End(Not run)

Generate sound intensity attenuation data

Description

This function generates dB data following theoretical spherical attenuation of sound.

Usage

attenuation(lref, dref = 1, dstop, n, plot = TRUE,
xlab = "Distance (m)", ylab = "dB", type = "l", ...)

Arguments

lref

reference intensity or pressure level (in dB).

dref

reference distance corresponding to lref (in m.) (by default = 1).

dstop

maximal distance of propagation (in m.).

n

number of points generated between dref and dstop.

plot

logical, if TRUE plots attenuation against distance of propagation (by default TRUE).

xlab

title of the x axis.

ylab

title of the y axis.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

...

other plot graphical parameters.

Value

If plot is FALSE return a numeric vector with the data generated.

Note

Sound attenuation in a free, unbounded medium behaves in accordance with the inverse square law. attenuation generates data following this rule from a reference point where sound intensity level (SIL) or sound pressure level (SPL) is known. Such theoretical data can be compared with experimental data collected in a real environment.

Author(s)

Jerome Sueur

References

Hartmann, W. M. 1998 Signals, sound and sensation. New York: Springer.

See Also

convSPL, moredB

Examples

# theoretical attenuation up to 150 m of a 100 dB/1m sound source
attenuation(lref=100, dref=1, dstop=150, n=200)

Reading and interpreting Audiomoth file name

Description

This function reads and decomposes the files names generated by an Audiomoth device, audio digal recorders produced by the society Open Acoustic Devices.

Usage

audiomoth(x, tz = "")

Arguments

x

a character vector with .wav file names.

tz

a character vector defining a time zone specification. See as.POSIXct

Details

The digital recorder Audiomoth produced by Open Acoustic Devices (https://www.openacousticdevices.info/) generates .wav files which names contains information about the time of recording. The information is encoded in hexadecimal (e.g. "5E9089F0"). The function audiomoth decodes this information so that time of recording can be retrieved in numeric or time format.

Value

The function returns a data.frame with the following columns:

year

year of recording, numeric

month

month of recording, numeric

day

day of recording, numeric

hour

hour of recording, numeric

min

minute of recording, numeric

sec

second of recording, numeric

time

time in POSIX format

Note

For the time zone see the 607 time zone names stored in OlsonNames.
The file names of Audiomoth may change with time. There is no guarantee that the function will be updated on time.

Author(s)

Jerome Sueur

References

See Open Acoustic Devices website for details regarding the Audiomoth: https://www.openacousticdevices.info/.

See Also

audiomoth.rename, as.POSIXct, OlsonNames, songmeter

Examples

## HEXADECIMAL EXAMPLES (OLD FORMAT)
## recording done on Friday 10 April 2020 16:54:44 UTC
## computer time zone (local time, Europe, Paris for the test)
audiomoth("5E90A4D4.WAV")
## UTC
audiomoth("5E90A4D4.WAV", tz="UTC")
## GMT (= UTC as UTC and GMT are synonyms)    
audiomoth("5E90A4D4.WAV", tz="GMT")
## UTC -2
audiomoth("5E90A4D4.WAV", tz="Etc/GMT-2")
## in Asia, Japan
audiomoth("5E90A4D4.WAV", tz="Japan")
## in South-America, Cayenne
audiomoth("5E90A4D4.WAV", tz="America/Cayenne")  
## several files
filenames <- c("5E914ED0.WAV", "5E915128.WAV",
"5E915380.WAV", "5E9155D8.WAV", "5E915830.WAV",
"5E915A88.WAV", "5E915CE0.WAV", "5E915F38.WAV",
"5E916190.WAV", "5E9163E8.WAV")
audiomoth(filenames)
## YYYYMMDD_HHMMSS.WAV FORMAT (ACTUAL FORMAT)
## single file
audiomoth("20230715_150000.wav")
## several files
filenames <- c("20230715_150000.wav", "20230715_151500.wav",
"20230715_153000.wav", "20230715_154500.wav")
audiomoth(filenames)

Rename audiomoth files in a readable format

Description

This function renames or copies files created with an Audiomoth device in a readable format including the data and time of recording.

Usage

audiomoth.rename(dir, overwrite = FALSE, tz = "", prefix = "")

Arguments

dir

a character vector, path to directory where the .WAV files are stored.

overwrite

a logical, to specify if the files should be renamed or copied, if TRUE the files are copied, if FALSE the files are renamed.

tz

a character vector defining a time zone specification. See as.POSIXct

prefix

a charcter vector for a prefix name to be added at the beginning of the file name.

Details

The format of the new file names follows the format of the SongMeter SM2/SM4 deveices: PREFIX_YYYYMMDD_HHMMSS.wav.

Value

1 logical vector indicating which operation succeeded for each of the files attempted.

Note

Be careful if you overwrite the files.

Author(s)

Jerome Sueur

See Also

audiomoth, songmeter


Short-term autocorrelation of a time wave

Description

This function returns the fundamental frequency of a harmonic time wave. This is achieved by computing a correlation of the signal with itself after a time delay.

Usage

autoc(wave, f, channel = 1, wl = 512, fmin, fmax, threshold = NULL, plot = TRUE,
xlab = "Time (s)", ylab = "Frequency (kHz)", ylim = c(0, f/2000), pb =
FALSE, ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

length of the window for the analysis (even number of points, by default = 512).

fmin

the minimum frequency to detect (in Hz). See details.

fmax

the maximum frequency to detect (in Hz). See details

threshold

amplitude threshold for signal detection (in %).

plot

logical, if TRUE plots the fundamental frequency against time (by default TRUE).

xlab

title of the x-axis.

ylab

title of the y-axis.

ylim

the range of y values.

pb

if TRUE returns a text progress bar in the console.

...

other plot graphical parameters.

Details

'fmin' and 'fmax' can help by reducing computing time but can also produce less accurate results.

Value

When plot is FALSE, autoc returns a two-column matrix, the first column corresponding to time in seconds (x-axis) and the second column corresponding to to fundamental frequency in kHz (y-axis).
NA corresponds to pause sections in wave (see threshold).

Author(s)

Jerome Sueur [email protected] and Thierry Aubin [email protected]

References

Hopp, S. L., Owren, M. J. and Evans, C. S. (Eds) 1998. Animal acoustic communication. Springer, Berlin, Heidelberg.

See Also

ceps, acf

Examples

data(sheep)
# fundamental frequency of a sheep
res <- autoc(sheep, f=8000, threshold=5, fmin=100, fmax=700, plot=FALSE)
spectro(sheep, f=8000, ovlp=75, scale=FALSE)
points(res, pch=20)
legend(0.5, 3.6, "Fundamental frequency", pch=20, bty=0, cex=0.7)

Beep sound

Description

Generate a simple beep to be used as an alert, for instance at the end of a loop of when ending up a long script.

Usage

beep(d = 0.5, f = 8000, cf = 1000)

Arguments

d

duration (in s)

f

sampling frequency (in Hz)

cf

carrier frequency (in Hz)

Value

Nothing returned, a pure tone sound is played back. The default duration is 0.5 s and the default frequency is 1000 Hz

Note

The function uses listen of seewave which calls play of tuneR. You might need to set up your sound player with setWavPlayer of tuneR.

Author(s)

Jerome Sueur

Examples

## Not run: 
# default settings
beep()
# change the duration and the frequency
beep(d=1, cf=880)

## End(Not run)

Butterworth frequency filter

Description

This function is a Butterworth frequency filter that filters out a selected frequency section of of a time wave (low-pass, high-pass, low-stop, high-stop, bandpass or bandstop frequency filter).

Usage

bwfilter(wave, f, channel = 1, n = 1, from = NULL, to = NULL,
bandpass = TRUE, listen = FALSE, output = "matrix")

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

n

Order of the filter. See details.

from

start frequency (in Hz) where to apply the filter.

to

end frequency (in Hz) where to apply the filter.

bandpass

if TRUE a band-pass filter is applied between from and to, if not NULL a band-stop filter is applied between from and to (by default NULL).

listen

if TRUE the new sound is played back.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

Details

The order of the filter determines the value of the roll-off value, that is the dB decrease per octave of the transfer function. A filter of order n will have a transfer function with a roll-off value of - n*6 dB.

Value

A new wave is returned. The class of the returned object is set with the argument output.

Note

This function mainly uses the functions filter() and filtfilt() from the package signal

Author(s)

Jerome Sueur, functions filter() and filtfilt() from the package signal.

References

Stoddard, P. K. (1998). Application of filters in bioacoustics. In: Hopp, S. L., Owren, M. J. and Evans, C. S. (Eds), Animal acoustic communication. Springer, Berlin, Heidelberg,pp. 105-127.

See Also

ffilter, bwfilter, preemphasis, lfs, afilter

Examples

require(signal)
f <- 8000
a <- noisew(f=f, d=1)
## low-pass
# 1st order filter
res <- bwfilter(a, f=f, n=1, to=1500)
# 8th order filter
res <- bwfilter(a, f=f, n=8, to=1500)
## high-pass
res <- bwfilter(a, f=f, from=2500)
## band-pass
res <- bwfilter(a, f=f, from=1000, to=2000)
## band-stop
res <- bwfilter(a, f=f, from=1000, to=2000,bandpass=FALSE)

Continuous coherence function between two time waves

Description

This function returns a two-dimension coherence representation between two time waves. The function corresponds to a sliding coherence function along the two signals. This produces a 2-D density plot. An amplitude contour plot can be overlaid.

Usage

ccoh(wave1, wave2, f, channel = c(1,1), wl = 512, ovlp = 0, plot = TRUE,
grid = TRUE, scale = TRUE, cont = FALSE,
collevels = seq(0, 1, 0.01), palette = reverse.heat.colors,
contlevels = seq(0, 1, 0.01), colcont = "black",
colbg="white", colgrid = "black",
colaxis = "black", collab="black",
xlab = "Time (s)", ylab = "Frequency (kHz)",
scalelab = "Coherence",
main = NULL,
scalefontlab = 1, scalecexlab =0.75, axisX = TRUE, axisY = TRUE,
flim = NULL, flimd = NULL,
...)

Arguments

wave1

a first R object

wave2

a second R object

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R objects, by default left channel (1) for each object.

wl

window length for the analysis (even number of points, by default = 512).

ovlp

overlap between two successive windows (in %).

plot

logical, if TRUE plots the continuous coherence function (by default TRUE).

grid

logical, if TRUE plots a y-axis grid (by default TRUE).

scale

logical, if TRUE plots a dB colour scale on the right side of the plot (by default TRUE).

cont

logical, if TRUE overplots contour lines on the plot (by default FALSE).

collevels

a set of levels which are used to partition the amplitude range of the coherence (should be between 0 and 1.

palette

a color palette function to be used to assign colors in the plot, see Details.

contlevels

a set of levels which are used to partition the amplitude range for contour overplot (in dB).

colcont

colour for cont plotting.

colbg

background colour.

colgrid

colour for grid plotting.

colaxis

color of the axes.

collab

color of the labels.

xlab

label of the time axis.

ylab

label of the frequency axis.

scalelab

label fo the amplitude scale.

main

label of the main title.

scalefontlab

font of the amplitude scale label.

scalecexlab

cex of the amplitude scale label.

axisX

logical, if TRUE plots time X-axis (by default TRUE).

axisY

logical, if TRUE plots frequency Y-axis (by default TRUE).

flim

modifications of the frequency Y-axis limits.

flimd

dynamic modifications of the frequency Y-axis limits. New wl and ovlp arguments are applied to increase time/frequency resolution.

...

other contour and oscillo graphical parameters.

Details

Coherence is a frequency domain function computed to show the degree of a relationship between two signals. The value of the coherence function ranges between zero and one, where a value of zero indicates there is no causal relationship between the signals. A value of one indicates the existence of linear frequency response between the two signals. This can be used, for instance, to compare the input and output signals of a system.
Any colour palette can be used. In particular, it is possible to use other palettes coming with seewave: temp.colors, reverse.gray.colors.1, reverse.gray.colors.2, spectro.colors, reverse.terrain.colors, reverse.topo.colors, reverse.cm.colors corresponding to the reverse of terrain.colors, topo.colors, cm.colors.
Use locator to identify points.

Value

This function returns a list of three items:

time

a numeric vector corresponding to the time axis.

freq

a numeric vector corresponding to the frequency axis.

amp

a numeric matrix corresponding to the coherence. Each column corresponds to a coherence function of length wl.

Note

This function is based on spec.pgram, contour and filled.contour. See spectro for graphical changes.

Author(s)

Jerome Sueur [email protected] but this function is mainly based on spec.pgram by Martyn Plummer, Adrian Trapletti and B.D. Ripley

See Also

coh, spectro, spec.pgram.

Examples

wave1<-synth(d=1,f=4000,cf=500)
wave2<-synth(d=1,f=4000,cf=800)
ccoh(wave1,wave2,f=4000)

Cepstrum or real cepstrum

Description

This function returns the cepstrum of a time wave allowing fundamental frequency detection.

Usage

ceps(wave, f, channel = 1, phase = FALSE, wl = 512, at = NULL, from = NULL, to = NULL,
tidentify = FALSE, fidentify = FALSE, col = "black", cex = 1, plot = TRUE,
qlab = "Quefrency (bottom: s, up: Hz)", alab = "Amplitude",
qlim = NULL, alim = NULL, type = "l", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

phase

if TRUE than the phase is taken into account in the computation of the cepstrum.

wl

if at is not null, length of the window for the analysis (even number of points, by defaults = 512).

at

position where to compute the cepstrum (in s).

from

start position where to compute the cepstrum (in s).

to

end position to compute the cepstrum (in s).

tidentify

to identify time values on the plot with the help of a cursor.

fidentify

to identify frequency values on the plot with the help of a cursor.

col

colour of the cepstrum.

cex

pitch size of the cepstrum.

plot

logical, if TRUE plots the cepstrum.

qlab

title of the quefrency axis (in s).

alab

title of the amplitude axis.

qlim

range of quefrency axis.

alim

range of amplitude axis.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

...

other plot graphical parameters.

Details

The cepstrum of a time wave is the inverse Fourier transform of the logarithm of the Fourier transform. The cepstrum of a wave s is then calculated as follows:

C(s)=Re[FFT1(log(FFT(s))]C(s) = Re[FFT^{-1}(\log{(|FFT(s)|)]}


The independent variable of a cepstral graph is called the quefrency. The quefrency is a measure of time, though not in the sense of a signal in the time domain. A correspondence with the frequency domain is obtained by simply computing the reverse of the temporal x coordinate. For instance if a peak appears at 0.005 s, this reveals a frequency peak at 200 Hz (=1/0.005). This explain the two scales plotted when plot is TRUE.
If at, from or to are FALSE then ceps computes the cepstrum of the whole signal.
When using tidentify or tidentify, press ‘stop’ tools bar button to return values in the console.

Value

When plot is FALSE, ceps returns the cesptral profile as a two-column matrix, the first column corresponding to quefrency (x-axis) and the second corresponding to amplitude (y-axis).

Warning

The argument peaks is no more available (version > 1.5.6). See the function fpeaks for peak(s) detection.

Note

Cepstral analysis is mainly used in speech processing. This analysis allows to extract the fundamental frequency, see the examples.
This function is based on fft.

Author(s)

Jerome Sueur [email protected]

References

Oppenheim, A.V. and Schafer, R.W. 2004. From frequency to quefrency: a history of the cepstrum. Signal Processing Magazine IEEE, 21: 95-106.

See Also

cepstro, fund, autoc

Examples

data(sheep)
par(mfrow=c(2,1))
# phase not taken into account
ceps(sheep,f=8000,at=0.4,wl=1024)
# phase taken into account
ceps(sheep,f=8000,at=0.4,wl=1024, phase=TRUE)

2D-cepstrogram of a time wave

Description

This function returns a two-dimension cepstrographic representation of a time wave. The function corresponds to a short-term cepstral transform. An amplitude contour plot can be overlaid.

Usage

cepstro(wave, f, channel = 1, wl = 512, ovlp = 0, plot = TRUE, grid = TRUE,
scale = TRUE, cont = FALSE, collevels = seq(0, 1, 0.01),
palette = reverse.heat.colors, contlevels = seq(0, 1, 0.01),
colcont = "black", colbg="white", colgrid = "black",
colaxis = "black", collab = "black",
xlab = "Time (s)", ylab = "Quefrency (ms)",
scalelab = "Amplitude", main = NULL, scalefontlab = 1, scalecexlab = 0.75,
axisX = TRUE, axisY = TRUE, tlim = NULL, qlim = NULL, ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

if at is not null, length of the window for the analysis (even number of points, by defaults = 512).

ovlp

overlap between two successive windows (in %).

plot

logical, if TRUE plots the cepstrogram (by default TRUE).

grid

logical, if TRUE plots a y-axis grid (by default TRUE).

scale

logical, if TRUE plots a dB colour scale on the right side of the cesptrogram (by default TRUE).

cont

logical, if TRUE overplots contour lines on the cepstrogram (by default FALSE).

collevels

a set of levels which are used to partition the amplitude range of the cepstrogram (in dB).

palette

a color palette function to be used to assign colors in the plot.

contlevels

a set of levels which are used to partition the amplitude range for contour overplot (in dB).

colcont

colour for cont plotting.

colbg

background colour.

colgrid

colour for grid plotting.

colaxis

color of the axes.

collab

color of the labels.

xlab

label of the time axis.

ylab

label of the quefrency axis.

main

label of the main title.

scalelab

amplitude scale label.

scalefontlab

font of the amplitude scale label.

scalecexlab

cex of the amplitude scale label.

axisX

if TRUE plots time X-axis (by default TRUE).

axisY

if TRUE plots frequency Y-axis (by default TRUE).

tlim

modifications of the time X-axis limits.

qlim

modifications of the quefrency Y-axis limits (in ms).

...

other contour graphical parameters.

Details

It is unfortunately not possible to turn the y-axis to a frequency scale.
See spectro for the use of the graphical arguments.

Value

This function returns a list of three items:

time

a numeric vector corresponding to the time axis.

freq

a numeric vector corresponding to the quefrency axis.

amp

a numeric matrix corresponding to the the successive cepstral profiles computed along time.

Note

This function is based on ceps.

Author(s)

Jerome Sueur [email protected].

References

Oppenheim, A.V. and Schafer, R.W. 2004. From frequency to quefrency: a history of the cepstrum. Signal Processing Magazine IEEE, 21: 95-106.

See Also

ceps, fund, autoc

Examples

data(sheep)
sheepc <- cutw(sheep, f=8000, from = 0.19, to = 2.3)
cepstro(sheepc,f=8000)

Coherence between two time waves

Description

This function returns the frequency coherence between two time waves.

Usage

coh(wave1, wave2, f, channel=c(1,1), plot =TRUE, xlab = "Frequency (kHz)",
ylab = "Coherence", xlim = c(0,f/2000), type = "l",...)

Arguments

wave1

a first R object.

wave2

a second R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R objects, by default left channel (1) for each object.

plot

logical, if TRUE plots the continuous coherence function (by default TRUE).

xlab

title of the frequency X-axis.

ylab

title of the coherence Y-axis.

xlim

range of frequency X-axis.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

...

other plot graphical parameters.

Details

Coherence is a frequency domain function computed to show the degree of a relationship between two signals. The value of the coherence function ranges between zero and one, where a value of zero indicates there is no causal relationship between the signals. A value of one indicates the existence of linear frequency response between the two signals. This can be used, for instance, to compare the input and output signals of a system.

Value

When plot is FALSE, this coh returns a two-column matrix, the first column being the frequency axis in kHz (x-axis) and the second column being the coherence (y-axis).

Note

This function is based on spec.pgram.

Author(s)

Jerome Sueur [email protected] but this function is based on spec.pgram by Martyn Plummer, Adrian Trapletti and B.D. Ripley.

See Also

ccoh, spectro, spec.pgram.

Examples

wave1<-synth(d=1,f=4000,cf=500)
wave2<-synth(d=1,f=4000,cf=800)
coh(wave1,wave2,f=4000)

Comb filter

Description

This function processes a feedforward comb filter and plots a spectrogram of the filtered wave asso- ciated with the frequency response of the filter.

Usage

combfilter(wave, f, channel = 1, alpha, K, units = c("samples", "seconds"),
plot = FALSE, output = "matrix", ...)

Arguments

wave

an R object

f

sampling frequency (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

alpha

a numeric vector of length 1 for the scaling factor. See Details.

K

a numeric vector of lenght 1 for the delay length, in units. See Details.

units

units in which K is given, the default is 'samples' but can be set to 'seconds'.

plot

a logical, if TRUE plots the spectrogram of the filtered wave and the frequency response of the comb filter.

output

character string, the class of the object to return, either 'matrix', 'Wave', 'Sample', 'audioSample' or 'ts'.

...

other arguments to be passed to spectro except scale and osc that are set by default to FALSE.

Details

A comb filter consists in adding a delayed version of a signal to itself resulting in constructive and destructive interference. The feedforward version of a comb filter can be written following:

y(n)=x(n)+α×x(nK)y(n) = x(n) + \alpha \times x(n - K)

where alpha is the scaling factor and K the delay length. The frequency response of the filter is obtained with:

H(f)=(1+α2)+2×cos(ωK)H(f) = \sqrt{(1+\alpha^2)+2 \times \cos(\omega K)}

The frequency response is periodic. The depth of the cycles is controlled with alpha and the number of cycles with K.

Value

A new wave is returned. The class of the returned object is set with the argument output.

Note

Setting K to high values may generate unwanted results.
The feedback form of the combfilter is not implemented yet.

Author(s)

Jerome Sueur

See Also

combfilter, fir, squarefilter, drawfilter, ffilter, bwfilter

Examples

## Not run: 
f <- 44100
## chirp
s1 <- synth(f=f, cf=1, d=2, fm=c(0,0,f/2,0,0), out="Wave")
combfilter(s1, alpha=1, K=50, plot=TRUE)
## harmonic sound
s2 <- synth(f=f, d=2, cf=600, harmonics=rep(1, 35), output="Wave")
combfilter(s2, alpha=1, K=10, plot=TRUE)
## noise, units in seconds
s3 <- noisew(d=2, f=44100, out="Wave")
combfilter(s3, alpha=0.5, K=1e-4, units="seconds", plot=TRUE)

## End(Not run)

Convert sound pressure level in other units

Description

This function converts sound pressure level (in dB) in sound power (Watt), intensity (Watt/m2) and pressure (Pa). By default, these conversions are applied to air-borne sound.

Usage

convSPL(x, d = 1, Iref = 10^-12, pref = 2*10^-5)

Arguments

x

a numeric vector or a matrix describind SPL values (in dB).

d

the distance from the sound source where SPL values have been measured (in meter) (by default = 1m)

Iref

reference intensity (in Watt/m2) (by default = 10^-12)

pref

reference pressure (in Pa) (by default = 2*10^-5)

Value

convSPL returns a list containing three components:

P

data converted in sound power (in Watt).

I

data converted in sound intensity (in Watt/m2).

p

data converted in sound pressure (in Pa).

Note

Iref and pref correspond to a 1 kHz sound in air.

Author(s)

Jerome Sueur [email protected]

References

Hartmann, W. M. 1998 Signals, sound and sensation. New York: Springer.

See Also

moredB, dBweight, attenuation

Examples

# conversion of two SPL measurements taken at 0.5 m from the source
convSPL(c(80,85),d=0.5)

Cross-correlation between two time wave envelopes

Description

This function tests the similarity between two time wave envelopes by returning their maximal correlation and the time shift related to it.

Usage

corenv(wave1, wave2, f, channel=c(1,1), envt="hil", msmooth = NULL, ksmooth = NULL,
ssmooth = NULL, plot = TRUE, plotval = TRUE,
method = "spearman", col = "black", colval = "red",
cexval = 1, fontval = 1, xlab = "Time (s)",
ylab = "Coefficient of correlation (r)", type = "l", pb = FALSE, ...)

Arguments

wave1

a first R object.

wave2

a second R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R objects, by default left channel (1) for each object.

envt

the type of envelope to be used: either "abs" for absolute amplitude envelope or "hil" for Hilbert amplitude envelope. See env.

msmooth

a vector of length 2 to smooth the amplitude envelope with a mean sliding window. The first component is the window length (in number of points). The second component is the overlap between successive windows (in %). See env.

ksmooth

kernel smooth via kernel. See env.

ssmooth

sum smooth. See env.

plot

logical, if TRUE plots r values against frequency shift (by default TRUE).

plotval

logical, if TRUE adds to the plot maximum r value and frequency offset (by default TRUE).

method

a character string indicating which correlation coefficient is to be computed ("pearson", "spearman", or "kendall") (see cor).

col

colour of r values.

colval

colour of r max and frequency offset values.

cexval

character size of r max and frequency offset values.

fontval

font of r max and frequency offset values.

xlab

title of the frequency axis.

ylab

title of the r axis.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

pb

if TRUE returns a text progress bar in the console.

...

other plot graphical parameters.

Details

Successive correlations between the envelopes of wave1 and wave2 are computed when regularly sliding forward and backward wave2 along wave1.
The maximal correlation is obtained at a particular shift (time offset). This shift may be positive or negative.
The higher smooth is set up, the faster will be the computation but less precise the results will be.
The corresponding p value, obtained with cor.test, is plotted. Inverting wave1 and wave2 may give slight different results.

Value

If plot is FALSE, corenv returns a list containing four components:

r

a two-column matrix, the first colum corresponding to the time shift (frequency x-axis) and the second column corresponding to the successive r correlation values between env1 and env2 (correlation y-axis).

rmax

the maximum correlation value between x and y.

p

the p value corresponding to rmax.

t

the time offset corresponding to rmax.

Author(s)

Jerome Sueur

See Also

env,corspec,covspectro, cor,cor.test.

Examples

## Not run: 
data(orni)
# cross-correlation between two echemes of a cicada song
wave1<-cutw(orni,f=22050,from=0.3,to=0.4,plot=FALSE)
wave2<-cutw(orni,f=22050,from=0.58,to=0.68,plot=FALSE)
corenv(wave1,wave2,f=22050)

## End(Not run)

Cross-correlation between two frequency spectra

Description

This function tests the similarity between two frequency spectra by returning their maximal correlation and the frequency shift related to it.

Usage

corspec(spec1, spec2, f = NULL, mel = FALSE, plot = TRUE, plotval = TRUE,
method = "spearman", col = "black", colval = "red",
cexval = 1, fontval = 1, xlab = NULL,
ylab = "Coefficient of correlation (r)", type="l",...)

Arguments

spec1

a first data set resulting of a spectral analysis obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

spec2

a first data set resulting of a spectral analysis obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

f

sampling frequency of waves used to obtain spec1 and spec2 (in Hz). Not necessary if spec1 and/or spec2 is a two columns matrix obtained with spec or meanspec.

mel

a logical, if TRUE the (htk-)mel scale is used.

plot

logical, if TRUE plots r values against frequency shift (by default TRUE).

plotval

logical, if TRUE adds to the plot maximum r value and frequency offset (by default TRUE).

method

a character string indicating which correlation coefficient is to be computed ("pearson", "spearman", or "kendall") (see cor).

col

colour of r values.

colval

colour of r max and frequency offset values.

cexval

character size of r max and frequency offset values.

fontval

font of r max and frequency offset values.

xlab

title of the frequency axis.

ylab

title of the r axis.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

...

other plot graphical parameters.

Details

It is important not to have data in dB.
Successive correlations between spec1 and spec2 are computed when regularly shifting spec2 towards lower or higher frequencies.
The maximal correlation is obtained at a particular shift (frequency offset). This shift may be positive or negative.
The corresponding p value, obtained with cor.test, is plotted.
Inverting spec1 and spec2 may give slight different results, see examples.

Value

If plot is FALSE, corspec returns a list containing four components:

r

a two-column matrix, the first colum corresponding to the frequency shift (frequency x-axis) and the second column corresponding to the successive r correlation values between spec1 and spec2 (correlation y-axis).

rmax

the maximum correlation value between spec1 and spec2.

p

the p value corresponding to rmax.

f

the frequency offset corresponding to rmax.

Author(s)

Jerome Sueur, improved by Laurent Lellouch

References

Hopp, S. L., Owren, M. J. and Evans, C. S. (Eds) 1998. Animal acoustic communication. Springer, Berlin, Heidelberg.

See Also

spec, meanspec, corspec, covspectro, cor, cor.test.

Examples

## Not run: data(tico)
## compare the two first notes spectra
a<-spec(tico,f=22050,wl=512,at=0.2,plot=FALSE)
c<-spec(tico,f=22050,wl=512,at=1.1,plot=FALSE)
op<-par(mfrow=c(2,1), mar=c(4.5,4,3,1))
spec(tico,f=22050,at=0.2,col="blue")
par(new=TRUE)
spec(tico,f=22050,at=1.1,col="green")
legend(x=8,y=0.5,c("Note A", "Note C"),lty=1,col=c("blue","green"),bty="o")
par(mar=c(5,4,2,1))
corspec(a,c, ylim=c(-0.25,0.8),xaxs="i",yaxs="i",las=1)
par(op)
## different correlation methods give different results...
op<-par(mfrow=c(3,1))
corspec(a,c,xaxs="i",las=1, ylim=c(-0.25,0.8))
title("spearmann correlation (by default)")
corspec(a,c,xaxs="i",las=1,ylim=c(0,1),method="pearson")
title("pearson correlation")
corspec(a,c,xaxs="i",las=1,ylim=c(-0.23,0.5),method="kendall")
title("kendall correlation")
par(op)
## inverting x and y does not give exactly similar results
op<-par(mfrow=c(2,1),mar=c(2,4,3,1))
corspec(a,c)
corspec(c,a)
par(op)
## mel scale
require(tuneR)
data(orni)
orni.mel <- melfcc(orni, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
orni.mel.mean <- apply(orni.mel$aspectrum, MARGIN=2, FUN=mean)
tico.mel <- melfcc(tico, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
tico.mel.mean <- apply(tico.mel$aspectrum, MARGIN=2, FUN=mean)
corspec(orni.mel.mean, tico.mel.mean, f=22050, mel=TRUE, plot=TRUE)

## End(Not run)

Covariance between two spectrograms

Description

This function tests the similarity between two spectrograms by returning their maximal covariance and the time shift related to it.

Usage

covspectro(wave1, wave2, f, channel = c(1,1), wl = 512, wn = "hanning", n,
plot = TRUE, plotval = TRUE,
method = "spearman", col = "black", colval = "red", cexval = 1,
fontval = 1, xlab = "Time (s)",
ylab = "Normalised covariance (cov)", type = "l", pb = FALSE, ...)

Arguments

wave1

a first R object.

wave2

a second R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R objects, by default left channel (1) for each object.

wl

length of the window for the analysis (even number of points, by default = 512).

wn

window name, see ftwindow (by default "hanning").

n

number of covariances computed between wave1 and wave2 when sliding wave2 along wave1.

plot

logical, if TRUE plots r values against frequency shift (by default TRUE).

plotval

logical, if TRUE adds to the plot maximum R value and frequency offset (by default TRUE).

method

a character string indicating which correlation coefficient is to be computed ("pearson", "spearman", or "kendall") (see cor).

col

colour of r values.

colval

colour of r max and frequency offset values.

cexval

character size of r max and frequency offset values.

fontval

font of r max and frequency offset values.

xlab

title of the frequency axis.

ylab

title of the r axis.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

pb

if TRUE returns a text progress bar in the console.

...

other plot graphical parameters.

Details

Successive covariances between the spectrogram of wave1 and the spectrogram of wave2 are computed when regularly sliding forward and backward wave2 along wave1.
The maximal covariance is obtained at a particular shift (time offset). This shift may be positive or negative.
n sets in how many steps wave2 will be slided along wave1. Time process can be then decreased by setting low n value.
Inverting wave1 and wave2 may give slight different results.

Value

If plot is FALSE, covspectro returns a list containing three components:

cov

the successive covariance values between wave1 and wave2.

covmax

the maximum covariance between wave1 and wave2.

t

the time offset corresponding to cov.

Author(s)

Jerome Sueur [email protected]

References

Hopp, S. L., Owren, M. J. and Evans, C. S. (Eds) 1998. Animal acoustic communication. Springer, Berlin, Heidelberg.

See Also

corspec, corenv, spectro, cor,

Examples

# covariance between two notes of a birdsong
## Not run: 
data(tico)
note1<-cutw(tico, f=22050, from=0.5, to=0.9)
note2<-cutw(tico, f=22050, from=0.9, to=1.3)
covspectro(note1,note2,f=22050,n=37)

## End(Not run)

Crest factor and visualization

Description

This function returns the crest factor and localizes the different crest(s).

Usage

crest(wave, f, channel = 1, plot = FALSE, col = 2, cex = 3, symbol = "*", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

plot

if TRUE plots the oscillogram of wave and indicates the location of the crest(s)

col

color of the symbol indicating the localisation of the crest(s)

cex

symbol magnification

symbol

symbol indicating the localisation of the crest(s)

...

other

Details

The crest factor of a time series s is calculated according to:

C=max(s)rms(s)C = \frac{max(s)}{rms(s)}

with rms the root-mean-square (see rms).

Value

The function returns a list of three items

C

crest factor

val

value of the crest(s)

loc

location of the crest(s)

Note

There might be several crests (maxima) along the time wave but there is a single crest factor.

Author(s)

Jerome Sueur [email protected]

References

Hartmann, W. M. 1998 Signals, sound and sensation. New York: Springer.

See Also

oscillo, rms

Examples

data(tico)
crest(tico, f=22050)
# see the crest location and change the default graphical parameters
crest(tico, f=22050, plot=TRUE, sym="-")

Continuous spectral entropy

Description

This function computes the continuous spectral entropy (H) of a time wave.

Usage

csh(wave, f, channel = 1, wl = 512, wn = "hanning", ovlp = 0,
fftw = FALSE, threshold = NULL,
plot = TRUE, xlab = "Times (s)", ylab = "Spectral Entropy",
ylim = c(0, 1.1), type = "l", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

if at is not null, length of the window for the analysis (even number of points, by default = 512).

wn

window name, see ftwindow (by default "hanning").

ovlp

overlap between two successive windows (in %).

fftw

if TRUE calls the function FFT of the library fftw. See Notes of the spectro.

threshold

amplitude threshold for signal detection (in %).

plot

logical, if TRUE plots the spectral entropy against time (by default TRUE).

xlab

title of the x axis.

ylab

title of the y axis.

ylim

the range of y values.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

...

other plot graphical parameters.

Details

See sh for computing method.

Value

When plot is FALSE, csh returns a two-column matrix, the first column being time in seconds (x-axis) and the second column being the spectral entropy (y-axis) computed along time.
NA corresponds to pause sections in wave (see threshold).

Note

The spectral entropy of a noisy signal will tend towards 1 whereas the spectral entropy of a pure tone signal will tend towards 0.

Author(s)

Jerome Sueur [email protected]

References

Toh, A. M., Togneri, R. & Nordholm, S. 2005 Spectral entropy as speech features for speech recognition. Proceedings of PEECS, pp. 60-65.

See Also

sh, th

Examples

data(orni)
csh(orni,f=22050,wl=512,ovlp=50)
# using the threshold argument can lead to some edge effets
# here sh=1 at the end of echemes
csh(orni,f=22050,wl=512,ovlp=50,threshold=5)

Cut a frequency spectrum

Description

This function can be used to select (cut) a specific part of a frequency spectrum.

Usage

cutspec(spec, f = NULL, flim, mel = FALSE, norm = FALSE, PMF = FALSE)

Arguments

spec

a vector or a two-column matrix set resulting of a spectral analysis. This can be the value obtained with spec or meanspec.

f

sampling frequency of spec (in Hz).

flim

a vector of length 2 to specify the new frequency range (in kHz).

mel

a logical, if TRUE the (htk-)mel scale is used.

norm

a logical, if TRUE the spectrum returned is normalised between 0 and 1.

PMF

a logical, if TRUE the spectrum returned is a probability mass function.

Value

A new spectrum is returned. The class of the returned object is the one of the input object (spec)

Note

The sampling frequency f is not necessary if spec has been obtained with either spec or meanspec.
This function can be used before calling analysis function like sh or sfm. See examples.

Author(s)

Jerome Sueur, improved by Laurent Lellouch

See Also

spec, meanspec

Examples

data(orni)
a <- meanspec(orni,f=22050,plot=FALSE)
b <- cutspec(a,flim=c(4,8))
## quick check with a plot
plot(b,type="l")
## effects on spectral entropy
sfm(a)
sfm(b)
## mel scale
require(tuneR)
mel <- melfcc(orni, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
melspec.mean <- apply(mel$aspectrum, MARGIN=2, FUN=mean)
c <- cutspec(melspec.mean, f=22050, flim=c(4000,8000), mel=TRUE)

Cut a section of a time wave

Description

This function selects and cuts a section of data describing a time wave. Original and cut sections can be plotted as oscillograms for comparison.

Usage

cutw(wave, f, channel=1, from = NULL, to = NULL, choose = FALSE,
plot = FALSE, marks = TRUE, output="matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

from

start mark (in s).

to

end mark (in s).

choose

logical, if TRUE start (=from) and end (=to) points can be graphically chosen with a cursor on the oscillogram.

plot

logical, if TRUE returns an oscillographic plot of original and cut sections (by default FALSE).

marks

logical, if TRUE shows the start and end mark on the plot (by default TRUE).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Details

If plot is TRUE returns a two-frame plot with both original and cut sections.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur

See Also

oscillo, addsilw,deletew, fadew,mutew,pastew,revw, zapsilw

Examples

# a 0.4 s section in a bird song
data(tico)
a<-cutw(tico,f=22050,from=0.5,to=0.9)
oscillo(a,22050)
# a direct way to see what has been cut
cutw(tico,f=22050,from=0.5,to=0.9,plot=TRUE)

dB colour scale for a spectrogram display

Description

This function displays a vertical or horizontal dB colour scale to be used with spectro plots.

Usage

dBscale(collevels, palette = spectro.colors, side = 4,
textlab = "Amplitude\n(dB)", cexlab = 0.75,
fontlab = 1, collab = "black", colaxis = "black",...)

Arguments

collevels

a set of levels which are used to partition the amplitude range of the spectrogram (in dB).

palette

a color palette function to be used to assign colors in the plot, see note.

side

side of the axis.

textlab

text of the label.

cexlab

character size of the label.

fontlab

font of the label.

collab

colour of the label.

colaxis

colour of the axis.

...

other axis arguments.

Note

This function, based on filled.contour by Ross Ihaka, is not supposed to be used by itself but as a legend of spectro.
Any colour palette can be used. In particular, it is possible to use other palettes coming with seewave: rev.gray.colors.1, rev.gray.colors.2, rev.heat.colors, rev.terrain.colors, rev.topo.colors, rev.cm.colors corresponding to the reverse of heat.colors, terrain.colors, topo.colors, cm.colors.

Author(s)

Jerome Sueur [email protected] and Caroline Simonis [email protected].

See Also

spectro.

Examples

data(pellucens)
# place the scale on the left and not on the right as spectro() does
def.par <- par(no.readonly = TRUE)
layout(matrix(c(1, 2), nc = 2), widths = c(1, 5))
par(mar=c(5,3,4,2))
dBscale(collevels=seq(-30,0,1),side=2)
par(mar=c(5,4,4,2))
spectro(pellucens, f=22050,wl=512,scale=FALSE)
par(def.par)
# place the scale on the top and not on the right as spectro() does
def.par <- par(no.readonly = TRUE)
layout(matrix(c(0,1,2,2), nc = 2, byrow=TRUE),widths=c(1,2),heights=(c(1,5.5)))
par(mar=c(0.5,3,4,2))
dBscale(collevels=seq(-30,0,1), textlab = "",side=3)
mtext("Amplitude (dB)",side=2,line = 1,at=0.6,cex=0.75)
par(mar=c(5,4,0.5,2))
spectro(pellucens, f=22050,wl=512,scale=FALSE)
par(def.par)

dB weightings

Description

This function returns the four most common dB weightings.

Usage

dBweight(f, dBref = NULL)

Arguments

f

frequency (in Hz).

dBref

dB reference level (by default NULL).

Details

By default, the function returns four weightings. When dBref is not NULL then the function returns the conversion from a dB reference level to four dB weighting levels.

Value

dBweight returns a list of five items corresponding to five dB weightings.

A

dB (A)

B

dB (B)

C

dB (C)

D

dB (D)

ITU

dB ITU-R 468

Note

The transfer equations used here come from Wipipedia but they were originally coming from the appendix of an international standard on the design performance of sound level meters IEC 651:1979 (Neil Glenister, pers. com.).

Author(s)

Jerome Sueur [email protected], Zev Ross, and Andrey Anikin

References

https://en.wikipedia.org/wiki/A-weighting, https://en.wikipedia.org/wiki/ITU-R_468_noise_weighting

See Also

convSPL, moredB

Examples

# weight for a 50 Hz frequency
dBweight(f=50)
# A weight for the 1/3 Octave centre frequencies.
dBweight(f=c(20,25,31.5,40,50,63,80,100,125,160,200,250,
315,400,500,630,800,1000,1500,
1600,2000,2500,3150,4000,5000,
6300,8000,10000,12500,16000,20000))$A
# correction for a 50 Hz sound emitted at 100 dB
dBweight(f=50, dB=100)
# weighting curves plot
f <- seq(10,20000,by=10)
par(las=1)
plot(f, dBweight(f)$A, type="n", log="x",
xlim=c(10,10^5),ylim=c(-80,20),xlab="",ylab="",xaxt="n",yaxt="n")
abline(v=c(seq(10,100,by=10),seq(100,1000,by=100),
seq(1000,10000,by=1000),seq(10000,100000,by=10000),
c(100,1000,10000,100000)),col="lightgrey",lty=2)
abline(v=c(100,1000,10000,100000),col="grey")
abline(h=seq(-80, 20, 20),col="grey")
par(new=TRUE)
plot(f, dBweight(f)$A, type="l", log="x",
xlab="Frequency (Hz)", ylab="dB",lwd=2, col="blue", xlim=c(10,10^5),ylim=c(-80,20))
title(main="Acoustic weighting curves (10 Hz - 20 kHz)")
lines(x=f, y=dBweight(f)$B, col="green",lwd=2)
lines(x=f, y=dBweight(f)$C, col="red",lwd=2)
lines(x=f, y=dBweight(f)$D, col="black",lwd=2)
legend("bottomright",legend=c("dB(A)","dB(B)","dB(C)","dB(D)"),
lwd=2,col=c("blue","green","red","black"),bty="o",bg="white")

Delete a section of a time wave

Description

This function selects and delete a section of data describing a time wave. Original section and section after deletion can be plotted as oscillograms for comparison.

Usage

deletew(wave, f, channel = 1, from = NULL, to = NULL, choose = FALSE, plot = FALSE,
marks = TRUE, output = "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

from

start position (in s).

to

end position (in s).

choose

logical, if TRUE start (=from) and end (=to) points can be graphically chosen with a cursor on the oscillogram.

plot

logical, if TRUE returns an oscillographic plot of original and cut sections (by default FALSE).

marks

logical, if TRUE shows the start and end mark on the plot (by default TRUE).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Details

If plot is TRUE returns a two-frame plot with both original and resulting sections.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected]

See Also

oscillo, addsilw,cutw, fadew, mutew, pastew, revw, zapsilw

Examples

# deletion a 0.4 s section in a bird song
data(tico)
a<-deletew(tico,f=22050,from=0.5,to=0.9)
oscillo(a,22050)
# a direct way to see what has been cut
deletew(tico,f=22050,from=0.5,to=0.9,plot=TRUE)

Dominant frequency of a time wave

Description

This function gives the dominant frequency (i. e. the frequency of highest amplitude) of a time wave.

Usage

dfreq(wave, f, channel = 1, wl = 512, wn = "hanning", ovlp = 0, fftw=  FALSE, at =
NULL, tlim = NULL, threshold = NULL, bandpass = NULL, clip = NULL,
plot = TRUE, xlab = "Times (s)", ylab = "Frequency (kHz)",
ylim = c(0, f/2000), ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

length of the window for the analysis (even number of points, by default = 512).

wn

window name, see ftwindow (by default "hanning").

ovlp

overlap between two successive analysis windows (in % ).

fftw

if TRUE calls the function FFT of the library fftw. See Notes of the spectro.

at

time position where the dominant frequency has to be computed (in s.).

tlim

modifications of the time X-axis limits.

threshold

amplitude threshold for signal detection (in % ).

bandpass

a numeric vector of length two, giving the lower and upper limits of a frequency bandpass filter (in Hz).

clip

a numeric value to select dominant frequency values according to their amplitude in reference to a maximal value of 1 for the whole signal (has to be >0 & < 1).

plot

logical, if TRUE plots the dominant frequency against time (by default TRUE).

xlab

title of the x axis.

ylab

title of the y axis.

ylim

the range of y values.

...

other plot graphical parameters.

Value

When plot is FALSE, dfreq returns a two-column matrix, the first column corresponding to time in seconds (x-axis) and the second column corresponding to to dominant frequency in kHz (y-axis).
NA corresponds to pause sections in wave (see threshold).

Note

This function is based on fft.

Author(s)

Jerome Sueur [email protected]

See Also

spec, meanspec,spectro.

Examples

data(tico)
f <- 22050
# default
dfreq(tico,f)
# using the amplitude threshold and changing the graphical output
dfreq(tico, f, ovlp=50,threshold=5, type="l", col=2)
# using 'at' argument for specific positions along the time axis
dfreq(tico, f, at=c(0.25, 0.75, 1.2, 1.6))
dfreq(tico, f, at=seq(0.5, 1.4, by=0.005), threshold=5)
# a specific number of measures on a single note
dfreq(tico, f, at=seq(0.5, 0.9, len=100), threshold=5, xlim=c(0.5,0.9))
# overlap on spectrogram
# and use of 'clip' argument to better track the dominant frequency
# in noisy conditions
op <- par()
ticon <- tico@left/max(tico@left) + noisew(d=length(tico@left)/f, f)
spectro(ticon, f)
res <- dfreq(ticon, f, clip=0.3, plot=FALSE)
points(res, col=2, pch =13)
par(op)

Difference between two cumulative frequency spectra

Description

This function compares two distributions (e.g. two frequency spectra) by computing the difference between two cumulative frequency spectra

Usage

diffcumspec(spec1, spec2, f = NULL, mel = FALSE, 
plot = FALSE, type = "l", lty = c(1, 2), col = c(2, 4, 8),
flab = NULL, alab = "Cumulated amplitude",
flim = NULL, alim = NULL,
title = TRUE, legend = TRUE, ...)

Arguments

spec1

any distribution, especially a spectrum obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

spec2

any distribution, especially a spectrum obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

f

sampling frequency of waves used to obtain spec1 and spec2 (in Hz). Not necessary if spec1 and/or spec2 is a two columns matrix obtained with spec or meanspec.

mel

a logical, if TRUE the (htk-)mel scale is used.

plot

logical, if TRUE plots both cumulative spectra and their distance.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

col

a vector of length 3 for the colour of spec1, spec2, and the difference between each of them.

lty

a vector of length 2 for the line type of spec1 and spec2 if type="l".

flab

title of the frequency axis.

alab

title of the amplitude axis.

flim

the range of frequency values.

alim

range of amplitude axis.

title

logical, if TRUE, adds a title with D and F values.

legend

logical, if TRUE adds a legend to the plot.

...

other plot graphical parameters.

Details

Both spectra are transformed into cumulative distribution functions (CDF).
Spectral difference is then computed according to:

Dcf(x,y)=i=1nXiYin,withwithXandYthespectrumCDFs,andD[0,1].D_{cf}(x, y) = \frac{\sum_{i=1}^{n}|X_{i} - Y_{i}|}{n}, with with X and Y the spectrum CDFs, and D \in [0,1].

Value

A numeric vector of length 1 returning the difference between the two spectra. No unit.

Note

This metric is sensitive not only to the spectral overlap between but also to the mean frequential distance between the different frequency peaks.

Author(s)

Laurent Lellouch, Jerome Sueur

References

Lellouch L, Pavoine S, Jiguet F, Glotin H, Sueur J (2014) Monitoring temporal change of bird communities with dissimilarity acoustic indices. Methods in Ecology and Evolution, in press.

See Also

kl.dist, ks.dist, simspec, diffspec, logspec.dist, itakura.dist

Examples

## Hz scale
data(tico)
data(orni)
orni.hz <- meanspec(orni, plot=FALSE)
tico.hz <- meanspec(tico, plot=FALSE)
diffcumspec(orni.hz, tico.hz, plot=TRUE)
## mel scale
require(tuneR)
orni.mel <- melfcc(orni, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
orni.mel.mean <- apply(orni.mel$aspectrum, MARGIN=2, FUN=mean)
tico.mel <- melfcc(tico, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
tico.mel.mean <- apply(tico.mel$aspectrum, MARGIN=2, FUN=mean)
diffcumspec(orni.mel.mean, tico.mel.mean, f=22050, mel=TRUE, plot=TRUE)

Difference between two amplitude envelopes

Description

This function estimates the surface difference between two amplitude envelopes.

Usage

diffenv(wave1, wave2, f, channel = c(1,1), envt = "hil", msmooth = NULL, ksmooth = NULL,
plot = FALSE, lty1 = 1, lty2 = 2, col1 = 2, col2 = 4, cold = 8,
xlab = "Time (s)", ylab = "Amplitude", ylim = NULL, legend = TRUE, ...)

Arguments

wave1

a first R object.

wave2

a second R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R objects, by default left channel (1) for each object.

envt

the type of envelope to be used: either "abs" for absolute amplitude envelope or "hil" for Hilbert amplitude envelope. See env.

msmooth

a vector of length 2 to smooth the amplitude envelope with a mean sliding window. The first component is the window length (in number of points). The second component is the overlap between successive windows (in %). See env.

ksmooth

kernel smooth via kernel. See env.

plot

logical, if TRUE plots both envelopes and their surface difference (by default FALSE).

lty1

line type of the first envelope (envelope of wave1).

lty2

line type of the second envelope (envelope of wave2).

col1

colour of the first envelope (envelope of wave1).

col2

colour of the second envelope (envelope of wave2).

cold

colour of the surface difference.

xlab

title of the time axis.

ylab

title of the amplitude axis.

ylim

range of amplitude axis.

legend

logical, if TRUE adds a legend to the plot.

...

other plot graphical parameters.

Details

D is a Manhattan distance (l1 norm).
Envelopes of both waves are first transformed as probability mass functions (PMF).
Envelope difference is then computed according to:

D=env1env22,withD[0,1].D = \frac{\sum{|env1-env2|}}{2}, with D \in [0,1].

Value

The difference is returned. This value is without unit. When plot is TRUE, both envelopes and their difference surface are plotted on the same graph.

Note

This method can be used as a relative distance estimation between different envelopes.

Author(s)

Jerome Sueur [email protected].

References

Sueur, J., Pavoine, S., Hamerlynck, O. & Duvail, S. (2008) - Rapid acoustic survey for biodiversity appraisal. PLoS ONE, 3(12): e4065.

See Also

env, corenv, diffspec, diffwave

Examples

data(tico) ; tico <- tico@left
data(orni) ; orni <- orni@left
# selection in tico of two waves with similar duration
tico2<-tico[1:length(orni)]
diffenv(tico2,orni,f=22050,plot=TRUE)
# smoothing the envelope gives a better graph but slightly changes the result
diffenv(tico2,orni,f=22050,msmooth=c(20,0),plot=TRUE)

Difference between two frequency spectra

Description

This function estimates the surface difference between two frequency spectra.

Usage

diffspec(spec1, spec2, f = NULL, mel = FALSE,
plot = FALSE, type="l", 
lty=c(1, 2), col =c(2, 4, 8),
flab = NULL, alab = "Amplitude",
flim = NULL, alim = NULL, title = TRUE, legend = TRUE, ...)

Arguments

spec1

a first data set resulting of a spectral analysis obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

spec2

a first data set resulting of a spectral analysis obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

f

sampling frequency of waves used to obtain spec1 and spec2 (in Hz). Not necessary if spec1 and/or spec2 is a two-column matrix obtained with spec or meanspec.

mel

a logical, if TRUE the (htk-)mel scale is used.

plot

logical, if TRUE plots both spectra and their surface difference (by default FALSE).

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

lty

a vector of length 2 for the line type of spec1 and spec2 if type="l".

col

a vector of length 3 for the colour of spec1, spec2, and the surface difference between each of them.

flab

title of the frequency axis.

alab

title of the amplitude axis.

flim

the range of frequency values.

alim

range of amplitude axis.

title

logical, if TRUE, adds a title with D value.

legend

logical, if TRUE adds a legend to the plot.

...

other plot graphical parameters.

Details

D is a Manhattan distance (l1 norm).
Both spectra are first transformed as probability mass functions (PMF).
Spectral difference is then computed according to:

D=spec1spec22,withD[0,1].D = \frac{\sum{|spec1-spec2|}}{2}, with D \in [0,1].

, with 0 < D < 1.

Value

The difference is returned. This value is without unit. When plot is TRUE, both spectra and their difference surface are plotted on the same graph.

Note

This method can be used as a relative distance estimation between different spectra.
The dB value obtained can be very different from the one visually estimated when looking at the graph (plot=TRUE).

Author(s)

Jerome Sueur, Sandrine Pavoine and Laurent Lellouch

References

Sueur, J., Pavoine, S., Hamerlynck, O. and Duvail, S. (2008). Rapid acoustic survey for biodiversity appraisal. PLoS One, 3(12): e4065.

See Also

spec, meanspec, corspec, simspec, diffcumspec, diffenv, kl.dist, ks.dist, logspec.dist, itakura.dist

Examples

a <- noisew(f=8000,d=1)
b <- synth(f=8000,d=1,cf=2000)
c <- synth(f=8000,d=1,cf=1000)
d <- noisew(f=8000,d=1)
speca <- spec(a,f=8000,wl=512,at=0.5,plot=FALSE)
specb <- spec(b,f=8000,wl=512,at=0.5,plot=FALSE)
specc <- spec(c,f=8000,wl=512,at=0.5,plot=FALSE)
specd <- spec(d,f=8000,wl=512,at=0.5,plot=FALSE)
diffspec(speca,speca,f=8000)
#[1] 0 => similar spectra of course !
diffspec(speca,specb)
diffspec(speca,specc,plot=TRUE)
diffspec(specb,specc,plot=TRUE)
diffspec(speca,specd,plot=TRUE)
## mel scale
require(tuneR)
data(orni)
data(tico)
orni.mel <- melfcc(orni, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
orni.mel.mean <- apply(orni.mel$aspectrum, MARGIN=2, FUN=mean)
tico.mel <- melfcc(tico, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
tico.mel.mean <- apply(tico.mel$aspectrum, MARGIN=2, FUN=mean)
diffspec(orni.mel.mean, tico.mel.mean, f=22050, mel=TRUE, plot=TRUE)

Difference between two time waves

Description

This function estimates the difference between two waves by computing the product between envelope surface difference and frequency surface difference.

Usage

diffwave(wave1, wave2, f, channel = c(1,1), wl = 512, envt = "hil",
msmooth = NULL, ksmooth = NULL)

Arguments

wave1

a first R object.

wave2

a second R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R objects, by default left channel (1) for each object.

wl

window length for spectral analysis (even number of points).

envt

the type of envelope to be used: either "abs" for absolute amplitude envelope or "hil" for Hilbert amplitude envelope. See env.

msmooth

a vector of length 2 to smooth the amplitude envelope with a mean sliding window. The first component is the window length (in number of points). The second component is the overlap between successive windows (in %). See env.

ksmooth

kernel smooth via kernel. See env.

Details

D is a Manhattan distance (l1 norm).
This function computes the product between the values obtained with diffspec and diffenv functions.
This then gives a global (time and frequency) estimation of dissimilarity.
The frequency mean spectrum and the amplitude envelope needed for computing respectively diffspec and diffenv are automatically generated. They can be controlled through wl, msmooth and ksmooth arguments respectively.
See examples below and examples in diffspec and diffenv for implications on the results.

Value

A single value varying between 0 and 1 is returned. The value has no unit.

Note

This method can be used as a relative distance estimation between different waves.

Author(s)

Jerome Sueur [email protected]

References

Sueur, J., Pavoine, S., Hamerlynck, O. & Duvail, S. (2008) - Rapid acoustic survey for biodiversity appraisal. PLoS ONE, 3(12): e4065.

See Also

diffspec, diffenv

Examples

data(tico) ; tico <- tico@left
data(orni) ; orni <- orni@left
# selection in tico to have two waves of similar duration (length)
tico <- tico[1:length(orni)]
diffwave(tico,orni,f=22050)
# changing the frequency parameter (wl)
diffwave(tico,orni,f=22050,wl=1024)
# changing the temporal parameter (msmooth)
diffwave(tico,orni,f=22050,msmooth=c(20,0))

Time series discretisation

Description

This function transforms a numeric (time) series into a sequence of symbols

Usage

discrets(x, symb = 5, collapse = TRUE, plateau=1)

Arguments

x

a vector, a matrix (first column), an object of class ts, Sample (left channel), or Wave (left channel).

symb

the number of symbols used for the discretisation, can be set to 3 or 5 only.

collapse

logical, if TRUE, the symbols are pasted in a character string of length 1.

plateau

a numeric vector of length 1 taking the values 1 or 2 only. See details.

Details

The function partitions the numeric (time) series into a sequence of finite number of symbols. These symbols result of the comparaison of each series value with its temporal neighbours.
They are two discretisations available:
when symb is set to 3, each value will be replaced by either:
- I if the series is Increasing,
- D if the series is Decreasing,
- F if the series remains Flat,
when symb is set to 5, each value will be replaced by either:
- I if the series is Increasing,
- D if the series is Decreasing,
- F if the series remains Flat,
- P if the series shows a Peak,
- T if the series shows a Trough.

The argument plateau can be used to control the way a plateau is encoded. A plateau is an elevated flat region that can be either considered a 'flat peak' encoded as PF...FP (plateau = 1) or as an increase, a flat region and a decrease encoded as IF...FD (plateau = 1. The default value (plateau = 1) refers to Cazelles et al. (2004).

Value

A character string of length 1 if collapse is TRUE. Otherwise, a character string of length n-2 if symbol=5 (the first and last values cannot be replaced with a symbol) or n-1 if symbol=3 (the first value cannot be replaced with a symbol.)

Author(s)

Jerome Sueur, improved by Laurent Lellouch

References

Cazelles, B. 2004 Symbolic dynamics for identifying similarity between rhythms of ecological time series. Ecology Letters, 7: 755-763.

See Also

symba

Examples

# a random variable
discrets(rnorm(30))
discrets(rnorm(30),symb=3)
# a frequency spectrum
data(tico)
spec1<-spec(tico,f=22050,at=0.2,plot=FALSE)
discrets(spec1[,2])

Draw the amplitude envelope of a time wave

Description

This function lets the user modifying the amplitude envelope of a time wave by drawing it with the graphics device

Usage

drawenv(wave, f, channel = 1, n = 20, plot = FALSE, listen = FALSE, output = "matrix")

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

n

the maximum number of points to draw the new envelope. Valid values start at 1.

plot

if TRUE returns the oscillogram of the new time wave (by default FALSE).

listen

if TRUE the new sound is played back.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

Details

The function first plots an oscillogram view of wave.
The user has then to choose points on the positive side of the y-axis (amplitude). The junction of these points will draw a new amplitude envelope.
The order of points along the x-axis (time) is not important but points cannot be cancelled. When this process is finished the new time wave is returned in the console or as an oscillogram in a second graphics device if plot is TRUE.
The function uses locator.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected]

See Also

setenv, env, synth

Examples

## Not run: 
a<-synth(d=1,f=22050,cf=1000)
# drawenv(a,f=22050,plot=TRUE)
# choose points on the oscillogram view to draw a new enveloppe
# stop (ESC on Windows; right mouse button on Linux)
# check the result on the second graphics device opened thanks to plot=TRUE

## End(Not run)

Draw the amplitude profile of a frequency filter

Description

This function lets the user drawing the amplitude profile of a frequency filter.

Usage

drawfilter(f, n = 256, continuous = TRUE, discrete = TRUE)

Arguments

f

a numeric vector of length 1 for the sampling frequency of the object to be filtered (in Hz).

n

a numeric vector of length 1 for the length (i.e. number of points) of the filter. By default = 256 to fit with a FIR with wl = 512.

continuous

a logical (TRUE by default) to draw a continuous filter.

discrete

a logical (TRUE by default) to draw a discrete filter.

Details

If the same frequency of a discrete filter is selected twice then the sum of the amplitudes of the two selections is used. If both arguments continuous and discrete are set to TRUE and if frequencies selected overlap between the two filters then only the frequencies of the discrete filter are considered.

Value

The function returns a two-column matrix, the first column is the frequency in kHz and the second column is the amplitude of the filter.

Note

This function can be used to prepare bandpass or bandstop custom filters to be used with fir and ffilter. See examples.

Author(s)

Laurent Lellouch

See Also

fir, squarefilter, combfilter, ffilter, drawenv

Examples

## Not run: 
f <- 8000
a <- noisew(f=f, d=1)
## bandpass continuous and discrete
cont.disc <- drawfilter(f=f/2)
a.cont.disc <- fir(a, f=f, custom=cont.disc)
spectro(a.cont.disc, f=f)
## bandpass continuous only
cont <- drawfilter(f=f/2, discrete=FALSE)
a.cont <- fir(a, f=f, custom=cont)
spectro(a.cont, f=f)
## bandstop continuous only
cont.stop <- drawfilter(f=f/2, discrete=FALSE)
a.cont.stop <- fir(a, f=f, custom=cont.stop, bandpass=FALSE)
spectro(a.cont.stop, f=f)
## bandpass discrete only
disc <- drawfilter(f=f/2, continuous=FALSE)
a.disc <- fir(a, f=f, custom=disc, bandpass=FALSE)
spectro(a.disc, f=f)

## End(Not run)

Duration of a time wave

Description

Returns the duration (in second) of a time wave

Usage

duration(wave, f, channel=1)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

Value

A numeric vector of length 1 returning the duration in second.

Author(s)

Jerome Sueur

Examples

data(tico)
duration(tico)

Dynamic oscillogram

Description

This graphical function displays a time wave as an windowed oscillogram.

Usage

dynoscillo(wave, f, channel = 1, wd = NULL, wl = NULL, wnb = NULL, title = TRUE, ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wd

a numerical vector, duration of the window (in seconds)

wl

a numerical vector, length of the window (in number of points).

wnb

a numerical vector, number of windows (no unit).

title

a logical, if TRUE displays a title with information regarding window size and number.

...

other plot graphical parameters.

Details

The arguments wd, wl and wn have to be used isolated, not in conjunction. They basically do the same, ie they set the duration of the zooming window that is slided along the signal. For instance, for a 5 seconds sound with a sampling rate (f) at 44.1 kHz, wl = 4096 is equivalent to wd = 4096 / 44100 = 0.093 s and equivalent to wnb = 5*4096 / 44100 = 53.

Note

This function requires the package rpanel.

Author(s)

Jerome Sueur

See Also

oscillo, oscilloST, dynspec.

Examples

## Not run: 
require(rpanel)
data(tico)
dynoscillo(tico, wn=4)
## End(Not run)

Dynamic sliding spectrum

Description

This function plots dynamically a sliding spectrum along a time wave. This basically corresponds to a short-term Fourier transform.

Usage

dynspec(wave, f, channel = 1, wl = 512, wn = "hanning", zp = 0,
ovlp = 0, fftw = FALSE, norm = FALSE, dB = NULL,  dBref = NULL, plot = TRUE,
title = TRUE, osc = FALSE, 
tlab = "Time (s)", flab = "Frequency (kHz)",
alab = "Amplitude", alim = NULL, flim = c(0, f/2000),
type = "l", from = NULL, to = NULL, envt = NULL,
msmooth = NULL, ksmooth = NULL, colspec = "black",
coltitle = "black", colbg = "white", colline = "black",
colaxis = "black", collab = "black", cexlab = 1,
fontlab = 1, colwave = "black",
coly0 = "lightgrey", colcursor = "red", bty = "l")

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

if at is not null, length of the window for the analysis (even number of points, by defaults = 512).

wn

window name, see ftwindow (by default "hanning").

zp

zero-padding (even number of points), see Details.

ovlp

overlap between two successive windows (in % ).

fftw

if TRUE calls the function FFT of the library fftw. See Notes of the spectro.

norm

logical, if TRUE compute a normalised sliding spectrum.

dB

a character string specifying the type dB to return: "max0" for a maximum dB value at 0, "A", "B", "C", "D", and "ITU" for common dB weights.

dBref

a dB reference value when dB is not NULL. NULL by default but should be set to 2*10e-5 for a 20 microPa reference (SPL).

plot

logical, if TRUE plots in an ew graphics device the successive spectra sliding along the time wave (by default TRUE).

title

logical, if TRUE adds a title with the time position of the current spectrum along the time wave.

osc

logical, if TRUE plots an oscillogram beneath the sliding spectrum with a cursor showing the position of the current spectrum (by default FALSE).

tlab

title of the time axis.

flab

title of the frequency axis.

alab

title of the amplitude axis.

flim

range of frequency axis.

alim

range of amplitude axis.

type

type of plot that should be drawn for the sliding spectrum. See plot for details (by default "l" for lines).

from

start mark where to compute the sliding spectrum (in s).

to

end mark where to compute the sliding spectrum (in s).

envt

the type of envelope to be plooted: either "abs" for absolute amplitude envelope or "hil" for Hilbert amplitude envelope. See env.

msmooth

when env is not NULL, a vector of length 2 to smooth the amplitude envelope with a mean sliding window. The first component is the window length (in number of points). The second component is the overlap between successive windows (in %). See env.

ksmooth

when env is not NULL, kernel smooth via kernel. See env.

colspec

colour of the sliding spectrum.

coltitle

if title is TRUE, colour of the title.

colbg

background colour.

colline

colour of axes line.

colaxis

colour of the axes.

collab

colour of axes title.

cexlab

character size for axes title.

fontlab

font for axes title.

colwave

colour of the oscillogram or of the envelope (only when osc is TRUE).

coly0

colour of the y=0 line (only when osc is TRUE).

colcursor

colour of oscillogram cursor (only when osc is TRUE).

bty

the type of box to be drawn around the oscillogram (only when osc is TRUE).

Details

Use the slider panel to move along the time wave.
Use the argument norm if you wish to have each spectrum normalised, i.e. with values between 0 and 1 or maximised to 0 dB when dB is TRUE.
The function requires the package rpanel that is based on the package tcltk.

Value

This function returns a list of three items:

time

a numeric vector corresponding to the time axis.

freq

a numeric vector corresponding to the frequency axis.

amp

a numeric matrix corresponding to the amplitude values. Each column is a Fourier transform of length wl/2.

Note

This function is very similar to a spectrogram. See the Details of spectro for some information regarding the short term Fourier transform.

Author(s)

Jerome Sueur and Caroline Simonis

See Also

spectro, spectro3D, wf, spec, dynspectro, fft, oscillo, env.

Examples

## Not run: 
data(sheep)
require(rpanel)
dynspec(sheep,f=8000,wl=1024,ovlp=50,osc=TRUE)

## End(Not run)

Dynamic sliding spectrogramn

Description

This function plots dynamically a sliding spectrogram along a time wave.

Usage

dynspectro(wave, f, channel = 1, slidframe = 10,
wl = 512, wn = "hanning", zp = 0, ovlp = 75,
fftw = FALSE, dB = TRUE, plot = TRUE,
title = TRUE, osc = FALSE,
tlab = "Time (s)", flab = "Frequency (kHz)", alab = "Amplitude",
from = NULL, to = NULL,
collevels = NULL, palette = spectro.colors,
envt = NULL, msmooth = NULL, ksmooth = NULL,
coltitle = "black", colbg = "white", colline = "black",
colaxis = "black", collab = "black", cexlab = 1,
fontlab = 1, colwave = "black",
coly0 = "lightgrey", colcursor = "red", bty = "l")

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

slidframe

size of the sliding frame (in percent of the wave duration).

wl

if at is not null, length of the window for the analysis (even number of points, by defaults = 512).

wn

window name, see ftwindow (by default "hanning").

zp

zero-padding (even number of points), see Details.

ovlp

overlap between two successive windows (in % ).

fftw

if TRUE calls the function FFT of the library fftw. See Notes of the spectro.

dB

a logical, if TRUE then uses dB values

plot

logical, if TRUE plots in an ew graphics device the successive spectrograms sliding along the time wave (by default TRUE).

title

logical, if TRUE adds a title with the time position of the current spectrogram along the time wave.

osc

logical, if TRUE plots an oscillogram beneath the sliding spectrogram with a cursor showing the position of the current spectrum (by default FALSE).

tlab

title of the time axis.

flab

title of the frequency axis.

alab

title of the amplitude axis.

from

start mark where to compute the sliding spectrogram (in s).

to

end mark where to compute the sliding spectrogram (in s).

collevels

a set of levels which are used to partition the amplitude range of the spectrogram.

palette

a color palette function to be used to assign colors in the plot.

envt

the type of envelope to be plooted: either "abs" for absolute amplitude envelope or "hil" for Hilbert amplitude envelope. See env.

msmooth

when env is not NULL, a vector of length 2 to smooth the amplitude envelope with a mean sliding window. The first component is the window length (in number of points). The second component is the overlap between successive windows (in %). See env.

ksmooth

when env is not NULL, kernel smooth via kernel. See env.

coltitle

if title is TRUE, colour of the title.

colbg

background colour.

colline

colour of axes line.

colaxis

colour of the axes.

collab

colour of axes title.

cexlab

character size for axes title.

fontlab

font for axes title.

colwave

colour of the oscillogram or of the envelope (only when osc is TRUE).

coly0

colour of the y=0 line (only when osc is TRUE).

colcursor

colour of oscillogram cursor (only when osc is TRUE).

bty

the type of box to be drawn around the oscillogram (only when osc is TRUE).

Details

Use the slider panel to move along the time wave.
The function requires the package rpanel that is based on the package tcltk.
The function is mainly written for inspecting long sounds.
The function is based on image for fast display when spectro is based on filled.contour. Displaying the amplitude envelope with the argument envt can slow down significantly the display.

Value

This function returns a list of three items:

time

a numeric vector corresponding to the time axis.

freq

a numeric vector corresponding to the frequency axis.

amp

a numeric matrix corresponding to the amplitude values. Each column is a Fourier transform of length wl/2.

Note

This function is very similar to a spectrogram. See the Details of spectro for some information regarding the short term Fourier transform.

Author(s)

David Pinaud and Jerome Sueur

See Also

spectro, spectro3D, wf, spec, dynspec, fft, oscillo, env.

Examples

## Not run: 
data(sheep)
require(rpanel)
dynspectro(sheep, ovlp=95, osc=TRUE)

## End(Not run)

Echo generator

Description

This function generate echoes of a time wave.

Usage

echo(wave, f, channel = 1, amp, delay, plot = FALSE,
listen = FALSE, output = "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

amp

a vector describing the relative amplitude of the successive echoes. Each value of the vector should be in [0,1]

delay

a vector describing the time delays of the successive echoes from the beginning of wave (in s.)

plot

logical, if TRUE returns an oscillographic plot of the wave modified (by default FALSE).

listen

if TRUE the new sound is played back.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Details

amp and delay should strictly have the same length corresponding to the number of desired echoes.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Note

This function is based on a convolution (convolve) between the input wave and a pulse echo filter.

Author(s)

Jerome Sueur [email protected]

References

Stoddard, P. K. (1998). Application of filters in bioacoustics. In: Hopp, S. L., Owren, M. J. and Evans, C. S. (Eds), Animal acoustic communication. Springer, Berlin, Heidelberg,pp. 105-127.

See Also

synth

Examples

# generation of the input wave
a <- synth(f=11025,d=1,cf=2000,shape="tria",am=c(50,10),fm=c(1000,10,1000,0,0))
# generation of three echoes
# with respectively a relative amplitude of 0.8, 0.4, and 0.2
# and with a delay of 1s, 2s, and 3s  from the beginning of the input wave
aecho <- echo(a,f=11025,amp=c(0.8,0.4,0.2),delay=c(1,2,3))
# another echo with time delays overlapping with the input wave
aecho <- echo(a,f=11025,amp=c(0.4,0.2,0.4),delay=c(0.6,0.8,1.5))

Amplitude envelope of a time wave

Description

This function returns the absolute or Hilbert amplitude envelope of a time wave.

Usage

env(wave, f, channel = 1, envt = "hil", 
msmooth = NULL, ksmooth = NULL, ssmooth = NULL,
asmooth = NULL,
fftw = FALSE, norm = FALSE,
plot = TRUE, k = 1, j = 1, ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

envt

the type of envelope to be returned: either "abs" for absolute amplitude envelope or "hil" for Hilbert amplitude envelope. See Details section.

msmooth

a vector of length 2 to smooth the amplitude envelope with a mean sliding window. The first component is the window length (in number of points). The second component is the overlap between successive windows (in %). See examples.

ksmooth

kernel smooth via kernel. See examples.

ssmooth

length of the sliding window used for a sum smooth.

asmooth

length of the sliding window used for an autocorrelation smooth.

fftw

if TRUE calls the function FFT of the library fftw for faster computation for the Hilbert amplitude envelope (envt="hil") and/or for kernell smoothing (ksmooth).

norm

a logical, if TRUE the amplitude of the envelope is normalised between 0 and 1.

plot

logical, if TRUE returns a plot of wave envelope (by default TRUE).

k

number of horizontal sections when plot is TRUE (by default =1).

j

number of vertical sections when plot is TRUE (by default =1).

...

other oscillo graphical parameters.

Details

When envt is set as "abs", the amplitude envelope returned is the absolute value of wave.
When envt is set as "hil", the amplitude envelope returned is the modulus (Mod) of the analytical signal of wave obtained through the Hilbert transform (hilbert).

Value

Data are returned as one-column matrix when plot is FALSE.

Note

Be aware that smoothing with either msmooth or ksmooth changes the original number of points describing wave.

Author(s)

Jerome Sueur. Implementation of 'fftw' argument by Jean Marchal and Francois Fabianek. Implementation of 'asmooth' by Thibaut Marin-Cudraz.

See Also

oscillo,hilbert

Examples

data(tico)
# Hilbert amplitude envelope
env(tico)
# absolute amplitude envelope
env(tico, envt="abs")
# smoothing with a 10 points and 50% overlaping mean sliding window
env(tico, msmooth=c(10,50))
# smoothing kernel
env(tico, ksmooth=kernel("daniell",10))
# sum smooth
env(tico, ssmooth=50)
# autocorrelation smooth
env(tico, asmooth=50)
# overplot of oscillographic and envelope representations
oscillo(tico)
par(new=TRUE)
env(tico, colwave=2)

Export sound data

Description

Export sound data as a text file that can be read by a sound player like 'Goldwave'

Usage

export(wave, f = NULL, channel = 1, filename = NULL, header=TRUE, ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

filename

name of the new file. (by default the name of wave).

header

either a logical or a character vector, if TRUE add a header to be read by Goldwave, if FALSE does not add any header, if a character vector add the character vector as a header.

...

other write.table parameters.

Details

Creates a new text file with a header describing the main features of the sound (wave). For instance, for a 2 s sound with a sampling frequency of 8000 Hz, the header will be: [ASCII 8000Hz, Channels: 1, Samples: 160000, Flags: 0]. This type of file can be read by sound players like Goldwave (http://www.goldwave.com/).

Author(s)

Jerome Sueur [email protected]

Examples

a<-synth(f=8000,d=2,cf=2000,plot=FALSE)
export(a,f=8000)
unlink("a.txt")

Fade in and fade out of a time wave

Description

This function applies a “fade in” and/or a “fade out” to a time wave following a linear, exponential or cosinus-like shape.

Usage

fadew(wave, f, channel = 1, din = 0, dout = 0, shape = "linear", plot = FALSE,
listen = FALSE, output = "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

din

fade in duration.

dout

fade out duration.

shape

fade shape, "linear", "exp" for exponential, "cos" for cosinus-like, (by default "linear").

plot

logical, if TRUE returns an oscillographic plot of the wave modified (by default FALSE).

listen

if TRUE the new sound is played back.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected]

See Also

oscillo, addsilw, cutw, deletew,mutew, pastew, revw, zapsilw

Examples

a<-noisew(d=5,f=4000)
op<-par(mfrow=c(3,1))
fadew(a,f=4000,din=1,dout=2,plot=TRUE,title="Linear",cexlab=0.8)
fadew(a,f=4000,din=1,dout=2,shape="exp",plot=TRUE,title="Exponential shape",
    colwave="blue",coltitle="blue",cexlab=0.8)
fadew(a,f=4000,din=1,dout=2,shape="cos",plot=TRUE,title="Cosinus-like shape",
    colwave="red",coltitle="red",cexlab=0.8)
par(op)

Frequency bands plot

Description

This graphical function returns a frequency spectrum as a bar plot.

Usage

fbands(spec, f = NULL, bands = 10, width = FALSE, mel = FALSE, plot = TRUE,
xlab = NULL, ylab = "Relative amplitude", ...)

Arguments

spec

a data set resulting of a spectral analysis obtained with spec or meanspec. Can be in dB.

f

sampling frequency of spec (in Hz). Not requested if the first column of spec contains the frequency axis.

bands

a numeric vector. If vector of length 1, then sets the number of bands dividing in equal parts the spectrum. If of length > 1, then takes the values as kHz limits of the bands dividing the spectrum. These bands can be of different size. See details and examples.

width

logical, if TRUE and that bands is an irregular series of values, then the width of the bands will be proportional to the frequency limits defined in bands.

mel

a logical, if TRUE the (htk-)mel scale is used.

plot

logical, if TRUE, a plot showing the peaks is returned.

xlab

label of the x-axis.

ylab

label of the y-axis.

...

other plot graphical parameters.

Details

The function proceeds as follows

  • divides the spectrum in bands. The limits of the bands are set with the argument bands. There are two options:

    • you set a number of bands with equal size by giving a single value to bands. For instance, setting bands to a value of 10 will slice the spectrum in 10 equal parts and return 10 local peaks.

    • you set the limits of the bands. This is achieve by giving a numeric vector to bands. The limits can follow a regular or irregular series. For instance attributing the vector c(0,2,4,8) will generate the following bands [0,2[, [2,4[, [4,8] kHz. Be aware that the last value should not exceed half the sampling frequency used to obtain the spectrum spec.

  • uses the function barplot.

Value

A two-column matrix, the first column corresponding to the frequency values (x-axis, mean of the bars limits) and the second column corresponding to height values (y-axis) of the bars.

Note

The value below bars is the mean between the corresponding frequency limits.

Author(s)

Jerome Sueur, improved by Laurent Lellouch

See Also

meanspec, spec, barplot.

Examples

data(sheep)
spec <- meanspec(sheep, f=8000, plot=FALSE)
# default plot
fbands(spec)
# setting a specific number of bands
fbands(spec, bands=6)
#setting specific regular bands limits
fbands(spec, bands=seq(0,4,by=0.25))
# some plot tuning
op <- par(las=1)
fbands(spec, bands=seq(0,4,by=0.1),
       horiz=TRUE, col=heat.colors(41),
       xlab="", ylab="",
       cex.axis=0.75, cex.names = 0.75,
       axes=FALSE)
par(op)
# showing or not the width of the bands
oct <- octaves(440,3)/1000
op <- par(mfrow=c(2,1))
fbands(spec, bands=oct, col="blue")
fbands(spec, bands=oct, width = TRUE, col="red")
par(op)
# kind of horizontal zoom
op <- par(mfrow=c(2,1))
fbands(spec, bands=seq(0,4,by=0.2), col=c(rep(1,10),
   rep("orange",5),rep(1,5)), main="all frequency range")
fbands(spec, bands=seq(2,3,by=0.2),
   col="orange", main="a subset or zoom in")
par(op)
# kind of dynamic frequency bands
specs <- dynspec(sheep, f=8000, plot= FALSE)$amp
out <- apply(specs, f=8000, MARGIN=2,
     FUN = fbands, bands = seq(0,4,by=0.2),
     col = 1, ylim=c(0,max(specs)))
# mel scale
require(tuneR)
mel <- melfcc(sheep, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
melspec.mean <- apply(mel$aspectrum, MARGIN=2, FUN=mean)
melspec.mean <- melspec.mean/max(melspec.mean) # [0,1] scaling 
fbands(melspec.mean, f=8000, bands=8)

Doppler effect

Description

This function computes the altered frequency of a moving source due to the Doppler effect.

Usage

fdoppler(f, c = 340, vs, vo = 0, movs = "toward", movo = "toward")

Arguments

f

original frequency produced by the source (in Hz or kHz)

c

speed of sound in meters/second.

vs

speed of the source in meters/second.

vo

speed of the observer in meters/second. The observer is static by default i.e. vo = 0

movs

movement direction of the source in relation with observer position, either "toward" (by default) or "away".

movo

movement direction of the observer in relation with the source position, either "toward" (by default, but be aware that the observer is static by default) or "away".

Details

The altered frequency f' is computed according to:

f=f×c±voc±vsf{'} = f\times{\frac{c \pm v_{o}}{c \pm v_{s}}}

with f = original frequency produced by the source (in Hz or kHz),
vs = speed of the source,
vo = speed of the observer.

Value

The altered frequency is returned in a vector.

Note

You can use wasp to have exact values of c. See examples.

Author(s)

Jerome Sueur [email protected]

See Also

wasp

Examples

# a 400 Hz source moving toward or away from the observer at 85 m/s
fdoppler(f=400,vs=85)
# [1] 533.3333
fdoppler(f=400,vs=85,movs="away")
# [1] 320
# use wasp() if you wish to have exact sound speed at a specific temperature
fdoppler(f=wasp(f=400,t=25)$c, vs=85)
# [1] 461.8667
# Doppler effect at different source speeds
f<-seq(1,10,by=1); lf<-length(f)
v<-seq(10,300,by=20); lv<-length(v)
res<-matrix(numeric(lf*lv),ncol=lv)
for(i in 1:lv) res[,i]<-fdoppler(f=f,vs=v[i])
op<-par(bg="lightgrey")
matplot(x=f,y=res,type="l",lty=1,las=1,col= spectro.colors(lv),
xlab="Source frequency (kHz)", ylab="Altered frequency (kHz)")
legend("topleft",legend=paste(as.character(v),"m/s"),
lty=1,col= spectro.colors(lv))
title(main="Doppler effect at different source speeds")
par(op)

Frequency filter

Description

This function filters out a selected frequency section of a time wave (low-pass, high-pass, low-stop, high-stop, bandpass or bandstop frequency filter).

Usage

ffilter(wave, f, channel = 1, from = NULL, to = NULL, bandpass = TRUE,
custom = NULL, wl = 1024, ovlp = 75, wn = "hanning", fftw = FALSE,
rescale=FALSE, listen=FALSE, output="matrix")

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

from

start frequency (in Hz) where to apply the filter.

to

end frequency (in Hz) where to apply the filter.

bandpass

if TRUE a band-pass filter is applied between from and to, if FALSE a band-stop filter is applied between from and to (by default TRUE).

custom

a vector describing the frequency response of a custom filter. This can be manually generated or obtained with spec and meanspec. The length of the vector should be half the length of wl. See examples.

wl

window length for the analysis (even number of points).

ovlp

overlap between successive FFT windows (in %).

wn

window name, see ftwindow (by default "hanning").

fftw

if TRUE calls the function FFT of the library fftw. See Notes of the spectro.

rescale

a logical, if TRUE then the sample values of new wave (output) are rescaled according to the sample values of wave (input).

listen

a logical, if TRUE the new sound is played back.

output

character string, the class of the object to return, either "matrix", "Wave", "audioSample" or "ts".

Details

A short-term Fourier transform is first applied to the signal (see spectro), then the frequency filter is applied and the new signal is eventually generated using the reverse of the Fourier Transform (istft).
There is therefore neither temporal modifications nor amplitude modifications.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur

See Also

afilter,lfs,fir, preemphasis, combfilter, bwfilter

Examples

a<-noisew(f=8000,d=1)
# low-pass
b<-ffilter(a,f=8000,to=1500)
spectro(b,f=8000,wl=512)
# high-pass
c<-ffilter(a,f=8000,from=2500)
spectro(c,f=8000,wl=512)
# band-pass
d<-ffilter(a,f=8000,from=1000,to=2000)
spectro(d,f=8000,wl=512)
# band-stop
e<-ffilter(a,f=8000,from=1500,to=2500,bandpass=FALSE)
spectro(e,f=8000,wl=512)
# custom
myfilter1<-rep(c(rep(0,64),rep(1,64)),4)
g<-ffilter(a,f=8000,custom=myfilter1)
spectro(g,f=8000)

Near field and far field limits

Description

This function helps in knowing whether you are working in the near or far field.

Usage

field(f, d)

Arguments

f

frequency (Hz)

d

distance from the sound source (m)

Details

Areas very close to the sound source are in the near-field where the contribution of particle velocity to sound energy is greater thant that of sound pressure and where these components are not in phase. Sound propagation properties are also different near or far from the source. It is therefore important to know where the microphone was from the source.
To know this, the product k*d is computed according to:

k×d=fc×dk\times{d} = \frac{f}{c}\times{d}

with d = distance from the source (m), f = frequency (Hz) and c = sound celerity (m/s).
If k*d is greatly inferior 1 then the microphone is in the near field.
The decision help returned by the function follows the rule:
far field:

k×d>1k\times{d} > 1

between near and far field limits:

0.1k×d10.1 \leq k\times{d} \leq 1

near field:

k×d<0.1k\times{d} < 0.1

.

Value

A list of two values is returned:

kd

the numeric value k*d used to take a decision

d

a character string giving the help decision.

Note

This function works for air-borne sound only.

Author(s)

Jerome Sueur [email protected]

Examples

# 1 kHz near field at 1 cm from the source
field(f=1000,d=0.01)
# playing with distance from source and sound frequency
op<-par(bg="lightgrey")
D<-seq(0.01,0.5,by=0.01); nD<-length(D)
F<-seq(100,1000,by=25); nF<-length(F)
a<-matrix(numeric(nD*nF),nrow=nD)
for(i in 1:nF) a[,i]<-field(f=F[i],d=D)$kd
matplot(x=D,y=a,type="l",lty=1,col= spectro.colors(nF),
  xlab="Distance from the source (m)", ylab="k*d")
title("Variation of the product k*d with distance and frequency")
text(x=c(0.4,0.15),y=c(0.02,1), c("Near Field","Far Field"),font=2)
legend(x=0.05,y=1.4,c("100 Hz","1000 Hz"),lty=1,
  col=c(spectro.colors(nF)[1],spectro.colors(nF)[nF]),bg="grey")
abline(h=0.1)
par(op)

Finite Impulse Response filter

Description

This function is a FIR filter that filters out a selected frequency section of a time wave (low-pass, high-pass, low-stop, high-stop, bandpass or bandstop frequency filter).

Usage

fir(wave, f, channel = 1, from = NULL, to = NULL, bandpass = TRUE, custom = NULL,
wl = 512, wn = "hanning", rescale=FALSE, listen = FALSE, output = "matrix")

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

from

start frequency (in Hz) where to apply the filter.

to

end frequency (in Hz) where to apply the filter.

bandpass

if TRUE a band-pass filter is applied between from and to, if not NULL a band-stop filter is applied between from and to (by default NULL).

custom

a vector describing the frequency response of a custom filter. This can be manually generated or obtained with spec and meanspec. wl is no more required. See examples.

wl

window length of the impulse filter (even number of points).

wn

window name, see ftwindow (by default "hanning").

rescale

a logical, if TRUE then the sample values of new wave (output) are rescaled according to the sample values of wave (input).

listen

a logical, if TRUE the new sound is played back.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

Details

This function is based on the reverse of the Fourier Transform (fft) and on a convolution (convolve) between the wave to be filtered and the impulse filter.

Value

A new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur

References

Stoddard, P. K. (1998). Application of filters in bioacoustics. In: Hopp, S. L., Owren, M. J. and Evans, C. S. (Eds), Animal acoustic communication. Springer, Berlin, Heidelberg,pp. 105-127.

See Also

ffilter, bwfilter, preemphasis, lfs, afilter

Examples

a<-noisew(f=8000,d=1)
# low-pass
b<-fir(a,f=8000,to=1500)
spectro(b,f=8000)
# high-pass
c<-fir(a,f=8000,from=2500)
spectro(c,f=8000)
# band-pass
d<-fir(a,f=8000,from=1000,to=2000)
spectro(d,f=8000)
# band-stop
e<-fir(a,f=8000,from=1500,to=2500,bandpass=FALSE)
spectro(e,f=8000)
# custom filter manually generated
myfilter1<-rep(c(rep(0,32),rep(1,32)),4)
g<-fir(a,f=8000,custom=myfilter1)
spectro(g,f=8000)
# custom filter generated using spec()
data(tico)
myfilter2<-spec(tico,f=22050,at=0.7,wl=512,plot=FALSE)
b<-noisew(d=1,f=22050)
h<-fir(b,f=22050,custom=myfilter2)
spectro(h,f=22050)

Frequency modulation analysis

Description

This function computes the Fourier analysis of the instantaneous frequency of a time wave. This allows to detect periodicity in frequency modulation.

Usage

fma(wave, f, channel = 1, threshold = NULL, plot = TRUE, ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

threshold

amplitude threshold for signal detection (in % ).

plot

logical, if TRUE the spectrum of the instantaneous frequency (by default TRUE).

...

other spec parameters.

Details

This function is based on ifreq and spec.
The instantaneous frequency of wave is first computed and the spectrum of this frequency modulation is then processed. All env and spec arguments can be set up.

Value

If plot is FALSE, fma returns a numeric vector corresponding to the computed spectrum. If peaks is not NULL, fma returns a list with two elements:

spec

the spectrum computed

peaks

the peaks values (in kHz).

Author(s)

Jerome Sueur [email protected]

See Also

ifreq, hilbert, spec, ama

Examples

# a sound with a 1 kHz sinusoid FM
a<-synth(d=1, f=8000, cf=1500, fm=c(1000,1000,0,0,0), output="Wave")
fma(a)

Frequency peak detection

Description

This function searches for peaks of a frequency spectrum.

Usage

fpeaks(spec, f = NULL,
nmax = NULL, amp = NULL, freq = NULL, threshold = NULL,
mel =FALSE,
plot = TRUE, title = TRUE,
xlab = NULL, ylab = "Amplitude",
labels = TRUE, digits = 2,
legend = TRUE, collab = "red", ...)

Arguments

spec

a data set resulting of a spectral analysis obtained with spec or meanspec. Can be in dB.

f

sampling frequency of spec (in Hz). Not requested if the first column of spec contains the frequency axis.

nmax

maximal number of peaks detected. Overrides amp and freq. See details.

amp

amplitude slope parameter, a numeric vector of length 2. Refers to the amplitude slopes of the peak. The first value is the left slope and the second value is the right slope. Only peaks with higher slopes than threshold values will be kept. See details.

freq

frequency threshold parameter (in Hz). If the frequency difference of two successive peaks is less than this threshold, then the peak of highest amplitude will be kept only. See details.

threshold

amplitude threshold parameter. Only peaks above this threshold will be considered. See details.

mel

a logical, if TRUE the (htk-)mel scale is used.

plot

logical, if TRUE, a plot showing the peaks is returned.

title

logical, if TRUE add the number of peaks detected as a plot title.

xlab

label of the x-axis.

ylab

label of the y-axis.

labels

logical, if TRUE peak labels are plotted.

digits

if labels is TRUE, the number of decimal places (round) for the peak labels.

legend

logical, if TRUE a legend returning the different selection parameters (nmax, amp, freq, threshold, threshold) is added to the plot.

collab

labels color.

...

other plot graphical parameters.

Details

Here are some details regarding the different selection parameters:

  • nmax: this parameter is to be used if you wish to get a specific number of peaks. The peaks selected are those with the highest slopes. It then does not work in conjunction with the other parameters.

  • freq: this parameter allows to remove from the selection successive peaks with a small frequency difference. Imagine you have two successive peaks at 1200 Hz and 1210 Hz and at 0.5 and 0.25 in amplitude. If you set freq to 50 Hz, then only the first peak will be kept.

  • amp: this parameter allows to remove from the selection peaks with low slopes. You can make the selection on both slopes or on a single one. Imagine you have an asymetric peak with a 0.01 left slope and a 0.02 right slope. The peak will be discarded for the following settings: both values higher than 0.02 (e.g. amp = c(0.03,0.04)), the first value higher than 0.01 (e.g. amp = c(0.02,0.001)), the second value higher than 0.02 (e.g. amp = c(0.001,0.03)). If you do not want apply the selection on one of the slope use 0. For instance, a selection on the left slope only will be achieved with: amp = c(0.02,0).

  • threshold: this parameter can be used to do a rough selection on the spectrum. Peaks with an amplitude value (not a slope) lower than this threshold will be automatically discarded. This can be useful when you want to remove peaks of a low-amplitude background noise.

Value

A two-column matrix, the first column corresponding to the frequency values (x-axis) and the second column corresponding to the amplitude values (y-axis) of the peaks.

Note

You can also use fpeaks with other kind of spectrum, for instance a cepstral spectrum. See examples.

Author(s)

Jerome Sueur and Amandine Gasc

See Also

localpeaks, meanspec, spec

Examples

data(tico)
spec <- meanspec(tico, f=22050, plot=FALSE)
specdB <- meanspec(tico, f=22050, dB="max0", plot=FALSE)
# all peaks
fpeaks(spec)
# 10 highest peaks
fpeaks(spec, nmax=10)
# highest peak (ie dominant frequency)
fpeaks(spec, nmax=1)
# peaks that are separated by more than 500 Hz
fpeaks(spec, freq=500)
# peaks with a left slope higher than 0.1
fpeaks(spec, amp=c(0.1,0))
# peaks with a right slope higher than 0.1
fpeaks(spec, amp=c(0,0.1))
# peaks with left and right slopes higher than 0.1
fpeaks(spec, amp=c(0.1,0.1))
# peaks above a 0.5 threshold
fpeaks(spec, threshold=0.5)
# peaks of a dB spectrum with peaks showing slopes higher than 3 dB
fpeaks(specdB, amp=c(3,3))
# comparing different parameter settings
meanspec(tico, f=22050)
col <- c("#ff000090","#0000ff75","#00ff00")
cex <- c(2,1.25,1.5)
pch <- c(19,17,4)
title(main="Peak detection \n (spectrum with values between 0 and 1)")
res1 <- fpeaks(spec, plot = FALSE)
res2 <- fpeaks(spec, amp=c(0.02,0.02), plot =FALSE)
res3 <- fpeaks(spec, amp=c(0.02,0.02), freq=200, plot = FALSE)
points(res1, pch=pch[1], col=col[1], cex=cex[1])
points(res2, pch=pch[2], col=col[2], cex=cex[2])
points(res3, pch=pch[3], col=col[3], cex=cex[3])
legend("topright", legend=c("all peaks","amp", "amp & freq"), pch=pch,
pt.cex=cex, col=col, bty="n")
# example with a cepstral spectrum
data(sheep)
res <- ceps(sheep,f=8000,at=0.4,wl=1024,plot=FALSE)
fpeaks(res, nmax=4, xlab="Quefrency (s)")
# melscale
require(tuneR)
mel <- melfcc(sheep, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
melspec.mean <- apply(mel$aspectrum, MARGIN=2, FUN=mean)
melspec.mean <- melspec.mean/max(melspec.mean) # [0,1] scaling 
fpeaks(melspec.mean, nmax=4, f=8000, mel=TRUE)
fpeaks(melspec.mean, freq=4, f=8000, mel=TRUE) # freq in Hz!
fpeaks(melspec.mean, threshold=0.3, f=8000, mel=TRUE)
fpeaks(melspec.mean, amp=c(0.1,0.1), f=8000, mel=TRUE)

Fourier transform windows

Description

Generates different Fourier Transform windows.

Usage

ftwindow(wl, wn = "hamming",
        correction = c("none", "amplitude", "energy"))

Arguments

wl

window length

wn

window name: bartlett, blackman, flattop, hamming, hanning, or rectangle (by default hamming).

correction

a character vector of length 1 to apply an amplitude ("amplitude") or an energy ("energy") correction to the FT window. By default no correction is applied ("none").

Value

A vector of length wl.

Note

Try the example to see windows shape.

Author(s)

Jerome Sueur [email protected]

References

Harris, F.J., 1978. On the use of windows for harmonic analysis with the discrete Fourier Transform. Proceedings of the IEEE, 66(1): 51-83.

See Also

covspectro, dfreq, meanspec, spec, spectro, spectro3D

Examples

a<-ftwindow(512)
b<-ftwindow(512,wn="bartlett")
c<-ftwindow(512,wn="blackman")
d<-ftwindow(512,wn="flattop")
e<-ftwindow(512,wn="hanning")
f<-ftwindow(512,wn="rectangle")
all<-cbind(a,b,c,d,e,f)
matplot(all,type="l",col=1:6,lty=1:6)
legend(legend=c("hamming","bartlett","blackman","flattop","hanning","rectangle"),
x=380,y=0.95,col=1:6,lty=1:6,cex=0.75)

Fundamental frequency track

Description

This function estimates the fundamental frequency through a short-term cepstral transform.

Usage

fund(wave, f, channel = 1, wl = 512, ovlp = 0, fmax = f/2, threshold = NULL,
at = NULL, from = NULL, to = NULL, 
plot = TRUE, xlab = "Time (s)", ylab = "Frequency (kHz)",
ylim = c(0, f/2000), pb = FALSE, ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

if at is not null, length of the window for the analysis (even number of points, by defaults = 512).

ovlp

overlap between two successive windows (in %).

fmax

the maximum frequency to detect (in Hz).

threshold

amplitude threshold for signal detection (in %).

at

position where the estimate the fundamental frequency (in s)

.

from

start position where to compute the fundamental frequency (in s).

to

end position to compute the fundamental frequency (in s).

plot

logical, if TRUE plots the fundamental frequency modulations against time (by default TRUE).

xlab

title of the time axis (s).

ylab

title of the frequency axis (Hz).

ylim

the range of frequency values.

pb

if TRUE returns a text progress bar in the console.

...

other plot graphical parameters.

Value

When plot is FALSE, fund returns a two-column matrix, the first column corresponding to time in seconds (x-axis) and the second column corresponding to to fundamental frequency in kHz (y-axis).
NA corresponds to pause sections in wave (see threshold).
No plot is produced when using at.

Note

This function is based on ceps.

Author(s)

Jerome Sueur [email protected].

References

Oppenheim, A.V. and Schafer, R.W. 2004. From frequency to quefrency: a history of the cepstrum. Signal Processing Magazine IEEE, 21: 95-106.

See Also

cepstro, ceps, autoc

Examples

data(sheep)
# estimate the fundamental frequency at a single position
fund(sheep, f=8000, fmax=300, at=1, plot=FALSE)
# track the fundamental frequency along time
fund(sheep,f=8000,fmax=300,type="l")
# with 50% overlap between successive sliding windows, time zoom and 
# amplitude filter (threshold)
fund(sheep,f=8000,fmax=300,type="b",ovlp=50,threshold=5,ylim=c(0,1),cex=0.5)
# overlaid on a spectrogram
spectro(sheep,f=8000,ovlp=75,zp=16,scale=FALSE,palette=reverse.gray.colors.2)
par(new=TRUE)
fund(sheep,f=8000,fmax=300,type="p",pch=24,ann=FALSE,
  xaxs="i",yaxs="i",col="black",bg="red",threshold=6)

Gammatone filter

Description

Generate gammatone filter in the time domain (impulse response).

Usage

gammatone(f, d, cfreq, n = 4, a = 1, p = 0, output = "matrix")

Arguments

f

sampling frequency (in Hz).

d

duration (in s).

cfreq

center frequency (in Hz).

n

filter order (no unit).

a

amplitude (linear scale, no unit).

p

initial phase (in radians).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

Details

The gammatone function in the time domain (impulse response) is obtained with:

g(t)=a×tn1×e2πβt×cos(2πcft+ϕ)g(t) = a \times t^{n-1} \times e^{-2\pi \beta t} \times \cos(2 \pi cf t + \phi)

with a the amplitude, t time, n the filter order, cf the center frequency, ϕ\phi the initial phase.
The parameter β\beta is the equivalent rectangular bandwidth (ERB) bandwidth which varies according to the center frequency cfcf following:

β=24.7×(4.37×cf1000+1)\beta = 24.7 \times (4.37 \times \frac{cf}{1000} + 1)

Value

A wave is returned. The class of the returned object is set with the argument output.

Note

Use the FFT based function, as spec or meanspec, to get the filter in the frequency domain. See examples.

Author(s)

Jerome Sueur

References

Holdsworth J, Nimmo-Smith I, Patterson R, Rice P (1988) Implementing a gammatone filter bank. Annex C of the SVOS Final Report: Part A: The Auditory Filterbank, 1, 1-5.

See Also

melfilterbank

Examples

## gammatone filter in the time domain (impulse response)
f <- 44100
d <- 0.05
res <- gammatone(f=f, d=d, cfreq=440, n=4)
## time display
oscillo(res, f=f)
## frequency display
spec(res, f=f)
## generate and plot a bank of 32 filters from 500 to 10000 Hz
n <- 32
cfreq <- round(seq(500, 10000, length.out=n))
res <- matrix(NA, nrow=f*d/2, ncol=n)
for(i in 1:n){
    res[,i] <- spec(gammatone(f=f, d=d, cfreq=cfreq[i]), f=f, dB="max0", plot=FALSE)[,2]
}
x <- seq(0,f/2,length.out=nrow(res))/1000
plot(x=x, y=res[,1],
     xlim=c(0,14), ylim=c(-60,0),
     type="l", col=2, las=1, 
     xlab="Frequency (kHz)", ylab="Relative amplitude (dB)")
for(i in 2:n) lines(x, res[,i], col=2)
## use the frequency domain to filter a white noise input
## here around the center frequency 2000 Hz
res <- gammatone(f=f, d=d, cfreq=2000, n=4)
gspec <- spec(res, f=f, plot=FALSE)[,2]
nw <- noisew(f=44100, d=1)
nwfilt <- fir(nw, f=44100, wl=length(gspec)*2, custom=gspec) 
spectro(nwfilt, f=f)

2D-spectrogram of a time wave using ggplot2

Description

This function returns a ggplot object to draw a spectrogram with the package ggplot2. This is an alternative to spectro.

Usage

ggspectro(wave, f, tlab = "Time (s)",
flab = "Frequency (kHz)", alab = "Amplitude\n(dB)\n", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

tlab

label of the time axis.

flab

label of the frequency axis.

alab

label of the amplitude axis.

...

other non-graphical arguments to be passed to spectro (wl, ovlp etc).

Details

This function return the fist layer (data and aesthetic mapping) of a ggplot2 plot.
See the example section to understand how to build a spectrogram and consult ggplot2 help to get what you exactly need.
There is no way to plot the oscillogram as spectro does.

Value

A ggpot layer.

Note

This function requires ggplot2 package.

Author(s)

Jerome Sueur

References

Wickham H (2009) – ggplot2: elegant graphics for data analysis. UseR! Springer.

See Also

spectro, spectro3D, dynspec

Examples

## Not run: 
require(ggplot2)
## first layer
v <- ggspectro(tico, ovlp=50)
summary(v)
## using geom_tile ##
v + geom_tile(aes(fill = amplitude)) + stat_contour()
## coordinates flip (interest?)
v + geom_tile(aes(fill = amplitude)) + stat_contour() + coord_flip()
## using stat_contour ##
# default (not nice at all)
v + stat_contour(geom="polygon", aes(fill=..level..))
# set up to 30 color levels with the argument bins
(vv <- v + stat_contour(geom="polygon", aes(fill=..level..), bins=30))
# change the limits of amplitude and NA values as transparent
vv + scale_fill_continuous(name="Amplitude\n(dB)\n", limits=c(-30,0), na.value="transparent")
# Black-and-white theme
(vv + scale_fill_continuous(name="Amplitude\n(dB)\n", limits=c(-30,0),
  na.value="transparent", low="white", high="black") + theme_bw())
# Other colour scale (close to spectro() default output)
v + stat_contour(geom="polygon", aes(fill=..level..), bins=30)
  + scale_fill_gradientn(name="Amplitude\n(dB)\n", limits=c(-30,0),
  na.value="transparent", colours = spectro.colors(30))

## End(Not run)

Total entropy

Description

This function estimates the total entropy of a time wave.

Usage

H(wave, f, channel = 1, wl = 512, envt="hil", msmooth = NULL, ksmooth = NULL)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

window length for spectral entropy analysis (even number of points). See sh.

envt

the type of envelope to be used: either "abs" for absolute amplitude envelope or "hil" for Hilbert amplitude envelope. See env.

msmooth

a vector of length 2 to smooth the amplitude envelope with a mean sliding window. The first component is the window length (in number of points). The second component is the overlap between successive windows (in %). See env.

ksmooth

kernel smooth via kernel. See env.

Details

This function computes the product between the values obtained with sh and th functions.
This then gives a global (time and frequency) estimation of signal entropy.
The frequency mean spectrum and the amplitude envelope needed for computing respectively sh and th are automatically generated. They can be controlled through wl and smooth arguments respectively. See examples below and examples in sh and th for implications on the results.

Value

A single value varying between 0 and 1 is returned. The value has no unit.

Note

The entropy of a noisy signal will tend towards 1 whereas the entropy of a pure tone signal will tend towards 0.

Author(s)

Jerome Sueur [email protected]

References

Sueur, J., Pavoine, S., Hamerlynck, O. & Duvail, S. (2008) - Rapid acoustic survey for biodiversity appraisal. PLoS ONE, 3(12): e4065.

See Also

sh, th, csh

Examples

data(orni)
H(orni,f=22050)
# changing the spectral parameter (wl)
H(orni,f=22050,wl=1024)
# changing the temporal parameter (msmooth)
H(orni,f=22050,msmooth=c(20,0))

Hilbert transform and analytic signal

Description

This function returns the analytic signal of a time wave through Hilbert transform.

Usage

hilbert(wave, f, channel = 1, fftw = FALSE)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

fftw

if TRUE calls the function FFT of the library fftw for faster computation. See Notes of the function spectro.

Details

The analytic signal is useful to get the amplitude envelope (see argument henv of oscillo and the instantaneous phase or frequency (see ifreq) of a time wave.

Value

hilbert returns the analytic signal as a complex matrix. The imaginary part of this matrix is the Hilbert transform.

Note

To get the Hilbert component only, use Im(Hilbert(wave)).

Author(s)

Jonathan Lees [email protected]. Implementation of 'fftw' argument by Jean Marchal and Francois Fabianek.

References

Mbu Nyamsi, R. G., Aubin, T. & Bremond, J. C. 1994 On the extraction of some time dependent parameters of an acoustic signal by means of the analytic signal concept. Its application to animal sound study. Bioacoustics, 5: 187-203.

See Also

ifreq

Examples

a<-synth(f=8000, d=1, cf=1000)
aa<-hilbert(a, f=8000)

Instantaneous frequency

Description

This function returns the instantaneous frequency (and/or phase) of a time wave through the computation of the analytic signal (Hilbert transform).

Usage

ifreq(wave, f, channel = 1, phase = FALSE, threshold = NULL,
plot = TRUE, xlab = "Time (s)", ylab = NULL,
ylim = NULL, type = "l", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

phase

if TRUE and plot is also TRUE plots the instantaneous phase instead of the instantaneous frequency.

threshold

amplitude threshold for signal detection (in % ).

plot

logical, if TRUE plots the instantaneous frequency or phase against time (by default TRUE).

xlab

title of the x axis.

ylab

title of the y axis.

ylim

the range of y values.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

...

other plot graphical parameters.

Details

The instantaneous phase is the argument of the analytic signal obtained throught the Hilbert transform.
The instantaneous phase is then unwrapped and derived against time to get the instantaneous frequency.
There may be some edge effects at both start and end of the time wave.

Value

If plot is FALSE, ifreq returns a list of two components:

f

a two-column matrix, the first column corresponding to time in seconds (x-axis) and the second column corresponding to instantaneous frequency in kHz (y-axis).

p

a two-column matrix, the first column corresponding to time in seconds (x-axis) and the second column corresponding to wrapped instantaneous phase in radians (y-axis).

Note

This function is based on the analytic signal obtained with the Hilbert transform (see hilbert).
The function requires the package signal.
The matrix describing the instantaneous phase has one more row than the one describing the instantaneous frequency.

Author(s)

Jerome Sueur [email protected]

References

Mbu Nyamsi, R. G., Aubin, T. & Bremond, J. C. 1994 On the extraction of some time dependent parameters of an acoustic signal by means of the analytic signal concept. Its application to animal sound study. Bioacoustics, 5: 187-203.

See Also

hilbert, zc

Examples

# generate a sound with sine and linear frequency modulations
a<-synth(d=1, f=8000, cf=1500, fm=c(200,10,1000,0,0))
# plot on a single graphical device the instantaneous frequency and phase
op<-par(mfrow=c(2,1))
ifreq(a,f=8000,main="Instantaneous frequency")
ifreq(a,f=8000,phase=TRUE,main="Instantaneous phase")
par(op)

Inverse of the short-term Fourier transform

Description

This function returns a wave object from a complex STFT matrix by computing the inverse of the short-term Fourier transform (STFT)

Usage

istft(stft, f, wl, ovlp=75, wn="hanning", output = "matrix")

Arguments

stft

a complex matrix resulting of a short-term Fourier transform.

f

sampling frequency of the original wave object (in Hz)

wl

FFT window length for the analysis (even number of points).

ovlp

overlap between successive FFT windows (in %, by default 75%, see the Details section).

wn

character string specifying the FFT window name, see ftwindow (by default "hanning").

output

character string, the class of the object to return, either "matrix", "Wave", "audioSample" or "ts".

Details

The function is based on the inverse of the FFT (see fft) and on the overlap add (OLA) method.
The overlap percentage must satisfy the Perfect Reconstruction OLA-constraint. For the most windows, this constraint is:

ovlp=100×(114×n),ovlp = 100 \times (1 - \frac{1}{4 \times n}),


with n being a positive integer.
A default value is set to 75%. We suggest not to change it.

Value

A new wave is returned. The class of the returned object is set with the argument output.

Note

The stft input data must be complex.
This function is used by ffilter, lfs to respectively filter in frequency and shift in frequency a sound.
The function can be used to reconstruct or modify a sound. See examples.

Author(s)

Original Matlab code by Hristo Zhivomirov (Technical University of Varna, Bulgaria), translated and adapted to R by Jerome Sueur

See Also

spectro, ffilter, lfs

Examples

## Not run: 
# STFT and iSTFT parameters
wl <- 1024
ovlp <- 75
# reconstruction of the tico sound from the stft complex data matrix
data(tico)
data <- spectro(tico, wl=wl, ovlp=ovlp, plot=FALSE, norm=FALSE, dB=NULL, complex=TRUE)$amp
res <- istft(data, ovlp=ovlp, wn="hanning", wl=wl, f=22050, out="Wave")
spectro(res)
# a strange frequency filter
n <- noisew(d=1, f=44100)
data <- spectro(n, f=44100, wl=wl, ovlp=ovlp, plot=FALSE, norm=FALSE, dB=NULL, complex=TRUE)$amp
data[64:192, 6:24] <- 0 
nfilt <- istft(data, f=8000, wl=wl, ovlp=ovlp, output="Wave")
spectro(nfilt, wl=wl, ovlp=ovlp)

## End(Not run)

Itakuro-Saito distance

Description

Compare two distributions (e.g. two frequency spectra) by computing the Itakuro-Saito distance

Usage

itakura.dist(spec1, spec2, scale=FALSE)

Arguments

spec1

any distribution, especially a spectrum obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

spec2

any distribution, especially a spectrum obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

scale

a logical, if TRUE the distance is scaled by dividing the distance by the length of spec1 (or spec2).

Details

The Itakura-Saito (I-S) distance is a non-symmetric measure of the difference between two probability distributions. It is here adapted for frequency spectra. The distance is asymmetric, ie computing the I-S distance between spec1 and spec2 is not the same as computing it between spec2 and spec1. A symmetry can be obtained by calculating the mean between the two directions.
The distance is obtained following:

DIS(spec1spec2)=spec1spec2log(spec1spec2)1D_{I-S}(spec1 \Vert spec2) = \sum{\frac{spec1}{spec2} - log(\frac{spec1}{spec2}) - 1}

Value

The function returns a list of three items:

D1

The I-S distance of 'spec2' with respect to 'spec1' (i.e. D(spec1 || spec2))

D2

The I-S distance of 'spec1' with respect to 'spec2' (i.e. D(spec2 || spec1))

D

The symmetric distance (i.e. D = 0.5*(D1+D2))

If scale = TRUE the distance is divided by the length of spec1 (or spec2).

Note

The function works for both Hz and (htk-)mel scales.

Author(s)

Jerome Sueur, improved by Laurent Lellouch

See Also

kl.dist, ks.dist, logspec.dist, simspec, diffspec

Examples

# Comparison of two spectra
data(tico)
tico1 <- spec(tico, at=0.65, plot=FALSE)
tico2 <- spec(tico, at=1.1, plot=FALSE)
itakura.dist(tico1, tico2)
itakura.dist(tico1, tico2, scale=TRUE)

Kullback-Leibler distance

Description

Compare two distributions (e.g. two frequency spectra) by computing the Kullback-Leibler distance

Usage

kl.dist(spec1, spec2, base = 2)

Arguments

spec1

any distribution, especially a spectrum obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

spec2

any distribution, especially a spectrum obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

base

the logarithm base used to compute the distance. See log.

Details

The Kullback-Leibler distance or relative entropy is a non-symmetric measure of the difference between two probability distributions. It is here adapted for frequency spectra. The distance is asymmetric, ie computing the K-L distance between spec1 and spec2 is not the same as computing it between spec2 and spec1. A symmetry can be obtained by calculating the mean between the two directions.
The distance is obtained following:

DKL(spec1spec2)=spec1×log(spec1spec2)D_{K-L}(spec1 \Vert spec2) = \sum{spec1 \times log(\frac{spec1}{spec2})}

Value

The function returns a list of three items:

D1

The K-L distance of 'spec2' with respect to 'spec1' (i.e. D(spec1 || spec2))

D2

The K-L distance of 'spec1' with respect to 'spec2' (i.e. D(spec2 || spec1))

D

The symmetric K-L distance (i.e. D = 0.5*(D1+D2))

Note

The base of the logarithm can be changed using the argument base. When sets to base 2, the information is measured in units of bits. When sets to base e, the information is measured in nats.
The function works for both Hz and (htk-)mel scales.

Author(s)

Jerome Sueur, improved by Laurent Lellouch

References

Kullback, S., Leibler, R.A. (1951). On information and sufficiency. Annals of Mathematical Statistics, 22: 79-86

See Also

ks.dist, logspec.dist, simspec, diffspec

Examples

# Comparison of two spectra
data(tico)
tico1 <- spec(tico, at=0.65, plot=FALSE)
tico2 <- spec(tico, at=1.1, plot=FALSE)
kl.dist(tico1, tico2)    # log2 (binary logarithm)
kl.dist(tico1, tico2, base=exp(1))  # ln (natural logarithm)

Kolmogorov-Smirnov distance

Description

This function compares two distributions (e.g. two frequency spectra) by computing the Kolmogorov-Smirnov distance

Usage

ks.dist(spec1, spec2, f = NULL, mel = FALSE,
plot = FALSE, type = "l",
lty = c(1, 2), col = c(2, 4), 
flab = NULL, alab = "Cumulated amplitude",
flim = NULL, alim = NULL,
title = TRUE, legend = TRUE, ...)

Arguments

spec1

any distribution, especially a spectrum obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

spec2

any distribution, especially a spectrum obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

f

sampling frequency of waves used to obtain spec1 and spec2 (in Hz). Not necessary if spec1 and/or spec2 is a two columns matrix obtained with spec or meanspec.

mel

a logical, if TRUE the (htk-)mel scale is used.

plot

logical, if TRUE plots both cumulated spectra and their maximal distance (i.e. the K-S distance.)

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

lty

a vector of length 2 for the line type of spec1 and spec2 if type="l".

col

a vector of length 2 for the colour of spec1 and spec2.

flab

title of the frequency axis.

alab

title of the amplitude axis.

flim

the range of frequency values.

alim

range of amplitude axis.

title

logical, if TRUE, adds a title with D and F values.

legend

logical, if TRUE adds a legend to the plot.

...

other plot graphical parameters.

Details

The Kolmogorov distance is the maximal distance between the cumulated spectra. The function returns this distance and the corresponding frequency. This is an adaptation of the statistic computed by the non-parametric Kolmogorov-Smirnov test (see ks.test).

Value

The function returns a list of two items

D

the Kolomogorov-Smirnov distance

F

the frequency (in KHz) where the Kolmogorov-Smirnov distance was found

Note

There is no p-value associated to the K-S distance.
If no frequency is provided, only the distance D.

Author(s)

Jerome Sueur, improved by Laurent Lellouch

See Also

kl.dist, simspec, diffspec, logspec.dist, diffcumspec, itakura.dist

Examples

## Comparison of two spectra and plot of the cumulated spectra with the K-S distance
data(tico)
tico1 <- spec(tico, at=0.65, plot=FALSE)
tico2 <- spec(tico, at=1.1, plot=FALSE)
ks.dist(tico1, tico2, plot=TRUE)
## mel scale
require(tuneR)
data(orni)
orni.mel <- melfcc(orni, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
orni.mel.mean <- apply(orni.mel$aspectrum, MARGIN=2, FUN=mean)
tico.mel <- melfcc(tico, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
tico.mel.mean <- apply(tico.mel$aspectrum, MARGIN=2, FUN=mean)
ks.dist(orni.mel.mean, tico.mel.mean, f=22050, mel=TRUE, plot=TRUE)

Linear Frequency Shift

Description

This function linearly shifts all the frequency content of a time wave.

Usage

lfs(wave, f, channel = 1, shift, wl = 1024, ovlp = 75,
wn = "hanning", fftw = FALSE, output = "matrix")

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

shift

positive or negative frequency shift to apply (in Hz).

wl

window length for the analysis (even number of points, by default = 1024).

ovlp

overlap between successive FFT windows (in %, by default 75%).

wn

window name, see ftwindow (by default "hanning").

fftw

if TRUE calls the function FFT of the library fftw. See Notes of the spectro.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

Details

A short-term Fourier transform is first applied to the signal (see spectro), then the frequency shift is applied and the new signal is eventually generated using the reverse of the Fourier Transform (istft).
There is therefore neither temporal modifications nor amplitude modifications.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected] and Thierry Aubin [email protected]

References

Hopp, S. L., Owren, M. J. and Evans, C. S. (Eds) 1998. Animal acoustic communication. Springer, Berlin, Heidelberg.

See Also

ffilter, spectro

Examples

data(orni)
a<-lfs(orni,f=22050,shift=1000)
spectro(a,f=22050)
# to be compared with the original signal
spectro(orni,f=22050)

Play a sound wave

Description

Play a sound wave

Usage

listen(wave, f, channel=1, from = NULL, to = NULL, choose = FALSE)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

from

start of play (in s).

to

end of play (in s).

choose

logical, if TRUE start (=from) and end (=to) points can be graphically chosen with a cursor on the oscillogram.

Note

This function is based on play but allows to read one-colum matrix, data.frame, time-series and Sample objects.

Author(s)

Jerome Sueur [email protected] but the original play function is by Uwe Ligges (package tuneR).

See Also

play

Examples

## NOT RUN
# data(tico)
# listen(tico,f=22050)
# listen(tico,f=22050,from=0.5,to=1.5)
# listen(noise(d=1,f=8000,Wave=TRUE))
## change f to play the sound a different speed
# data(sheep)
## normal
# listen(sheep,f=8000)
## two times faster
# listen(sheep,f=8000*2)
## two times slower
# listen(sheep,f=8000/2)

Local maximum frequency peak detection

Description

This functions searches for local peaks of a frequency spectrum

Usage

localpeaks(spec, f = NULL, bands = 10, mel = FALSE, plot = TRUE,
xlab = NULL, ylab = "Amplitude", labels = TRUE, ...)

Arguments

spec

a data set resulting of a spectral analysis obtained with spec or meanspec. Can be in dB.

f

sampling frequency of spec (in Hz). Not requested if the first column of spec contains the frequency axis.

bands

a numeric vector. If vector of length 1, then sets the number of bands dividing in equal parts the spectrum. If of length > 1, then takes the values as kHz limits of the bands dividing the spectrum. These bands can be of different size. See details and examples.

mel

a logical, if TRUE the (htk-)mel scale is used.

plot

logical, if TRUE, a plot showing the peaks is returned.

xlab

label of the x-axis.

ylab

label of the y-axis.

labels

logical, if TRUE peak labels are plotted.

...

other plot graphical parameters.

Details

The function proceed as follows

  • divides the spectrum in bands. The limits of the bands are set with the argument bands. There are two options:

    • you set a number of bands with equal size by giving a single value to bands. For instance, setting bands to a value of 10 will slice the spectrum in 10 equal parts and return 10 local peaks.

    • you set the limits of the bands. This is achieve by giving a numeric vector to bands. The limits can follow a regular or irregular series. For instance attributing the vector c(0,2,4,8) will generate the following bands [0,2[, [2,4[, [4,8] kHz. Be aware that the last value should not exceed half the sampling frequency used to obtain the spectrum spec.

  • uses the function fpeaks with the argument nmax set to 1.

Value

A two-column matrix, the first column corresponding to the frequency values (x-axis) and the second column corresponding to the amplitude values (y-axis) of the peaks.

Author(s)

Jerome Sueur

See Also

fpeaks, meanspec, spec

Examples

data(sheep)
spec <- meanspec(sheep, f=8000)
# a specific number of bands with all the same size
localpeaks(spec, bands=5)
# bands directly specified  with a regular sequence
localpeaks(spec, bands=seq(0,8/2,by=0.5))
# bands directly specified  with an irregular sequence
localpeaks(spec, bands=c(0,0.5,1,1.5,3,4))
# Amaj octave bands, note that there is no peak detection
# in the higher part of the spectrum as sequence stops at 3520 Hz
localpeaks(spec, bands=octaves(440, below=3, above=3)/1000)
# melscale
require(tuneR)
mel <- melfcc(sheep, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
melspec.mean <- apply(mel$aspectrum, MARGIN=2, FUN=mean)
melspec.mean <- melspec.mean/max(melspec.mean) # [0,1] scaling 
localpeaks(melspec.mean, f=8000, bands=8)

Log-spectral distance

Description

Compare two distributions (e.g. two frequency spectra) by computing the log-spectral distance

Usage

logspec.dist(spec1, spec2, scale=FALSE)

Arguments

spec1

any distribution, especially a spectrum obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

spec2

any distribution, especially a spectrum obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

scale

a logical, if TRUE the distance is scaled by dividing by the square-root of the length of spec1 (or spec2).

Details

The distance is computed according to:

DLS(spec1spec2)=DLS(spec2spec1)=10×log10(spec1spec2)2D_{LS}(spec1 \Vert spec2) = D_{LS}(spec2 \Vert spec1) = \sqrt{\sum{10 \times log_{10}(\frac{spec1}{spec2})^{2}}}


If scale = TRUE the distance is divided by the length of spec1 (or spec2).

Value

A numeric vector of length 1 returning the D distance.

Note

The function works for both Hz and (htk-)mel scales.

Note

The distance is symmetric.

Author(s)

Jerome Sueur, improved by Laurent Lellouch

See Also

ks.dist, kl.dist, itakura.dist, simspec, diffspec

Examples

# Comparison of two spectra
data(tico)
tico1 <- spec(tico, at=0.65, plot=FALSE)
tico2 <- spec(tico, at=1.1, plot=FALSE)
logspec.dist(tico1, tico2)
logspec.dist(tico1, tico2, scale=TRUE)

Long-term spectrogram

Description

A spectrogram computed over several survey files obtained with a Wildlife Acoustics SongMeter recorder

Usage

lts(dir, f, wl = 512,
wn = "hanning", ovlp = 0, rmoffset = TRUE, FUN = mean, col = spectro.colors(30),
fftw = FALSE, norm = FALSE, verbose = TRUE,
tlab = "Time", ntann = NULL, flab = "Frequency (kHz)",
recorder = c("songmeter", "audiomoth"), plot = TRUE, ...)

Arguments

dir

a character vector, the path to the directory where the .wav files are stored or directly the names of the .wav files to be processed.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in the .wav files contained in dir.

wl

window length for the analysis (even number of points) (by default = 512).

wn

window name, see ftwindow (by default "hanning").

ovlp

overlap between two successive windows (in %).

rmoffset

a logical to sepcify whether DC offset should be removed. By default TRUE.

FUN

the function to apply to compute the successive frequency spectra, by default mean for a mean spectrum but could be other as median or var for a median spectrum or variance spectrum.

col

a list of colors or the color palette with a number of colors

fftw

if TRUE calls the function FFT of the library fftw. See Notes.

norm

a logical, to specify if each mean spectrum should be normalised between 0 and 1 (default FALSE) before to concatenate the image.

verbose

a logical, if TRUE (default) the file number and name processed are displayed in the console.

tlab

label of the time axis.

ntann

a numeric of length 1, the number of axis annotations (all annotations by default).

flab

label of the frequency axis.

recorder

the type of automatic recorder used, either a Wildlife SongMeter or a Open Audio deveices Audiomoth.

plot

logical, if TRUE plots the spectrogram (by default TRUE).

...

other image graphical parameters.

Details

The function reads each .wav file and computes its mean spectrum with meanspec. The successive mean spectra are then concatenated into a single image with the function image. The parameters wl, ovlp, and wn are those of the function meanspec.

Value

This function returns a list of three items:

time

a numeric vector corresponding to the time axis.

freq

a numeric vector corresponding to the frequency axis.

amp

a numeric or a complex matrix corresponding to the amplitude values. Each column is a Fourier transform of length wl/2.

Author(s)

Jerome Sueur

See Also

spectro, meanspec, image, spectro3D, ggspectro, songmeter, audiomoth

Examples

## Not run: 
## if 'dir' contains a set of files recorded with a Wildlife Acoustics
# songmeter recorder then a direct way to obtain
# the spectrogram of all .wav files is
dir <- "pathway-to-directory-containing-wav-files"
lts(dir)
# to normalise each mean spectrum
lts(dir, norm=TRUE)
# to change the STFT parameters used to obtain each mean spectrum
lts(dir, wl=1024, wn="hamming", ovlp=50)
# to change the colors and the number of time labels and to make it quiet
lts(dir, col=cm.colors(20), ntann=10, verbose=FALSE)
## direct use of files names stored in the working directory
files <- c("S4A09154_20190213_150000.wav", "S4A09154_20190213_153000.wav",
"S4A09154_20190213_160000.wav", "S4A09154_20190213_163000.wav",
"S4A09154_20190213_170000.wav", "S4A09154_20190213_173000.wav",
"S4A09154_20190213_180000.wav", "S4A09154_20190213_183000.wav",
"S4A09154_20190213_190000.wav", "S4A09154_20190213_193000.wav")
lts(files)

## End(Not run)

Median of the amplitude envelope

Description

This function computes an acoustic index based on the median of the amplitude envelope.

Usage

M(wave, f, channel = 1, envt = "hil", plot = FALSE, ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

envt

the type of envelope to be used: either "abs" for absolute amplitude envelope or "hil" for Hilbert amplitude envelope. See env.

plot

logical, if TRUE returns a plot of the amplitude envelope of wave (by default FALSE).

...

other env parameters, in particular smoothing parameters. See env.

Details

This amplitude index M is computed according to:

M=Aˉ(t)×21depthM = \bar{A}(t) \times 2^{1-depth}

with

0M10 \leq M \leq 1

where A(t) is the amplitude envelope and depth is the signal digitization depth in number of bits.

Value

A numeric vector of length 1 between 0 and 1, without unit.

Author(s)

Jerome Sueur and Marion Depraetere

References

Depraetere M, Pavoine S, Jiguet F, Gasc A, Duvail S, Sueur J (2012) Monitoring animal diversity using acoustic indices: implementation in a temperate woodland. Ecological Indicators, 13, 46-54.

See Also

env, AR

Examples

data(tico)
M(tico)
# smoothing the amplitude may change slightly the result
M(tico, msmooth=c(500,50), plot=TRUE)

Mean of dB values

Description

This function calculates the mean of dB values

Usage

meandB(x, level="IL")

Arguments

x

a numeric vector or a numeric matrix.

level

intensity level ("IL") or sound pressure level ("SPL")

Details

The mean of dB values is not linear. See examples.

Value

A numeric vector of length 1 is returned.

Author(s)

Jerome Sueur and Zev Ross

References

Hartmann, W. M. 1998 Signals, sound and sensation. New York: Springer.

See Also

sddB, moredB, convSPL, dBweight

Examples

meandB(c(89,90,95))

Mean frequency spectrum of a time wave

Description

This function returns the mean frequency spectrum (i.e. the mean relative amplitude of the frequency distribution) of a time wave. Results can be expressed either in absolute or dB data.

Usage

meanspec(wave, f, channel = 1, wl = 512, wn = "hanning", ovlp = 0, fftw = FALSE,
norm = TRUE, PSD = FALSE, PMF = FALSE, FUN = mean, correction = "none", dB = NULL,
dBref = NULL, from = NULL, to = NULL, identify = FALSE,
col = "black", cex = 1, plot = 1, flab = "Frequency (kHz)",
alab = "Amplitude", flim = NULL, alim = NULL, type ="l", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

length of the window for the analysis (even number of points, by default = 512).

wn

window name, see ftwindow (by default "hanning").

ovlp

overlap between two successive analysis windows (in %).

fftw

if TRUE calls the function FFT of the library fftw. See Notes of spectro.

norm

if TRUE the mean spectrum is normalised (i. e. scaled) by its maximum.

PSD

if TRUE return Power Spectra Density, i. e. the square of the spectra.

PMF

if TRUE return Probability Mass Function, i. e. the probability distribution of frequencie.

FUN

the function to apply on the rows of the STFT matrix, by default mean for a mean spectrum but could be other as median or var for a median spectrum or variance spectrum.

correction

a character vector of length 1 to apply an amplitude ("amplitude") or an energy ("energy") correction to the FT window. This argument is useful only when one wish to obtain absolute values that is when norm=FALSE and PMF=FALSE. By default no correction is applied ("none").

dB

a character string specifying the type dB to return: "max0" for a maximum dB value at 0, "A", "B", "C", "D", and "ITU" for common dB weights.

dBref

a dB reference value when dB is not NULL. NULL by default but should be set to 2*10e-5 for a 20 microPa reference (SPL).

from

start mark where to compute the spectrum (in s).

to

end mark where to compute the spectrum (in s).

identify

to identify frequency and amplitude values on the plot with the help of a cursor.

col

colour of the spectrum.

cex

pitch size.

plot

if 1 returns frequency on x-axis, if 2 returns frequency on y-axis, (by default 1).

flab

title of the frequency axis.

alab

title of the amplitude axis.

flim

range of frequency axis (in kHz).

alim

range of amplitude axis.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

...

other plot graphical parameters.

Details

See examples of spec. This function is based on fft.

Value

If plot is FALSE, meanspec returns a two columns matrix, the first column corresponding to the frequency axis, the second column corresponding to the amplitude axis.
If identify is TRUE, spec returns a list with two elements:

freq

the frequency of the points chosen on the spectrum


amp

the relative amplitude of the points chosen on the spectrum


Warning

The argument peaks is no more available (version > 1.5.6). See the function fpeaks for peak(s) detection.

Note

The argument fftw can be used to try to speed up process time. When set to TRUE, the Fourier transform is computed through the function FFT of the package fftw. This package is a wrapper around the fastest Fourier transform of the free C subroutine library FFTW (http://www.fftw.org/). FFT should be then installed on your OS.

Author(s)

Jerome Sueur [email protected]

See Also

spec,fpeaks, localpeaks, dynspec, corspec, diffspec, simspec, fft.

Examples

data(orni)
# compute the mean spectrum of the whole time wave
meanspec(orni,f=22050)
# compute the mean spectrum of a time wave section (from 0.32 s to 0.39 s)
meanspec(orni,f=22050,from=0.32,to=0.39)
# different window lengths
op<-par(mfrow=c(3,1))
meanspec(orni,f=22050,wl=256)
title("wl=256")
meanspec(orni,f=22050,wl=1024)
title("wl=1024")
meanspec(orni,f=22050,wl=4096)
title("wl=4096")
par(op)
# different overlap values (almost no effects here...)
op<-par(mfrow=c(3,1))
meanspec(orni,f=22050)
title("ovlp=0")
meanspec(orni,f=22050,ovlp=50)
title("ovlp=50")
meanspec(orni,f=22050,ovlp=95)
title("ovlp=95")
par(op)
# use of flim to zoom in
op<-par(mfrow=c(2,1))
meanspec(orni,f=22050)
title("zoom in")
meanspec(orni,f=22050,wl=512,flim=c(4,6))
par(op)
# comparaison of spectrum and mean spectrum
op<-par(mfrow=c(2,1))
spec(orni,f=22050)
title("spec()")
meanspec(orni,f=22050)
title("meanspec()")
par(op)
# log scale on frequency axis
meanspec(orni, f=22050, log="x")
# median spectrum
meanspec(orni,f=22050, FUN=median)
# variance spectrum
meanspec(orni,f=22050, FUN=var)

Hertz / Mel conversion

Description

This function converts Hertz data in Mel data.

Usage

mel(x, inverse = FALSE)

Arguments

x

a value in Hertz (or in Mel if inverse is TRUE)

inverse

logical, if TRUE converts the Mel data in Hertz data.

Details

Hertz to mel conversion is computed according to:

m=1127.01048×log(1+(f700))m = 1127.01048 \times {\log{(1+(\frac{f}{700}))}}

with m in Mel and f in Hertz.

Mel to Hertz conversion (when inverse is TRUE) is therefore computed according to:

f=700×(em1127.010481)f = 700 \times{(e^{\frac{m}{1127.01048}}-1)}

with f in Hertz and m in Mel.

Value

A corresponding R object is returned.

Note

The Mel scale is a perceptual scale of pitches judged by listeners to be equal in distance from one another. The name Mel comes from the word melody to indicate that the scale is based on pitch comparisons. The reference point between this scale and normal frequency measurement is defined by equating a 1000 Hz tone, 40 dB above the listener's threshold, with a pitch of 1000 mels.

Author(s)

Jerome Sueur [email protected]

References

Stevens, S. S., Volkman, J. and Newman, E. B. 1937. A scale for the measurement of psychological magnitude pitch. Journal of the Acoustical Society of America, 8: 185-190.

See Also

melfilterbank

Examples

x<-seq(0,10000,by=50)
y<-mel(x)
plot(x,y,type="l",xlab = "f (hertz)", ylab = "f (mel)",
  main = "Mel scale", col="red")

Mel-filter bank for MFCC computation

Description

This functions returns graphically and numerically the Mel-filters used to compute MFCC.

Usage

melfilterbank(f = 44100, wl = 1024,
minfreq = 0, maxfreq = f/2, m = 20,
palette, alpha = 0.5, plot = FALSE)

Arguments

f

sammpling frequency (in Hz).

wl

the Fourier window length (in number of samples).

minfreq

the minimum (or lower) frequency of the filter bank (in Hz).

maxfreq

the maximum (or upper) frequency of the filter bank (in Hz).

m

the total number of filters.

palette

an optional colour palette if plot is TRUE.

alpha

alpha-transparency when a colour palette is used.

plot

if TRUE all filters are displayed in a single plot.

Value

A list of 3 items:

central.freq

the kHz central frequencies of the filters,

freq

the kHz frequency scale,

amp

the amplitude of the filters, scaled between 0 and 1.

Note

These triangular filters are used for computing MFCCs.

Author(s)

Jerome Sueur

References

Sharan RV & Moir TJ (2016) Applications and advancements in automatic sound recognition. Neurocomputing.

See Also

mel, gammatone

Examples

## default values
melfilterbank(plot=TRUE)
## with color surfaces
melfilterbank(palette=cm.colors, plot=TRUE)
## values changed
res <- melfilterbank(f=16000, wl=512, minfreq=300, plot=TRUE)
## plot the 1st filter only
plot(res$freq, res$amp[,1], type="l", xlab="Frequency (kHz)", ylab="Amplitude")
## plot the last filter only
plot(res$freq, res$amp[,ncol(res$amp)], type="l", xlab="Frequency (kHz)", ylab="Amplitude")
## get the kHz central frequencies of the succesive filters
res$central.freq

Microphone sensitivity and conversion

Description

This function converts microphone sensitivity from mV/Pa to dB.

Usage

micsens(x, sref = 1, inverse = FALSE)

Arguments

x

a measured sensitivity in mV/Pa (or in dB if inverse is TRUE)

sref

the sensitivity reference (by default equals to 1 V/Pa)

inverse

logical, if TRUE, the inverse conversion from dB to mV/Pa is computed.

Details

The sensitivity S in dB is calculated according to:

SdB=20×log10(ssref)S_{dB} = 20 \times log_{10}(\frac{s}{s_{ref}})

with s the measured sensitivity in mv/Pa and sref the reference sensitivity (by default 1 mV/Pa).

Value

A numeric value in dB re 1V/Pa with default settings, in mV/Pa if inverse is set to FALSE.

Author(s)

Jerome Sueur [email protected]

See Also

convSPL

Examples

# conversion of a sensitivity of 2 mV/Pa
micsens(2)
# conversion of a sensitivity of -54 dB re 1V/Pa
micsens(-54,inverse=TRUE)

Addition of dB values

Description

This functions calculates the sum of dB values

Usage

moredB(x, level="IL")

Arguments

x

a numeric vector or numeric matrix.

level

intensity level ("IL") or sound pressure level ("SPL")

Details

The addition of dB values is not linear. See examples.

Value

A numeric vector of length 1.

Author(s)

Jerome Sueur

References

Hartmann, W. M. 1998 Signals, sound and sensation. New York: Springer.

See Also

meandB, sddB, convSPL, dBweight

Examples

# two sources of 60 dB give an intensity level of 63 dB
moredB(c(60,60))
# addition of three sources
moredB(c(89,90,95))

Replace time wave data by 0 values

Description

This functions replaces a time wave or a section of a time wave by 0 values. For a time wave describing a sound, this corresponds in muting the sound or a section of it.

Usage

mutew(wave, f, channel = 1, from = NULL, to = NULL, choose = FALSE, plot = TRUE,
output = "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

from

start of the silence section (in s).

to

end of the silence section (in s).

choose

logical, if TRUE start (=from) and end (=to) points can be graphically chosen with a cursor on the oscillogram.

plot

logical, if TRUE returns an oscillographic plot of wave with the new silence section (by default TRUE).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Details

By default, from and from are NULL, this results in completely muting wave.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected]

See Also

oscillo, addsilw, cutw, deletew,fadew, pastew, revw, zapsilw

Examples

data(tico)
mutew(tico,f=22050,from=0.5,to=0.9)

Normalized Difference Soundscape Index

Description

This function computes the Normalized Difference Soundscape Index as described by Kasten et al. (2012).

Usage

NDSI(x, anthropophony = 1, biophony = 2:8, max = FALSE)

Arguments

x

a two-column numeric matrix computed with soundscapespec.

anthropophony

a numeric vector defining the frequency band(s) of the anthropophony (in kHz).

biophony

a numeric vector defining the frequency band(s) of the biophony (in kHz).

max

a logical, if TRUE then defines the biophony as the maximum - not the sum - of the 2 and 8 kHz frequency bands

Details

NDSI aims at estimating the level of anthropogenic disturbance on the soundscape by computing the ratio of human-generated (anthropophony) to biological (biophony) acoustic components found in field collected sound samples. In terms of frequency, the anthropophony is defined as the [1-2[ kHz frequency bin and the biophony as the [2-8[ kHz frequency bins of a soundscape frequency spectrum (see soundscapespec).

NDSI is computed according to:

NDSI=(biophonyanthropophony)(biophony+anthropophony)NDSI = \frac{(biophony - anthropophony)}{(biophony + anthropophony)}


NDSI varies between -1 and +1, where +1 indicates a signal containing no anthropophony.

Value

A numeric vector of length 1 giving the NDSI value.

Author(s)

Jerome Sueur

References

Kasten, E.P., Gage, S.H., Fox, J. & Joo, W. (2012). The remote environmental assessment laboratory's acoustic library: an archive for studying soundscape ecology. Ecological Informatics, 12, 50-67.

See Also

soundscapespec, SAX, NDSI

Examples

## Note that 'tico' is not a soundscape recording...
data(tico)
spec <- soundscapespec(tico, plot=FALSE)
NDSI(spec)
NDSI(spec, max=TRUE)

Generate noise

Description

This function generates noise.

Usage

noisew(f, d, type="unif", listen = FALSE, output = "matrix")

Arguments

f

sampling frequency of the signal to be generated (in Hz)

d

duration of the signal to be generated.

type

a character string to specify the type of noise, either "unif" or "gaussian".

listen

if TRUE the new sound is played back.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

Details

Uniform noise is generated using runif and gaussian noise is based on rnorm

Value

A new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected]

See Also

synth, pulse

Examples

# add noise to a synthetic signal
a<-noisew(d=1,f=8000)
b<-synth(f=8000,d=1,cf=2000,plot=FALSE)
c<-a+b
spectro(c,f=8000)

Frequency of a muscical note

Description

This function computes the frequency of a musical note (Equal temperament)

Usage

notefreq(note, ref = 440, octave = 3)

Arguments

note

a numerical or a character vector. See Note.

ref

a numerical vector of length 1 for the reference frequency.

octave

a numerical vector of length for the octave number.

Details

The frequency is computed according to:

f=ref×2octave3+note1012f = ref \times 2 ^{octave - 3 + \frac{note-10}{12}}

with:
ref = reference frequency,
octave = octave number, and
note = rank of the note along the scale.

Value

The frequency in Hz is returned.

Note

The note can be given in two ways. The first solution is to give the rank of the note along the scale (e.g. rank 10 for A) or to give its names in characters with the following notation: C, D, E, F, G, A, B.

Author(s)

Jerome Sueur

See Also

octaves

Examples

# Some notes frequency (use apply-like functions when dealing with character strings)
sapply(c("C", "A", "Gb"), notefreq)

# C major scale plot
n <- 1:12
freq <- notefreq(n)
names <- c("C", "C#", "D", "D#", "E", "F", "F#", "G", "G#", "A", "A#", "B") 
plot(n, freq, pch=19, cex=1.5,
     xlab = "Note name",
     ylab = "Frequency (Hz)",
     xaxt="n", las=1, main="Third octave")
axis(side=1, at=n, labels=names)
abline(h=freq, col="lightgrey")

# C major scale sound
f <- 2000 # sampling rate
s <- NULL
for (i in 1:length(freq))
  {
    tmp <- synth(d=0.5, f=f, cf=freq[i])
    s <- pastew(s, tmp, at="start", f)
  }
spectro(s, f, ovlp=75)

Octave values

Description

This functions returns the frequency values of the octaves below and above a specific frequency

Usage

octaves(x, below = 3, above = 3)

Arguments

x

a numeric vector, frequency of the note in Hz or kHz.

below

the number of octaves below x.

above

the number of octaves above x.

Value

A numeric vector with the octave series in frequency (Hz or kHz depending on x unit).

Author(s)

Jerome Sueur

See Also

notefreq

Examples

names <- c("C","D","E","F","G","A","B")
values <- c(261.63, 293.66, 329.64, 349.23, 392, 440, 493.88)
res <- sapply(values, FUN=octaves)/1000
op <- par(las=1,mfrow=c(2,1))
par(mar=c(0,4,1,1))
matplot(x=1:7, y=res, t="o", pch=names, xlab="",
    ylab="Frequency (kHz) [linear scale]", col=rainbow(7), xaxt="n")
par(mar=c(4.5,4,0,1))
matplot(x=1:7, y=res, t="o", pch=names, xlab="Octave",
    ylab="Frequency (kHz) [log scale]", col=rainbow(7), ylog=TRUE, log="y")
par(op)

Song of the cicada Cicada orni

Description

Recording of a calling song section of the Mediterranean cicada Cicada orni.

Usage

data(orni)

Format

A Wave object.

Details

Duration = 0.719 s. Sampling frequency = 22050 Hz.

Source

Recording by Jerome Sueur.

Examples

data(orni)
oscillo(orni,f=22050)

Show a time wave as an oscillogram

Description

This graphical function displays a time wave as an oscillogram in a single or multi-frame plot. The envelope of the wave can also be shown.

Usage

oscillo(wave, f, channel = 1, from = NULL, to = NULL, fastdisp = FALSE,
scroll = NULL, zoom = FALSE, k=1, j=1, cex,
labels = TRUE,  tlab = "Time (s)", alab = "Amplitude",            
byrow = TRUE, identify = FALSE, nidentify = NULL, 
plot = TRUE, colwave = "black", 
coltitle = "black", cextitle = 1.2, fonttitle = 2,
collab = "black", cexlab = 1, fontlab = 1,
colline = "black",
colaxis = "black", cexaxis = 1, fontaxis = 1,
coly0 = "lightgrey",
tcl = 0.5, title = FALSE, xaxt="s", yaxt="n", type="l", bty = "l")

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

from

start of the oscillogram (in s).

to

end of the oscillogram (in s).

fastdisp

faster graphic display for long wave. The oscillogram is displayed/saved faster in the graphic device/ graphic file when set to TRUE, with a cost on graphic resolution.

scroll

a numeric of length 1 allowing to move along the time wave using a slider panel. This numeric corresponds to the number of successive windows dividing the time wave.

zoom

time zoom in with start and end points chosen on the oscillogram with a cursor.

k

number of horizontal sections (by default =1).

j

number of vertical sections (by default =1).

cex

pitch size if type = "p".

labels

if TRUE plots time and amplitude labels (by default TRUE).

tlab

label of time axis.

alab

label of amplitude axis.

byrow

logical, if TRUE, the sections are filled by rows, otherwise the sections are filled by colmuns (by default TRUE).

identify

returns the time and amplitude coordinates of points chosen with a cursor on the oscillogram.

nidentify

a numeric vector of length 1, specifies the number of points to identified on wave if identify is TRUE.

plot

logical, if TRUE returns an oscillographic or envelope plot of wave(by default TRUE).

colwave

colour of the oscillogram or of the envelope.

coltitle

if title is TRUE, colour of the title.

cextitle

character size for the title.

fonttitle

font for the title.

cexlab

character size for axes labels.

fontlab

font for axes labels.

collab

colour of axes labels.

colline

colour of axes line.

colaxis

colour of the axis annotation.

fontaxis

font of axis annotation.

cexaxis

magnification for axis annotation.

coly0

colour of the y=0 line.

tcl

length of tick marks.

title

TRUE to add a title with information on wave duration and f, FALSE to live it blank, or a character string to add any desired title.

xaxt

equivalent to xaxt of par (by default ="s").

yaxt

equivalent to yaxt of par (by default ="n").

type

type of plot, by default "l". Use "n" for no plot.

bty

the type of box to be drawn around the oscillogram.

Value

Data are returned as one-column matrix if plot is FALSE. identify returns a two-column matrix with the time and amplitude coordinates of points successively chosen on the oscillogram.

Note

zoom is similar to but more visual than from and/or to. zoom and identify do work with a single-frame window only (i. e. with k = 1 and j = 1).
Press ‘Stop’ button of the tools bar after choosing the appropriate points on the oscillogram.

Author(s)

Jerome Sueur [email protected] and Caroline Simonis [email protected].

See Also

dynoscillo, oscilloST, oscilloEQ, cutw, pastew, timer

Examples

data(tico)
# a simple oscillogram of a bird song
oscillo(tico)
# zoom in
op<-par(mfrow=c(4,1),mar=c(4.5,4,2,2))
oscillo(tico,22050,cexlab=0.75)
oscillo(tico,22050,from=0.5,to=0.9,cexlab=0.75)
oscillo(tico,22050,from=0.65,to=0.75,cexlab=0.75)
oscillo(tico,22050,from=0.68,to=0.70,cexlab=0.75)
par(op)
# the same divided in four lines
oscillo(tico,f=22050,k=4,j=1)
# the same divided in different numbers of lines and columns
oscillo(tico,f=22050,k=4,j=4)
oscillo(tico,f=22050,k=2,j=2,byrow=TRUE)
oscillo(tico,f=22050,k=2,j=2,byrow=FALSE)
# overplot of oscillographic and envelope representations
oscillo(tico,f=22050)
par(new=TRUE)
env(tico,f=22050,colwave=2)
# full colour modifications in a two-frame oscillogram
op<-par(bg="grey")
oscillo(tico,f=22050,k=4,j=1,title=TRUE,colwave="black",
    coltitle="yellow",collab="red",colline="white",
    colaxis="blue",coly0="grey50")
par(op)
# change the title
data(orni)
oscillo(orni,f=22050,title="The song of a famous cicada")
# move along the signal using scroll
## Not run: 
require(rpanel)
oscillo(tico,f=22050,scroll=8)
## End(Not run)

Oscillogram 'equalizer'

Description

A multipanel plot of a time wave displaying the oscillogram of a bank of frequency filters like in an 'equalizer'.

Usage

oscilloEQ(wave, f, channel = 1, flim = NULL, colwave = 1,
xlab = "Time (s)", ylab = "Frequency band (kHz)",
cexlab = 1, collab = 1, fontlab = 1,
savedir = ".", plot = TRUE, ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

flim

a numeric vector giving the ordered limites of the frequency filters to be applied. By default, 1 kHz frequency filters.

colwave

colour of the oscillogram.

xlab

label of the x axis.

ylab

label of the y axis.

cexlab

character size for axes labels.

collab

color for axes labels.

fontlab

font for axes labels.

savedir

the path were the .wav files will be stored if plot is FALSE. By default, the working directory.

plot

a logical, if TRUE a plot is created, if FALSE then a series of .wav files are saved. Each file corresponds to a frequency band.

...

other oscillo graphical parameters.

Details

The function applies a bank of filters as delimited with the argument flim. If plot is TRUE, then the function displays the wave on a multiframe plot so that the time*amplitude dynamics of each frequency filter can be estimated. The filtered waves are generated using the function fir. If plot is FALSE, then the corresponding waves are saved as separated .wav file. Each file corresponds to a frequency filter.

Value

If plot is FALSE then a series of .wav files are saved. Each file corresponds to a frequency filter.

Author(s)

Jerome Sueur

See Also

oscillo, oscilloST

Examples

data(peewit)
## default 1 kHz frequency filter
oscilloEQ(peewit)
## change de frequency filter limits
oscilloEQ(peewit, flim=c(0, 4, 8, 10))
oscilloEQ(peewit, flim=seq(2, 10, by=0.5))
## play with colors
oscilloEQ(peewit, colwave=c(1,2))
oscilloEQ(peewit, colwave=heat.colors)
blue.gray  <- colorRampPalette(c("darkblue", "lightgrey"))
oscilloEQ(peewit, colwave=blue.gray)
## save files instead of visualizing them
## Not run: 
oscilloEQ(peewit, plot=FALSE)

## End(Not run)

Show a stereo time wave as oscillograms

Description

This graphical function displays a stereo (2 channels) time wave as an oscillogram in a two-frame plot. The envelope of the wave can also be shown.

Usage

oscilloST(wave1, wave2 = NULL, f, from = NULL, to = NULL,
fastdisp = FALSE,
identify = FALSE, plot = TRUE, colwave1 = "black",
colwave2 = "blue", coltitle = "black",
collab = "black", cexlab = 1, fontlab = 1, colaxis = "black",
cexaxis = 1, coly01 = "grey47", coly02 = "black", title = FALSE,
bty = "l")

Arguments

wave1

a first R object.

wave2

a second R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

from

start of the oscillogram (in s).

to

end of the oscillogram (in s).

fastdisp

faster graphic display for long wave. The stereo oscillogram is displayed/saved faster in the graphic device/ graphic file when set to TRUE, with a cost on the graphic resolution.

identify

returns the time coordinate of points chosen with a cursor on the bottom oscillogram.

plot

logical, if TRUE returns an oscillographic or envelope plot of wave(by default TRUE).

colwave1

colour of the oscillogram or of the envelope of wave1.

colwave2

colour of the oscillogram or of the envelope of wave2.

coltitle

if title is TRUE, colour of the title.

collab

colour of axes title.

cexlab

character size for axes title.

fontlab

font for axes title.

colaxis

colour of the axes

cexaxis

mangification for axes annotation.

coly01

colour of the y=0 line of wave1.

coly02

colour of the y=0 line of wave1.

title

logical, if TRUE plots the title with information on time and f (by default FALSE).

bty

the type of box to be drawn around the oscillogram.

Value

Data are returned as two-column matrix if plot is FALSE. identify returns a numeric object with the time coordinate of points successively chosen on the bottom oscillogram.

Author(s)

Jerome Sueur and Caroline Simonis.

See Also

oscillo, oscilloEQ, dynoscillo

Examples

a<-synth(f=8000,d=1,cf=2000,am=c(50,10),plot=FALSE)
b<-synth(f=8000,d=1,cf=1000,fm=c(0,0,2000,0,0),plot=FALSE)
oscilloST(a,b,f=8000)

Paste a time wave to another one

Description

This function pastes a first time wave to a second one. The time wave to be pasted, the time wave to be completed and the resulting time wave can be displayed in a three-frame oscillographic plot.

Usage

pastew(wave1, wave2, f, channel = c(1,1), at = "end",
join = FALSE, tjunction = 0,
choose = FALSE, plot = FALSE,
marks = TRUE, output = "matrix", ...)

Arguments

wave1

a first R object.

wave2

a second R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R objects, by default left channel (1) for each object.

at

wave2 position in seconds where wave1 will be pasted into. Can be also specified as "start", "middle" or "end".

join

if TRUE the two waves will be pasted and jointed by removing the last point of wave2. See examples.

tjunction

a numeric vector to remove clicks at the junction of ‘wave1’ and ‘wave2’. The value specifies the duration in seconds where the real vales will be replaced by a linear interpolation. This duration should be a few milliseconds.

choose

logical, if TRUE the point where wave1 will be pasted into wave2 (=at) can be graphically chosen with a cursor.

plot

logical, if TRUE returns an oscillographic plot of wave1, wave2 and wave1 + wave2 (by default FALSE).

marks

logical, if TRUE shows where wave1 has been pasted (by default TRUE).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Details

If plot is TRUE returns a two-frame plot with three waves:
(1) the wave to be pasted (wave1),
(2) the wave to be completed (wave2),
(3) the resulting wave.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur, improved by Laurent Lellouch

See Also

oscillo, addsilw, cutw, deletew, fadew, mutew , revw, repw, timelapse , zapsilw

Examples

data(tico)
# double a data set describing a bird song
a<-pastew(tico,tico,f=22050)
oscillo(a,f=22050)
# a direct way to see what has been pasted
pastew(tico,tico,f=22050,plot=TRUE)
# cut a section and then paste it at the beginning
a<-cutw(tico, f=22050, from=0.5, to=0.9)
pastew(a,tico,f=22050,at="start",plot=TRUE)
# or paste it at a specific location
pastew(a,tico,f=22050,at=1.4,plot=TRUE)
# setting the argument 'join' to TRUE might be useful
# to smooth pasting when some phase problem occur
# generate two sine waves
a <- synth(cf=50, f=400, d=0.1)
b <- synth(cf=100, f=400, d=0.1)
# paste it with 'join' turned to FALSE
# there is a click at the junction between the two waves
pastew(a, b, f=400, plot=TRUE)
# that can be removed by setting 'join' to TRUE
pastew(a, b, f=400, join=TRUE, plot=TRUE)
# or by using the argument 'tjunction'
pastew(a, b, f=400, tjunction=0.01, plot=TRUE)

Song of the bird Vanellus vanellus

Description

Recording of a song emitted by a peewit (lapwing) male Vanellus vanellus

Usage

data(peewit)

Format

A Wave object.

Details

Duration = 0.706 s. Sampling frequency = 22050 hz.

Source

Recording by Thierry Aubin.

Examples

data(peewit)
oscillo(peewit,f=22050)

Calling song of the tree cricket Oecanthus pellucens

Description

Recording of a calling song section emitted by the European tree cricket Oecanthus pellucens.

Usage

data(pellucens)

Format

A Wave object.

Details

Duration = 3.309 s. Sampling frequency = 11025 hz.

Source

Recording by Jerome Sueur.

Examples

data(pellucens)
oscillo(pellucens,f=11025)

Phase-phase 2D or 3D plot of a time wave

Description

This function returns a 2D or 3D representation of a time wave according to its first, second and possibly third derivatives.

Usage

phaseplot(wave, f, channel = 1, dim = 3, plot = TRUE, type = "l",
xlab = "1st derivative",
ylab = "2nd derivative",
zlab = "3rd derivative", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

dim

a vector of lenght 1, the number of dimensions of the plot. Can be either 2 or 3.

plot

logical, if TRUE plots phase-phase plot (by default TRUE).

type

type of plot that should be drawn. See plot for details (by default "l" for lines).

xlab

title of the x axis.

ylab

title of the y axis.

zlab

title of the z axis.

...

other plot or plot3d graphical parameters of the package rgl.

Value

If plot is FALSE then a 2 or 3 column matrix is returned. The position of the column is related to the order of the derivative (i. e. first colum = first derivative.

Note

Phase-phase plot can be used to test non-linearity.

Author(s)

Jerome Sueur

References

For use of such plots see: Rice AN, Land BR, Bass AH (2011) - Nonlinear acoustic complexity in a fish 'two-voice' system. Proceedings of the Royal Society B, in press.

See Also

phaseplot2

Examples

## Not run: 
require(rgl)
data(tico)
phaseplot(tico)

## End(Not run)
s <- synth(d=0.05, f=44100, cf=440, out="Wave")
n <- noisew(d=0.05, f=44100, out="Wave")
par(mfrow=c(2,1))
phaseplot(s, dim=2)
phaseplot(n, dim=2)

Phase-phase 2D plot of a time wave

Description

This functions returns a 2D representation of a time wave against a delayed version of itself.

Usage

phaseplot2(wave, f, channel = 1, tau = 1, type = "l",
xlab = "x(t)",
ylab = paste("x(t+", tau, ")", sep = ""), ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

tau

the time delay to apply in number of samples.

type

type of plot that should be drawn. See plot for details (by default "l" for lines).

xlab

title of the x axis.

ylab

title of the y axis.

...

other plot parameters.

Details

The principle consists in displaying in a single x-y graph the original time wave with a delayed version of itself. The delay is controlled with the argument tau that needs to be specified in number of samples. The conversion of tau in second is obtained by calculating tau/f, with f the sampling frequency.

Value

Nothing is returned except an x-y plot.

Note

Phase-phase plot can be used to test non-linearity.

Author(s)

Jerome Sueur

References

Kantz H, Schreiber T (2003) Non linear time series analysis. Cambridge University Press.

See Also

phaseplot

Examples

s <- synth(d=0.05, f=44100, cf=440, out="Wave")
n <- noisew(d=0.05, f=44100, out="Wave")
par(mfrow=c(2,1))
phaseplot2(s)
phaseplot2(n)

Play a list of sound files

Description

This function works as a playlist, ie it plays back a list of sound files.

Usage

playlist(directory, sample = FALSE, loop = 1)

Arguments

directory

a character vector indicating the path to the directory where sound files to played are saved.

sample

a logical, if TRUE the order of sounds files to be played back is shuffled.

loop

a numeric vector of length 1, number of loops.

Details

The success of using this function depends on the wave player in use. This works particularly well with SoX under Linux. The type of files (.mp3, .wav, .ogg etc) depends on the wave player as well)

Value

None. Listen and enjoy!

Note

The function is mainly based on play

Author(s)

Jérôme Sueur

See Also

play, listen

Examples

## Not run: 
playlist("MyMusic", sample = TRUE, loop=2)

## End(Not run)

Pre-emphasis speech filter

Description

A pre-emphasis frequency filter for speech

Usage

preemphasis(wave, f, channel = 1, alpha = 0.9,
plot = FALSE, output = "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

alpha

time constant, see Details.

plot

a logical, if TRUE plots the spectrogram of the filtered wave and the frequency response of the comb filter.

output

character string, the class of the object to return, either 'matrix', 'Wave', 'Sample', 'audioSample' or 'ts'.

...

other arguments to be passed to spectro except scale and osc that are set by default to FALSE.

Details

The function applies a pre-emphasis filter usually applied in speech analysis. The filter is a kind of high-pass frequency filter that amplifies the high-frequency content of the sample. The filter is defined with:

y(n)=x(n)α×x(n1)y(n) = x(n) - \alpha \times x(n - 1)

where alpha is a time constant usually set between 0.9 and 1.

The frequency response of the filter is obtained with:

H(f)=1+a22×α×cos(2×π×f/fs)H(f)=1+a^{2}-2 \times \alpha \times \cos(2 \times \pi \times f/f_{s})

Value

A new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur

See Also

bwfilter, combfilter, ffilter, fir,lfs, afilter

Examples

data(sheep)
fc <- 150
f <- sheep@samp.rate
alpha <- exp(-2*pi*fc/f)
res <- preemphasis(sheep, alpha=alpha, output="Wave")

Generate rectangle pulse

Description

This function generates a rectangle pulse.

Usage

pulsew(dbefore, dpulse, dafter, f, plot = FALSE, output = "matrix", ...)

Arguments

dbefore

duration of the silent period before the pulse

dpulse

duration of the pulse to generate

dafter

duration of silent period after the pulse

f

sampling frequency of the signal to be generated (in Hz)

plot

logical, if TRUE returns an oscillographic plot of the pulse generated (by default FALSE).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other plot parameters.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected]

See Also

synth, noisew

Examples

pulsew(dbefore=0.5,dpulse=0.1,dafter=0.3,f=8000,plot=TRUE)

Resonance quality factor of a frequency spectrum

Description

This function estimates the frequency pureness of a time wave by returning the resonant quality factor Q at a specific dB level.

Usage

Q(spec, f = NULL, level = -3, mel = FALSE, plot = TRUE, colval = "red",
cexval = 1, fontval = 1, flab = NULL,
alab = "Relative amplitude (dB)", type = "l", ...)

Arguments

spec

a data set resulting of a spectral analysis obtained with spec, or meanspec (in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

f

sampling frequency of the wave used to obtain spec (in Hz). Not necessary if spec is a two columns matrix obtained with spec or meanspec.

level

frequency bandwidth set by an amplitude value relative to spectrum (in dB).

mel

a logical, if TRUE the (htk-)mel scale is used.

plot

logical, if TRUE returns the spectrum with Q plotted (by default TRUE).

colval

colour of plotting Q.

cexval

character size of plotting Q.

fontval

font of plotting Q.

flab

title of the frequency axis.

alab

title of the amplitude axis.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

...

other plot graphical parameters.

Details

A high Q value indicates a highly resonant system.

Value

A list is returned with the following four items:

Q

a numeric vector of length 1 returning the Q factor (no units)

dfreq

a numeric vector of length 1 the dominant frequency (kHz)

fmin

a numeric vector of length 1 returning the minimum frequency of the -dB level bandwidth (kHz)

fmax

a numeric vector of length 1 returning the minimum frequency of the -dB level bandwidth (kHz)

bwd

a numeric vector of length 1 returning the bandwidth, i. e. fmax-fmin (kHz)

Note

This function is based on an linear interpolation of the spectrum so that the result should be considered as an estimation, not an exact measure.

Author(s)

Jerome Sueur, improved by Laurent Lellouch

See Also

spec, meanspec, corspec, fft.

Examples

# bird song
data(tico)
t<-spec(tico,f=22050,at=1.1,plot=FALSE,dB="max0")
op<-par(mfrow=c(2,1),las=1)
Q(t,type="l")
Q(t,type="l",xlim=c(3.8,4.2),ylim=c(-60,0))
title("zoom in")
par(op)
# cricket, changing the dB level
data(pellucens)
p<-spec(pellucens,f=11025,at=0.5,plot=FALSE,dB="max0")
op<-par(mfrow=c(3,1))
Q(p,type="l",xlim=c(1.8,2.6),ylim=c(-70,0))
title("level = - 3 (default value)",col.main="red")
Q(p,type="l",level=-6,
    xlim=c(1.8,2.6),ylim=c(-70,0),colval="blue")
title("level = - 6",col.main="blue")
Q(p,type="l",level=-9,
    xlim=c(1.8,2.6),ylim=c(-70,0),colval="green")
title("level = - 9",col.main="green")
par(op)

Audacity audio markers import

Description

Read audio markers as exported by Audacity.

Usage

read.audacity(file, format)

Arguments

file

A .txt file produced by Audacity when exporting time or time x frequency markers.

format

The format of the file name that will appear in the value, that is in the first column of the data frame returned. if "dir" then the full path to the file is returned, if "base" only the base name of the file is returned.

Details

Audacity opens the possibility to annotate sound files with a marker channel. These markers can be exported as .txt files. The function read.audacity import such .txt files whether they contain time markers or time x frequency markers.

Value

A data.frame. The size of the data.frame differs whether the .txt file contains time markers or time x frequency markers.
For time markers, the data.frame contains 4 columns:

  1. file returning the name of the input file either with the full path or with the base name only (see argument format),

  2. label the text label,

  3. t1 the start time in seconds,

  4. t2the end time in seconds.

For time x frequency markers, the data.frame contains 6 columns:

  1. file returning the name of the input file either with the full path or with the base name only (see argument format),

  2. label the text label,

  3. t1 the start time in seconds,

  4. t2 the end time in seconds,

  5. f1 the lower frequency in Hz,

  6. f2 the upper frequency in Hz.

Author(s)

Jerome Sueur

References

Audacity is a free software distributed under the terms of the GNU General Public License.
Web site: https://www.audacityteam.org/

See Also

write.audacity

Examples

## Not run: 
## If 'markers.txt' is an export of Audacity markers
x <- read.audacity("markers.txt")

## End(Not run)

Repeat a time wave

Description

This function repeats a time wave

Usage

repw(wave, f, channel = 1, times = 2, join = FALSE, plot = FALSE, output= "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

times

a numeric of length 1 describing the number of times the wave has to be repeated.

join

if TRUE the last point of wave will be removed for smoothing junction between repetitions. See examples.

plot

logical, if TRUE plots the repeated time wave.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected]

See Also

oscillo, addsilw, cutw, deletew, fadew, mutew, pastew, revw, zapsilw

Examples

data(tico)
repw(tico,f=22050,plot=TRUE)
# use 'join' for smooth pasting
par(mfrow=c(2,1))
a <- synth(cf=50, f=400, d=0.1)
repw(a, f=400, plot=TRUE)
title(main="join is FALSE")
points(x=0.1, y=0, cex=2, col=2)
repw(a, f=400, join=TRUE, plot=TRUE)
title(main="join is TRUE")
points(x=0.1, y=0, cex=2, col=2)

Resample a time wave

Description

This function resamples (down- or over-samples) a time wave. This corresponds to a sampling frequency change.

Usage

resamp(wave, f, g, channel = 1, output="matrix")

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

g

new sampling frequency of wave (in Hz).

channel

channel of the R object, by default left channel (1).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Note

Resampling might change frequency properties of the time wave.

Author(s)

Jerome Sueur [email protected]

Examples

data(peewit)
# downsampling
a<-resamp(peewit,f=22050,g=11025)
# oversampling
b<-resamp(peewit,f=22050,g=44100)

Time reverse of a time wave

Description

Reverse the wave along the time axis.

Usage

revw(wave, f, channel = 1, env = TRUE, ifreq = TRUE,
plot = FALSE, output = "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

env

logical, if TRUE the amplitude envelope is reversed.

ifreq

logical, if TRUE the instantaneous frequency is reversed.

plot

logical, if TRUE returns an oscillographic plot of the reversed wave (by default FALSE).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Details

If plot is TRUE returns an oscillogram of the reversed wave. The amplitude and the instantaneous frequency can be independently reversed thanks to the arguments env and ifreq. See the examples.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected]

References

Beeman, K. 1998. Digital signal analysis, editing and synthesis in Hopp, S. L., Owren, M. J. and Evans, C. S. (Eds) 1998. Animal acoustic communication, pp. 59-103. Springer, Berlin, Heidelberg.

See Also

oscillo, addsilw, deletew, fadew, pastew, mutew

Examples

data(tico)
# simple reverse
revw(tico,f=22050,plot=TRUE)
# envelope reverse only
revw(tico,f=22050,ifreq=FALSE, plot=TRUE)
# instantaneous frequency reverse only
revw(tico,f=22050,env=FALSE, plot=TRUE)

Remove the amplitude modulations of a time wave

Description

This functions removes the amplitude modulation of a time wave through the Hilbert amplitude envelope.

Usage

rmam(wave, f, channel = 1, plot = FALSE, listen = FALSE, output = "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

plot

logical, if TRUE returns an oscillographic plot of the nwe time wave (by default FALSE).

listen

if TRUE the new sound is played back.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Details

The new time wave is obtained by dividing the original time wave by its Hilbert amplitude envelope.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected]

References

Mbu Nyamsi, R. G., Aubin, T. & Bremond, J. C. 1994 On the extraction of some time dependent parameters of an acoustic signal by means of the analytic signal concept. Its application to animal sound study. Bioacoustics, 5: 187-203.

See Also

hilbert.

Examples

# generate a new sound with amplitude modulation
a<-synth(f=8000, d=1, cf=1500, am=c(50,10))
# remove the amplitude modulation and plot the result
rmam(a,f=8000,plot=TRUE)

Remove noise

Description

This function removes background noise by smoothing

Usage

rmnoise(wave, f, channel = 1, output = "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other smooth.spline arguments.

Details

This function is based on smooth.spline. You can use the arguments of the later to modify the smoothing.

Value

A new wave is returned. The class of the returned object is set with the argument output.

Note

Low frequency noise might not be removed out properly.

Author(s)

Jerome Sueur [email protected]

See Also

afilter, noisew

Examples

# synthesis of a 440 Hz sound with background noise
n <- noisew(d=1,f=8000)
s <- synth(d=1,f=8000,cf=440)
ns <- n+s
# remove noise (but low frequency content still there)
a <- rmnoise(ns,f=8000)

Remove the offset of a time wave

Description

This function removes the offset of a time wave.

Usage

rmoffset(wave, f, channel = 1, FUN = mean, plot = FALSE, output = "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

FUN

a function used to apply the offset correction. See Details.

plot

logical, if TRUE returns an oscillographic plot of the wave after removing the offset (by default FALSE).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Value

The offset is removed by substracting the wave by its mean (argument FUN). But other function can be used. For instance, it can be more approriate to use the median to remove the offtset and transients. See Examples.
If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected]

See Also

oscillo

Examples

data(tico)
# artifically generates an offset
tico2<-tico+0.1
# see the wave with an offset
oscillo(tico2, f=22050)
# remove the offset with the mean (by default)
rmoffset(tico2, f=22050, plot=TRUE)
# remove the offset with the median
rmoffset(tico2, f=22050, FUN=median, plot=TRUE)

Root Mean Square

Description

This function computes the root mean square or quadratic mean.

Usage

rms(x, ...)

Arguments

x

an R object

...

further arguments passed to mean

Details

The Root Mean Square or quadratic mean is computed according to:

RMS=1n×i=1Nxi2RMS = \sqrt{\frac{1}{n} \times \sum_{i=1}^{N} x{_i}{^2}}

Value

A numeric vector of length 1

Author(s)

Jerome Sueur [email protected]

See Also

mean

Examples

# simple rms
rms(1:10)
# rms of a normalized envelope
data(sheep)
env <- env(sheep, f=8000)
rms(env)

Roughness or total curvature

Description

This function computes the roughness or total curvature of a curve, i.e. of a time wave or of a spectrum

Usage

roughness(x, std = FALSE)

Arguments

x

a vector

std

a logical, if set to TRUE then x is standardized by its maximum.

Details

Roughness or total curvature is the integrated squared second derivative :

roughness=[D2x(t)]2dtroughness = \int [D^2x(t)]^2 \, \mathrm{d} t

.

Value

A vector of length 1.

Note

The value has not unit.

Author(s)

Jerome Sueur

References

Ramsay JO, Silverman BW (2005) Functional data analysis. Springer, Berlin.

See Also

rugo, rms, sh, th, H.

Examples

data(tico)
spec <- meanspec(tico, plot=FALSE)[,2]
roughness(spec)

Rugosity of a time wave

Description

This function computes the rugosity of a time wave or time series

Usage

rugo(x, ...)

Arguments

x

a vector

...

other mean parameters.

Details

The formula has been slightly modified from Mezquida & Martinez (2009: 826) to fit with the classical definition of the root-mean-square (see rms).
The rugosity is then computed as following:

rugo=i=1n1(xi+1xi)2nrugo = \sqrt{\sum_{i=1}^{n-1} \frac{(x_{i+1}-x_{i})^2}{n}}

for a vector x of length n.

Value

A vector of length 1.

Note

The rugosity of a noisy signal will tend to be higher than that of a pure tone signal, all other things being equal.

Author(s)

Jerome Sueur

References

Mezquida DA, Martinez JL (2009) - Platform for bee-hives monitoring based on sound analysis. A perpetual warehouse for swarm's daily activity. Spanish Journal of Agricultural Research 7, 824-828.

See Also

roughness, rms, sh, th, H.

Examples

data(tico) ; tico <-tico@left
# rugosity of the original recording normalised
rugo(tico/max(tico))
# synthesis of white noise with the same duration as tico
noise <- noisew(d=length(tico)/22050, f=22050)
# tico is normalised to get similar amplitude with the noise
tico.norm <- tico/max(tico)
# addition of noise to tico
tico.noisy <- tico.norm + 0.5*noise
# new rugosity (higher) on normalised signal
rugo(tico.noisy/max(tico.noisy))

Save a .wav file

Description

Save sound data as .wav file

Usage

savewav(wave, f, channel = 1, filename = NULL, rescale = NULL, ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

filename

name of the new file. (by default the name of wave).

rescale

a numeric vector of length 2 giving the lower (negative value) and upper (positive value) amplitude limits of the .wav file to be exported.

...

other arguments to be passed to writeWave

.

Details

This function uses three functions from the package tuneR: Wave, normalize and writeWave.

Note

The file automatically owerwrites an existing file with the same name.
The amplitude (volume) of the .wav file is normalized by defaults but can be changed with the argument rescale. See examples

Author(s)

Jerome Sueur [email protected], Ethan C. Brown for the argument 'rescale'

See Also

export.

Examples

require(tuneR)
a<-synth(f=8000,d=2,cf=2000,plot=FALSE)
# the name of the file is automatically the name of the object
# here: "a.wav"
savewav(a,f=22050)
unlink("a.wav")
# if you wish to change the name, use the 'file' argument
savewav(a,f=22050,file="b.wav")
unlink("b.wav")
# if you wish to change the amplitude of the file, use the argument 'rescale'
# this will turn down the volume of a 16 bit sound
# which amplitude was originally ranging between -2^15 and +2^15
savewav(a, f=22050, file="c.wav", rescale=c(-1500,1500))
unlink("c.wav")

Symbolic Aggregate approXimation

Description

This function converts a numeric times seris into a series of letters with a specific length and alphabet.

Usage

SAX(x, alphabet_size, PAA_number,
breakpoints = "gaussian", collapse = NULL)

Arguments

x

a numeric vector.

alphabet_size

a numeric vector of length 1 setting the size of the alphabet.

PAA_number

a numeric vector of length 1 setting the number of elements (subsequences) of the Piecewise Aggregate Approximation (PAA).

breakpoints

either a character vector ("gaussian", "quantiles") or a numeric vector specifying the sorted values of the breakpoints along the distribution of x. See details and examples.

collapse

a character vector of length 1, specifying the way to collapse the output letters, see paste. By default letters are returned separated.

Details

The SAX method has been developed to reduce the dimensionality of a numerical series into a short chain of characters. SAX follows a two-step process: (1) Piecewise Aggregate Approximation (PAA) and (2) conversion a PAA sequence into a series of letters.

PAA consists in a Z-normalisation, a segmentation of the series of length n into w segments, and the computation of each segment average.

The conversion of the PAA into a series of letters is achieved by attributing with equiprobability each value of the PAA to a letter in reference to a Gaussian distribution. This process therefore assumes that the distribution of the numeric series x follows a Gaussian distribution. To relax the constraints of normality we here added the possibility to directly work on the quantiles of the original data distribution or to specify particular breakpoints along the distribution of x. See the examples.

Value

A character vector of length (when collapse is NULL) or number of character (when collapse is not NULL) corresponding to PAA_number argument.

Note

SAX has been used recently to search similar times series in a soundcape data base (Kasten et al., 2012).

Author(s)

Laurent Lellouch. An improvement added by Pavel Senin.

References

Kasten, E.P., Gage, S.H., Fox, J. & Joo, W. (2012). The remote environmental assessment laboratory's acoustic library: an archive for studying soundscape ecology. Ecological Informatics, 12, 50 - 67.

Lin, J., Keogh, E., Lonardi, S., Chiu, B., June (2003). A symbolic representation of time series with implications for streaming algorithms. Proceedings of the 8th ACM SIGMOD Workshop on Research Issues in Data Mining and Knowledge Discovery. San Diego, California, USA.

See Also

discrets, symba, soundscapespec

Examples

data(tico)
spec <- soundscapespec(tico, plot=FALSE)[,2]
SAX(spec, alphabet = 5, PAA = 10)

# change breakpoints
SAX(spec,  alphabet = 5, PAA = 10, breakpoints="quantiles")
SAX(spec,  alphabet = 5, PAA = 10, breakpoints=c(0, 0.5, 0.75, 1))
SAX(spec,  alphabet = 5, PAA = 10, breakpoints=c(0, 0.33, 0.66, 1))

# different output formats
SAX(spec,  alphabet = 5, PAA = 10, collapse="")
SAX(spec,  alphabet = 5, PAA = 10, collapse="-")

Soundcape chord diagram

Description

Computes and displays a chord diagram of a set of audio files or of a set segments extracted from a single audio file.

Usage

scd(input, f,  sl, wl = 512, wn = "hanning", ovlp = 0, flim = NULL,
rmoffset = TRUE, threshold = NULL, HCA = TRUE,
grid.col = terrain.colors, names, plot = TRUE, verbose = TRUE, ...)

Arguments

input

a character vector, either (i) the path to the directory where .wav files are stored, (ii) directly the names of the .wav files to be processed, or (iii) a single .wav file to be segmented by the duration set with the argument sl.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in the .wav files contained in input.

sl

segment length in duration if input is a single file.

wl

window length for the analysis spectral (even number of points) (by default = 512).

wn

window name for the spectral analysis, see ftwindow (by default "hanning").

ovlp

overlap between two successive windows (in %) for the spectral analysis.

flim

a numeric vector of length 2 to select a frequency band (in kHz).

rmoffset

a logical to sepcify whether DC offset should be removed. By default TRUE.

threshold

a numeric value in ]0,1[ to be applied to the similarity distance. All similairty distances below this threshold will not depicted.

HCA

logical, if TRUE the sectors are colored according to clusters automatically obtained with a hierarchical cluster analysis (HCA).

grid.col

name of color palette to color the sectors and the links). By default terrain.colors.

names

names of the sectors, if empty then the names of the .wav files or the time stamps of the segments.

plot

logical, if TRUE plots the chord diagram.

verbose

logical, if TRUE prints the computation progress of the mean spectra.

...

other chordDiagram parameters.

Details

The soundscape chord diagram (SCD) aims at representing similarities between audio files or audio segments extracted from a single audio file. The mean frequency spectrum of each file/segment is computed using a STFT. These frequency spectra are then (1) pairwised compared using a similarity distance (see function diffcumspec, and (2) automatically clustered with a hierarchical cluster analysis (HCA) (see function HCPC of FactoMiner). The resulting similarity matrix is then given as an input to the function chordDiagram. The width of the sectors and the links are based on the spectral similarity matrix. The color of the sectors and the links follow the HCA classification.

Value

THe function returns a list of two items:

m

spectral similarity matrix

resHCA

the classification result of the HCA, if HCA is TRUE

Note

The function call the function HCPC of the package FactoMineR and the function chordDiagram of the package circlize.

Author(s)

Adèle de Baudouin, Jérôme Sueur

References

de Baudouin, A, Couprie P, Michaud F, Haupert S, Sueur J – Similarity visualization of nature and music soundscapes, in prep.

See Also

diffcumspec

Examples

## Not run: 
## 1 ##
# if 'dir' contains a set of files recorded with a Wildlife Acoustics
# songmeter recorder or an Audiomoth  then a direct way to obtain
# the soundscape chord diagram (SCD)  of all .wav files is
dir <- "pathway-to-directory-containing-wav-files"
scd(dir)
# to change the STFT parameters used to obtain each mean spectrum
lts(dir, wl=1024, wn="hamming", ovlp=50)
# to select only high similarities, here above 0.6
scd(dir, threshold=0.6)
# to change the colors
scd(dir, grid.col=colorRampPalette(c("darkblue", "yellow", "grey")))
# to name manually the sectors
scd(dir, names=as.character(0:23))
# to name automatically the sectors from the name of songmeter files
# here according to hour of recording 
scd(dir, names=as.character(songmeter(files)$hour))  

## 2 ##
# to directly use files names stored in the working directory
files <- c("S4A09154_20190213_150000.wav", "S4A09154_20190213_153000.wav",
"S4A09154_20190213_160000.wav", "S4A09154_20190213_163000.wav",
"S4A09154_20190213_170000.wav", "S4A09154_20190213_173000.wav",
"S4A09154_20190213_180000.wav", "S4A09154_20190213_183000.wav",
"S4A09154_20190213_190000.wav", "S4A09154_20190213_193000.wav")
scd(files)

## 3 ##
# to  use of single files which is segmented in successive time segments
# lasting each 60 s
file <- "a-very-nice-soundscape.wav")
scd(file, sl = 60)

## End(Not run)

Standard deviation of dB values

Description

This function estimates the standard deviation of dB values

Usage

sddB(x, level = "IL")

Arguments

x

a numeric vector.

level

intensity level ("IL") or sound pressure level ("SPL")

Details

The standard deviation of dB values is not linear. The function is an estimation not an exact computation which is not possible.

Value

A numeric vector of length 1.

Author(s)

Jérôme Sueur

References

Wikipedia, https://en.wikipedia.org/wiki/Propagation_of_uncertainty

See Also

meandB, moredB, convSPL, dBweight

Examples

sddB(c(89,90,95))
sddB(c(89,90,95), level="SPL")

A quick look at quantitative data

Description

See quantitative data at a glance

Usage

seedata(data, na.rm = FALSE, col = "grey")

Arguments

data

a numeric vector describing quantitative data.

na.rm

logical, if TRUE removes NA.

col

main color.

Details

The red curves depict the corresponding Normal law (same mean and sd as data).

Value

A multi-plot graphic is returned.

Author(s)

Caroline Simonis [email protected] and Jerome Sueur [email protected].

Examples

seedata(rnorm(1000))

Sound analysis and synthesis

Description

seewave provides functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes in particular time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, frequency coherence, dominant frequency, analytic signal, 2D and 3D spectrograms.

Details

Package: seewave
Type: Package
Version: 2.2.3
Date: 2023-10-15
License: GPL version 2 or newer
Contributors : Pierre Aumond, Ethan C. Brown,
Adèle de Baudouin,
Guillaume Corbeau, Camille Desjonqueres,
Marion Depraetere, Francois Fabianek,
Amandine Gasc, Sylvain Haupert,
Eric Kasten, Laurent Lellouch,
Stefanie LaZerte, Jonathan Lees,
Jean Marchal, Thibaut Marin-Cudraz,
Andre Mikulec, Sandrine Pavoine,
David Pinaud, Luis J. Villanueva-Rivera
Zev Ross, Carl G. Witthoft,
Hristo Zhivomirov
Acknowledgments: Marianna Anichini, Andrey Anikin, Michel Baylac,
Charlotte Cure, Denis Dupeyron,
Kurt Fristrup, Arnold Fertin,
Sylvain Haupert, Kurt Hornik,
Yannick Jadoul, Emiliano A. Laca,
Uwe Ligges, Duncan Murdoch, Morgane Papin,
Emmanuel Paradis, Daniel Ridley-Ellis,
Brian Ripley, Jesse Ross,
Zev Ross, Pavel Senin, David Savage,
Arvind Sowmyan, Simon Urbanek
Maria A. Wis, George Zhang
Webpage: https://rug.mnhn.fr/seewave/
Discussion group : https://groups.google.com/g/seewave
Source reference: Sueur J, Aubin T, Simonis C (2008) - seewave: a free modular tool for sound analysis and synthesis.
Bioacoustics, 18: 213-226.
Book: Sueur J (2018) - Sound analysis and synthesis with R. Springer.

Author(s)

Jerome Sueur <[email protected]>
Thierry Aubin
Caroline Simonis
Maintainer: Jerome Sueur <[email protected]>


Set the amplitude envelope of a time wave to another one

Description

This function sets the amplitude envelope of a time wave to another one

Usage

setenv(wave1, wave2, f, channel = c(1,1), envt="hil", msmooth = NULL, ksmooth = NULL,
plot = FALSE, listen = FALSE, output = "matrix", ...)

Arguments

wave1

a first R object.

wave2

a second R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R objects, by default left channel (1) for each object.

envt

the type of envelope to be used for wave2: either "abs" for absolute amplitude envelope or "hil" for Hilbert amplitude envelope. See env.

msmooth

a vector of length 2 to smooth the amplitude envelope of wave2 with a mean sliding window. The first component is the window length (in number of points). The second component is the overlap between successive windows (in %). See env.

ksmooth

kernel smooth via kernel to apply to the amplitude envelope ofwave2. See env.

plot

if TRUE returns the oscillogram of the new time wave (by default FALSE).

listen

if TRUE the new sound is played back.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Details

wave1 and wave2 can have different duration (length)
Smoothing the envelope with smooth or ksmooth can significantly change the value returned.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur [email protected]

See Also

drawenv, env, synth

Examples

data(tico)
a<-synth(d=1,f=22050,cf=1000)
# apply 'tico' ammplitude envelope to 'a' that has a square amplitude envelope
setenv(a,tico,f=22050,plot=TRUE)
# the same but with smoothing the envelope
setenv(a,tico,f=22050,ksmooth=kernel("daniell",50),plot=TRUE)

Spectral Flatness Measure

Description

This function estimates the flatness of a frequency spectrum.

Usage

sfm(spec)

Arguments

spec

a data set resulting of a spectral analysis obtained with spec or meanspec (not in dB).

Details

SFM is calculated as the ratio between the geometric mean and the arithmetic mean :

F=N×i=1NyiNi=1NyiF = N\times{\frac{\sqrt[N]{\prod_{i=1}^N{y_i}}}{\sum_{i=1}^N{y_i}}}

with:
y = relative amplitude of the i frequency,
and N = number of frequencies.

Value

A single value varying between 0 and 1 is returned. The value has no unit.

Note

The SFM of a noisy signal will tend towards 1 whereas the SFM of a pure tone signal will tend towards 0.
See sh for another measure of signal noisiness/pureness.

Author(s)

Jerome Sueur [email protected]

See Also

sh, csh

Examples

a<-synth(f=8000,d=1,cf=2000,plot=FALSE)
speca<-spec(a,f=8000,at=0.5,plot=FALSE)
sfm(speca)
# [1] 0
b<-noisew(d=1,f=8000)
specb<-spec(b,f=8000,at=0.5,plot=FALSE)
sfm(specb)
# [1] 0.8233202

Shannon and Renyi spectral entropy

Description

This function computes the Shannon or Renyi entropy of a frequency spectrum

Usage

sh(spec, alpha = "shannon")

Arguments

spec

a data set resulting of a spectral analysis obtained with spec or meanspec (not in dB).

alpha

a character string, by default "shannon" to compute Shannon entropy, "simpson" to compute Simpson entropy otherwise a numeric vector of length 1 with a value superior to 0 but different to 1 to compute Renyi entropy. See the examples.

Details

. Shannon spectral entropy is calculated according to:

S=i=1Nyilog2(yi)log2(N)S = -\frac{\sum_{i = 1}^{N} y_i log_2(y_i)}{log_2(N)}

. Simpson or Gini-Simpson spectral entropy (or index) is computed according to:

GS=1i=1Nyi2GS = 1 - \sum_{i=1}^{N} y_{i}^2

. Renyi spectral entropy of order alpha is calucalted according to:

R=11α×log2(i=1Nyiα)R = \frac{1}{1-\alpha} \times log_2(\sum_{i = 1}^{N} y_{i}^{\alpha})

with

α0\alpha \geq 0

α1\alpha \neq 1

y = relative amplitude of the i frequency,

i=1Nyi=1\sum_{i = 1}^{N} y_i = 1


and N = number of frequencies.

Value

A numeric vector of length 1 is returned. The value has no unit.

Note

The Shannon entropy scaled between 0 and 1 is also known as Pielou's evenness index

Note

The Shannon spectral entropy of a noisy signal will tend towards 1 whereas the Shannon spectral entropy of a pure tone signal will tend towards 0. See Han et al. for details regarding the Renyi entropy.

Author(s)

Jerome Sueur and Laurent Lellouch

References

Han, NC, Muniandy SV, Dayou J (2011) Acoustic classification of Australian anurans based on hybrid spectral-entropy approach. Applied Acoustics.

Nunes RR, Almeida de MP, Sleigh JW (2004) - Spectral entropy: a new method for anesthetic adequacy. Revista Brasileira de Anestesiologia, 54, 413-422.

Renyi A (1961) - On measures of information and entropy. Proceedings of the 4th Berkeley Symposium on Mathematics, Statistics and Probability 1960. pp. 547-561.

Simpson EH (1949) - Measurement of diversity. Nature, 163, 688.

See Also

csh,th, H, sfm

Examples

a<-synth(f=8000,d=1,cf=2000,plot=FALSE)
speca<-spec(a,f=8000,at=0.5,plot=FALSE)
## Shannon spectral entropy
sh(speca)
# [1] 0.2336412
b<-noisew(d=1,f=8000)
specb<-spec(b,f=8000,at=0.5,plot=FALSE)
sh(specb)
# close to 1
## Renyi spectral entropy
sh(speca, alpha=2)
sh(speca, alpha=3)

Sheep bleat

Description

Recording of a sheep bleat.

Usage

data(sheep)

Format

A Wave object.

Details

Duration = 2.47 s. Sampling frequency = 8000 hz.

Source

Recording by Frederic Sebe.

Examples

data(sheep)
oscillo(sheep,f=8000)

Similarity between two frequency spectra

Description

This function estimates the similarity between two frequency spectra.

Usage

simspec(spec1, spec2, f = NULL, mel = FALSE,
norm = FALSE, PMF = FALSE,
plot = FALSE, type = "l",
lty =c(1, 2, 3), col = c(2, 4, 1),
flab = NULL, alab = "Amplitude (percentage)",
flim = NULL, alim = NULL,
title = TRUE, legend = TRUE, ...)

Arguments

spec1

a first data set resulting of a spectral analysis obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

spec2

a first data set resulting of a spectral analysis obtained with spec or meanspec (not in dB). This can be either a two-column matrix (col1 = frequency, col2 = amplitude) or a vector (amplitude).

f

sampling frequency of waves used to obtain spec1 and spec2 (in Hz). Not necessary if spec1 and/or spec2 is a two columns matrix obtained with spec or meanspec.

mel

a logical, if TRUE the (htk-)mel scale is used.

norm

a logical, if TRUE spec1 and spec2 are normalised (scaled) between 0 and 1.

PMF

a logical, if TRUE spec1 and spec2 are transformed into probability mass functions.

plot

logical, if TRUE plots both spectra and similarity function (by default FALSE).

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

lty

a vector of length 3 for the line type of spec1, spec2 and of the similarity function if type="l".

col

a vector of length 3 for the colour of spec1, spec2, and the similarity function.

flab

title of the frequency axis.

alab

title of the amplitude axis.

flim

the range of frequency values.

alim

range of amplitude axis.

title

logical, if TRUE, adds a title with S value.

legend

logical, if TRUE adds a legend to the plot.

...

other plot graphical parameters.

Details

Spectra similarity is assessed according to:

S=100/N×i=1Nminspec1(i),spec2(i)maxspec1(i),spec2(i)S = \frac{100/N} \times{\sum_{i=1}^N{\frac{\min{spec1(i),spec2(i)}} {\max{spec1(i),spec2(i)}}}}

with S in %.

Value

The similarity index is returned. This value is in %.
When plot is TRUE, both spectra and the similarity function are plotted on the same graph. The similarity index is the mean of this function.

Author(s)

Jerome Sueur, improved by Laurent Lellouch

References

Deecke, V. B. and Janik, V. M. 2006. Automated categorization of bioacoustic signals: avoiding perceptual pitfalls. Journal of the Acoustical Society of America, 119: 645-653.

See Also

spec, meanspec, corspec, diffspec, diffenv, kl.dist, ks.dist, logspec.dist, itakura.dist

Examples

a<-noisew(f=8000,d=1)
b<-synth(f=8000,d=1,cf=2000)
c<-synth(f=8000,d=1,cf=1000)
d<-noisew(f=8000,d=1)
speca<-spec(a,f=8000,at=0.5,plot=FALSE)
specb<-spec(b,f=8000,at=0.5,plot=FALSE)
specc<-spec(c,f=8000,at=0.5,plot=FALSE)
specd<-spec(d,f=8000,at=0.5,plot=FALSE)
simspec(speca,speca)
simspec(speca,specb)
simspec(speca,specc,plot=TRUE)
simspec(specb,specc,plot=TRUE)
#[1] 12.05652
simspec(speca,specd,plot=TRUE)
## mel scale
require(tuneR)
data(orni)
data(tico)
orni.mel <- melfcc(orni, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
orni.mel.mean <- apply(orni.mel$aspectrum, MARGIN=2, FUN=mean)
tico.mel <- melfcc(tico, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
tico.mel.mean <- apply(tico.mel$aspectrum, MARGIN=2, FUN=mean)
simspec(orni.mel.mean, tico.mel.mean, f=22050, mel=TRUE, plot=TRUE)

A function to tentativily smooth a time wave

Description

This function tries to smooth with a sum sliding window a time wave, and then to remove residual noise.

Usage

smoothw(wave, f, channel = 1, wl, padding=TRUE, output = "matrix")

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

window length in number of points (samples).

padding

a logical, if TRUE add 0 values at the start and end of the file to match wave length (duration).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

Details

A window slides along the signal and sums up the sample amplitude values. Zero values are added at the end of the wave to keep wave length (duration).

Value

A new wave is returned. The class of the returned object is set with the argument output. If padding is TRUE, the new wave starts and ends up with 0 values to match the size of wave.

Warning

This function should be used with care as this kind of filter may change the frequency content of the sound. See the examples section for an illustration.

Author(s)

Jerome Sueur

See Also

fir, filter

Examples

# An example to show that smoothw() may change
# the frequency content of your sound
data(orni)
orni2 <- smoothw(orni, wl=2, out="Wave")
orni10 <- smoothw(orni, wl=10, out="Wave")
orni50 <- smoothw(orni, wl=50, out="Wave")
orni100 <- smoothw(orni, wl=100, out="Wave")
meanspec(orni)
lines(meanspec(orni2, plot=FALSE), col=2)
lines(meanspec(orni10, plot=FALSE), col=3)
lines(meanspec(orni50, plot=FALSE), col=4)
lines(meanspec(orni100, plot=FALSE), col=5)
legend("topright", col=1:5, lty=1, legend=c("original","wl=2","wl=10","wl=50","wl=100"))

Reading and interpreting SongMeter file name

Description

This function reads and decomposes the files names generated by a SongMeter device, audio digal recorders produced by the society Wildlife Acoustics.

Usage

songmeter(x)

Arguments

x

a character vector with file names, either .wac or .wav

Details

The digital recorder SongMeter (either SM2, SM3, or SM4 device model) produced by the society 'Wildlife Acoustics' (https://www.wildlifeacoustics.com/) generates '.wav' files which names include useful information. Here are the character format of the files:

  • SM2 or SM4: PREFIX_YYYYMMDD_HHMMSS.wav

  • SM3:

    • without geolocalisation PREFIX_XXX_YYYYMMDD_HHMMSS.wav

    • with geolocalisation PREFIX_XXX_YYYYMMDD$HHMMSS.wav

with:

  • PREFIX: prefix set when programming the SongMeter

  • XXX: microphone information

  • YYYY: year

  • MM: month

  • DD: day

  • HH: hour

  • MM: month

  • SS: minute

This information is read and decomposed by the function songmeter().
Please note that the function does not read the content of audio file but the name of the file.

Value

The function returns a data.frame with the following columns:

model

device model, either "SM2/SM4" or "SM3"

prefix

prefix of the file, specifying for instance to recording site

mic

microphone information specifying if the recording is mono left channel ("monoL"), mono right ("monoR") or stereo ("stereo"). This works for SM3 only, NA for SM2

year

year of recording, numeric

month

month of recording, numeric

day

day of recording, numeric

hour

hour of recording, numeric

min

minute of recording, numeric

sec

second of recording, numeric

time

time in POSIX format

geo

logical, TRUE if the device was GPS synchronized

Note

The file names of Songmeters may change with time. There is no guarantee that the function will be updated on time.

Author(s)

Jerome Sueur

References

See Wildlife Acoustics website for details regarding the SongMeters 2, 3 and 4: https://www.wildlifeacoustics.com/

See Also

songmeterdiag, audiomoth, strptime for the POSIX time format.

Examples

file1 <- "MNHN_20141225_234500.wav"      # SM2 file
file2 <- "CNRS_0+1_20130824_153000.wav"  # SM3 file without geolocalisation
file3 <- "PARIS_-0-_20150410$195550.wav" # SM3 file with geolocalisation
file4 <- "MNHN_20141225_234500.txt"      # not a .wav or a .wac file
file5 <- "myfile.wav"                    # not a Wildlife Acoustics filename
files <- c(file1, file2, file3, file4, file5)
songmeter(files)

Songmeter file diagnostics and diagram

Description

This function looks for files generated by a SongMeter device (audio digal recorders produced by the society Wildlife Acoustics) and checks for possible missing or small files according to a predefined recording schedule.

Usage

songmeterdiag(dir, start, end, frequency,
pch.exi = 1, pch.mis = 19,
col.exi = 1, col.mis = 2,
cex.exi = NULL, cex.mis = 0.5,
limits = FALSE, output="file", plot = FALSE)

Arguments

dir

a character vector, path to directory(ies) where the .wav files are stored. Typically a "Data" folder as generated by SongMeter devices.

start

a character vector, start date/time of the recording schedule as programmed on the SongMeter device, must be in the format "year-month-day hour:minute:second".

end

a character vector, end date/time of the recording schedule as programmed on the SongMeter device, must be in the format "year-month-day hour:minute:second".

frequency

a numeric vector, frequency of the recording schedule expressed in minute.

pch.exi

symbol for plotting the existing file(s).

pch.mis

symbol for plotting the missing file(s)

col.exi

colour of the symbol for plotting the existing file(s).

col.mis

colour of the symbol for plotting the missing file(s).

cex.exi

size of the symbol for plotting the existing file(s), by default NULL so that the size of the symbol corresponds to the size of the .wav file in Mb divided by the average size of all .wav files found in the directory. If not NA then symbol size as in plot.

cex.mis

size of the symbol for plotting the missing file(s).

limits

a logical, if TRUE adds to the plot the limits (start and end date/time) of the recording schedule as programmed on the SongMeter device.

output

a character vector of length 1, either "file" or "time" to get the file name or the time slot in POSIXct format respectively.

plot

a logical, if TRUE plots a time plot indicating the existing and missing files (by default TRUE).

Details

The function works for a single or several directories so that the operation of several SongMeters can be compared visually. This function should be helpful to check quickly how the devices worked.

Value

A character vector with the names of the missing files.

Note

The file names of Songmeters may change with time. There is no guarantee that the function will be perfectly updated.

Author(s)

Jerome Sueur and Sylvain Haupert

References

See Wildlife Acoustics website for details regarding the SongMeters 2, 3 and 4: https://www.wildlifeacoustics.com/

See Also

songmeter

Examples

## Not run: 
##################
# simulated data
##################
# a recording schedule programmed on four SongMeters SM4
# named "S4A03895", "S4A03998", "S4A03536", and "S4A04430"
# starting the 1st of January 2019 at 00:00:00
# and stopping the 31st January 2019 at 23:30:00
# with a recording frequency of 30 minutes
# all directories stored in a single directory named "project" 
# recorder names
recorders <- c("S4A03895", "S4A03998", "S4A03536", "S4A04430")
n <- length(recorders)
# schedule as programmed on the devices
format <- "
start <- strptime("20190101_000000", format) 
end <- strptime("20190131_233000", format)
schedule <- seq(from=start, to=end, by=30*60)
schedule <- paste(format(schedule, "
# directories and files
dir.create("project")
for(i in 1:n) {
dir.create(paste("project", recorders[i], sep="/"))
}
for(i in 1:n) {
file.create(paste("project", recorders[i],
paste(recorders[i], each=schedule, sep="_"), sep="/"))
}
# removing some files to simulate missing files
dirs <- paste("project", recorders, sep="/")
file.remove(paste(dirs[1], dir(dirs[1])[200:500], sep="/"))

######################
# use of the function
######################
# directories where the .wav files are stored (as above)
dirs <- paste("project", recorders, sep="/")
# function call with a plot, cex.exi is here specify because we deal
# with ghost files (the .wav file are not truly created)
res <- songmeterdiag(dirs,
                     start="2019-01-01 00:00:00", end="2019-01-31 23:30:00", frequency=30,
                     cex.exi=1,  plot=TRUE)
# clear out
unlink("project", recursive=TRUE)

## End(Not run)

Soundscape frequency spectrum of a time wave

Description

This function returns a kHz binned spectrum as described by Kasten et al. (2012) for the description of a soundscape.

Usage

soundscapespec(wave, f, channel = 1, wl = 1024, wn = "hamming", ovlp = 50,
plot = TRUE, xlab = "Frequency (kHz)", ylim = c(0, 1), ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

length of the window for the analysis (even number of points, by default = 1024).

wn

window name, see ftwindow (by default "hamming").

ovlp

overlap between two successive analysis windows (in %), by default = 50%.

plot

if TRUE returns a barplot.

xlab

title of the barplot x axis.

ylim

range of the barplot y axis.

...

other barplot graphical parameters.

Details

The soundscape frequency spectrum is based on the computation of a spectrogram power spectral density using Welch'smethod (Welch & June, 1967). Parameters used in Kasten et al. (2012) were a Hamming window of 1024 samples with 50% of overlap and are used here as default values.

Value

A two-column numeric matrix, the first column returning the frequency (kHz) bands and the second column returning the power value within each frequency band.
A barplot is returned when plot is TRUE.

Author(s)

Jerome Sueur and Eric Kasten

References

Kasten, E.P., Gage, S.H., Fox, J. & Joo, W. (2012). The remote environmental assessment laboratory's acoustic library: an archive for studying soundscape ecology. Ecological Informatics, 12, 50-67.
Welch, P.D., June (1967). The use of the fast Fourier transform for the estimation of power spectra: a method based on time-averaging over short, modified periodograms. IEEE Transactions on Audio and Electroacoustics, 15: 70-73.

See Also

spec, meanspec, SAX, NDSI

Examples

## Note that 'tico' is not a soundscape recording...
data(tico)
soundscapespec(tico, plot=TRUE, col="darkgreen")

Calls SoX

Description

This function calls SoX, the Swiss Army knife of sound processing programs.

Usage

sox(command, exename = NULL, path2exe = NULL, option = NULL,
shQuote_type = NULL)

Arguments

command

the SoX command to invoke.

exename

a character string specifying the name of the SoX binary file. If NULL, the default name "sox" will be used for Linux OS.

path2exe

a character string giving the path to the SoX binary file

g

option

option to be passed to the SoX command

shQuote_type

type of shell quotes ("cmd" or "cmd2", for Windows OS; "sh" or "csh" Unix OS)

Details

See the documentation of SoX for proper use.

Note

Sox must be installed to use this function but not to install the package seewave. As mentioned on the SoX webpage, the primary development platform is Linux. Using SoX with Windows from R might not be straightforward. In particular, it is advisable to pay attention to file path and exe name.

Author(s)

Jerome Sueur, Stefanie LaZerte, Andre Mikulec

References

https://en.wikipedia.org/wiki/SoX

Examples

## Not run: 
##########
## data ##
##########
## Generate a simple sound file at 440 Hz
s <- synth(cf=440, f=8000, d=1, fm=c(0,0,1000,0,0), output="Wave")
savewav(s, file="mysound.wav")
##############
## Linux OS ##
##############
## Play the file
sox("mysound.wav", exename="play")
## Slow down  the  audio  tempo  (but  not  its  pitch)
sox("mysound.wav myslowsound.wav tempo 0.5")
## Cut the file
sox("myslowsound.wav myslowcutsound.wav trim 0.25 0.75")
################
## Windows OS ##
################
## path with simple slash
path <- "C:/Program Files (x86)/sox-14-4-2"
## or path with double backslash
## path <- "C:\Program Files (x86)\sox-14-4-2"
sox("mysound.wav", path2exe=path, option="-t waveaudio")
## with the option directly passed to the command 
sox("mysound.wav -t waveaudio", path2exe=path)
## Slow down  the  audio  tempo  (but  not  its  pitch)
sox("mysound.wav myslowsound.wav tempo 0.5", path2exe=path)
## Cut the file
sox("myslowsound.wav myslowcutsound.wav trim 0.25 0.75", path2exe=path)
###########
## clean ##
###########
file.remove("mysound.wav", "myslowsound.wav", "myslowcutsound.wav")

## End(Not run)

Frequency spectrum of a time wave

Description

This function returns the frequency spectrum (i.e. the relative amplitude of the frequency content) of a time wave. Results can be obtained either as absolute or dB data.

Usage

spec(wave, f, channel = 1, wl = 512, wn = "hanning", fftw = FALSE, norm = TRUE,
scaled = FALSE, PSD = FALSE, PMF = FALSE, correction="none", dB = NULL, dBref = NULL,
at = NULL, from = NULL, to = NULL,
identify = FALSE, col = "black", cex = 1,
plot = 1, flab = "Frequency (kHz)",
alab = "Amplitude", flim = NULL,
alim = NULL, type="l",...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

if at is not null, length of the window for the analysis (by default = 512).

wn

window name, see ftwindow (by default "hanning").

fftw

if TRUE calls the function FFT of the library fftw for faster computation. See Notes of the function spectro.

norm

if TRUE the spectrum is normalised by its maximum.

scaled

if TRUE the spectrum is scaled by the length of the FFT.

PSD

if TRUE return Power Spectrum Density, i. e. the square of the spectrum.

PMF

if TRUE return Probability Mass Function, i. e. the probability distribution of frequencies.

correction

a character vector of length 1 to apply an amplitude ("amplitude") or an energy ("energy") correction to the FT window. This argument is useful only when one wish to obtain absolute values that is when norm=FALSE, scaled=FALSE, and PMF=FALSE. By default no correction is applied ("none").

dB

a character string specifying the type dB to return: "max0" for a maximum dB value at 0, "A", "B", "C", "D", and "ITU" for common dB weights.

dBref

a dB reference value when dB is not NULL. NULL by default but should be set to 2*10e-5 for a 20 microPa reference (SPL).

at

position where to compute the spectrum (in s).

from

start mark where to compute the spectrum (in s).

to

end mark where to compute the spectrum (in s).

identify

to identify frequency and amplitude values on the plot with the help of a cursor.

col

colour of the spectrum.

cex

pitch size of the spectrum.

plot

if 1 returns frequency on x-axis, if 2 returns frequency on y-axis, (by default 1).

flab

title of the frequency axis.

alab

title of the amplitude axis.

flim

range of frequency axis.

alim

range of amplitude axis.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

...

other plot graphical parameters.

Details

If at, from or to are FALSE then spec computes the spectrum of the whole signal.

Value

This function returns a two-column matrix, the first column corresponding to the frequency axis, the second column corresponding to the amplitude axis.
If identify is TRUE, spec returns a list with two elements:

freq

the frequency of the points chosen on the spectrum


amp

the relative amplitude of the points chosen on the spectrum


Warning

The argument peaks is no more available (version > 1.5.6). See the function fpeaks for peak(s) detection.

Note

This function is based on fft.

Author(s)

Jerome Sueur

See Also

meanspec, fpeaks, localpeaks, dynspec, corspec, fft.

Examples

data(tico)
# spectrum of the whole signal, in absolute or dB amplitude,
# horizontaly or vertically
op<-par(mfrow=c(2,2))
spec(tico,f=22050)
spec(tico,f=22050,col="red",plot=2)
spec(tico,f=22050,dB="max0",col="blue")
spec(tico,f=22050,dB="max0",col="green",plot=2)
par(op)
# an indirect way to compare spectra 
a<-spec(tico,f=22050,wl=512,at=0.2,plot=FALSE)
b<-spec(tico,f=22050,wl=512,at=0.7,plot=FALSE)
c<-spec(tico,f=22050,wl=512,at=1.1,plot=FALSE)
d<-spec(tico,f=22050,wl=512,at=1.6,plot=FALSE)
all<-cbind(a[,2],b[,2],c[,2],d[,2])
matplot(x=a[,1],y=all,yaxt="n",
    xlab="Frequency (kHz)",ylab="Amplitude",xaxs="i",type="l")
legend(8,0.8,c("Note A","Note B", "Note C", "Note D"),bty="o",
    lty=c(1:4),col=c(1:4))
# spectrum from a particular position to another one
op<-par(mfrow=c(2,1))
oscillo(tico,f=22050)
abline(v=c(0.5,0.9),col="red",lty=2)
spec(tico,f=22050,wl=512,from=0.5,to=0.9,col="red")
title("Spectrum of the note B")
par(op)
# spectrum and spectrogram
data(orni)
orni1<-cutw(orni,f=22050,from=0.32,to=0.39)
layout(matrix(c(1,2),nc=2),widths=c(3,1))
par(mar=c(5,4,3,0.5))
spectro(orni1,f=22050,wl=128,zp=8,ovlp=85,scale=FALSE)
par(mar=c(5,1,3,0.5))
spec(orni1,f=22050,col="red",plot=2,flab="",yaxt="n")

Spectral flux

Description

Compute spectral flux

Usage

specflux(wave, f, channel = 1,
         wl = 512, ovlp = 0, wn = "rectangle", flim = NULL,
         norm = FALSE,  p = 2,
         plot = TRUE, xlab = "Times (s)", ylab = "Flux", type = "l", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

window length for the analysis (even number of points) (by default = 512).

ovlp

overlap between two successive windows (in %).

wn

window name, see ftwindow (by default "rectangle").

flim

a numeric vector of length 2 to select a frequency band (in kHz).

norm

if is TRUE then the normalised spectra are used. The spectra are normalised by their sum.

p

the norm type, by default = 2.

plot

logical, if TRUE the spectral flux is displayed against time (s) (by default TRUE).

xlab

title of the x axis.

ylab

title of the y axis.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

...

other plot parameters.

Details

The spectral flux (FF) is the sum of the time (tt) derivative of the columns – that is the successive spectra – (ss) of the normalized short-term Fourier transform (zz).
F is then computed according to:

F=(s(t+1)s(t)p)1pF = (\sum |s(t+1) - s(t)|^{p})^{\frac{1}{p}}

Value

When plot is FALSE, specflux returns a two-column matrix, the first column being time in seconds (x-axis) and the second column being the spectral flux (y-axis) computed along time.

Note

The sum of the successive spectral flux values could be used as an ecoacoustic index, quite close to the acoustic complexity index (ACI). See examples.

Author(s)

Jérôme Sueur

References

Scheirer E, Slaney M (1997). Construction and evaluation of a robust multifeature speech/music discriminator. IEEE International Conference on Acoustics, Speech, and Signal Processing, 2, 1221-1224.

See Also

spectro, ACI

Examples

## default use
data(tico)
specflux(tico)
## norm 1
specflux(tico, p = 1)
## frequency limit between 2 and 4 kHz
specflux(tico, flim = c(2,4))
## index computation
sum(specflux(tico, plot=FALSE)[,2])

Spectral properties

Description

This function returns a list of statistical properties of a frequency spectrum.

Usage

specprop(spec, f=NULL,
str = FALSE, flim=NULL, mel=FALSE,
plot = FALSE, type = "l", xlab=NULL, ylab = NULL,
col.mode = 2, col.quartiles = 4, ...)

Arguments

spec

a data set resulting of a spectral analysis obtained with spec or meanspec (not in dB).

f

sampling frequency of spec (in Hz).

str

logical, if TRUE returns the results in a structured table.

flim

a vector of length 2 to specifgy the frequency limits of the analysis (in kHz)

mel

a logical, if TRUE the (htk-)mel scale is used.

plot

if 1 returns the spectrum , if 2 returns the cumulative spectrum, both of them with the first quartile, the third quartile, the median and the mode plotted (by default FALSE).

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

xlab

label of the x axis.

ylab

label of the y axis.

col.mode

colour of the mode segments (by default blue).

col.quartiles

colour of the quartiles segments (by default red).

...

other arguments to be passed to plot

Details

The spectrum is converted in a probability mass function (PMF).
If a selected value has to be selected with $, the argument str has to be set to FALSE.

Value

A list of 15 values is returned

mean

mean frequency (see mean)

sd

standard deviation of the mean (see sd)

sem

standard error of the mean

median

median frequency (see median)

mode

mode frequency, i.e. the dominant frequency

Q25

first quartile (see quantile)

Q75

third quartile (see quantile)

IQR

interquartile range (see IQR)

cent

centroid, see note

skewness

skewness, a measure of asymmetry, see note

kurtosis

kurtosis, a measure of peakedness, see note

sfm

spectral flatness measure (see sfm)

sh

spectral entropy (see sh)

prec

frequency precision of the spectrum

Note

Centroid is computed according to:

C=i=1Nxi×yiC = \sum_{i = 1}^{N} x_i\times{y_i}


with:
x = frequencies, y = relative amplitude of the i frequency,
N = number of frequencies.

Skewness is computed according to:

S=i=1N(xixˉ)3N1×1σ3S = \frac{\sum_{i = 1}^{N}(x_i-\bar{x})^{3}}{N-1}\times{\frac{1}{\sigma^{3}}}

.
S < 0 when the spectrum is skewed to left,
S = 0 when the spectrum is symetric,
S > 0 when the spectrum is skewed to right.
Spectrum asymmetry increases with |S|.

Kurtosis is computed according to:

K=i=1N(xixˉ)4N1×1σ4K = \frac{\sum_{i = 1}^{N}(x_i-\bar{x})^{4}}{N-1}\times{\frac{1}{\sigma^{4}}}

.
K < 3 when the spectrum is platikurtic, i.e. it has fewer items at the center and at the tails than the normal curve but has more items in the shoulders,
K = 3 when the spectrum shows a normal shape,
K > 3 when the spectrum is leptokurtic, i.e. it has more items near the center and at the tails, with fewer items in the shoulders relative to normal distribution with the same mean and variance.

Author(s)

Jerome Sueur and Caroline Simonis, and a patch by Jesse Ross (Dec. 2012)

Examples

data(orni)
a<-meanspec(orni,f=22050,plot=FALSE)
specprop(a,f=22050)
# to get a single measure of the list
specprop(a,f=22050)$mode
# to get the results structured
specprop(a,f=22050,str=TRUE)
# to limit the analysis between 4 and 6 kHz
specprop(a,f=22050,flim=c(4,6),str=TRUE)
# plots
specprop(a,f=22050,plot=1)
specprop(a,f=22050,plot=2)
# (htk-)mel scale
require(tuneR)
mel <- melfcc(orni, nbands = 256, dcttype = "t3", fbtype = "htkmel", spec_out=TRUE)
melspec.mean <- apply(mel$aspectrum, MARGIN=2, FUN=mean)
specprop(melspec.mean, f=22050, mel=TRUE)
# be aware that flim is always given in kHz even if mel=TRUE
specprop(melspec.mean, f=22050, flim=c(4,6), mel=TRUE, plot=TRUE)

2D-spectrogram of a time wave

Description

This function returns a two-dimension spectrographic representation of a time wave. The function corresponds to short-term Fourier transform. An amplitude contour plot can be overlaid.

Usage

spectro(wave, f, channel = 1, wl = 512, wn = "hanning", zp = 0,
ovlp = 0, noisereduction = NULL, fastdisp = FALSE,
complex = FALSE, norm = TRUE, correction="none",
fftw = FALSE, dB = "max0", dBref = NULL, plot = TRUE,
flog = FALSE, grid = TRUE, osc = FALSE, scale = TRUE, cont = FALSE,
collevels = NULL, palette = spectro.colors,
contlevels = NULL, colcont = "black",
colbg = "white", colgrid = "black",
colaxis = "black", collab="black",
cexlab = 1, cexaxis = 1, 
tlab = "Time (s)",
flab = "Frequency (kHz)",
alab = "Amplitude",
scalelab = "Amplitude\n(dB)",
main = NULL,
scalefontlab = 1, scalecexlab =0.75,
axisX = TRUE, axisY = TRUE, tlim = NULL, trel = TRUE,
flim = NULL, flimd = NULL,
widths = c(6,1), heights = c(3,1),
oma = rep(0,4),
listen=FALSE,
...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

window length for the analysis (even number of points) (by default = 512).

wn

window name, see ftwindow (by default "hanning").

zp

zero-padding (even number of points), see Details.

ovlp

overlap between two successive windows (in %).

noisereduction

a numeric vector of length 1, if 1 a noise reduction is applied along the rows of the spectrogram, if 2 a noise reduction applied along the columns. See Details.

fastdisp

faster graphic display for long wave. The spectrogram/oscillogram is displayed/saved faster in the graphic device/ graphic file when set to TRUE, with a cost on graphical resolution.

complex

if TRUE the STFT will be returned as complex numbers.

norm

if TRUE the STFT is normalised (i. e. scaled) by its maximum.

correction

a character vector of length 1 to apply an amplitude ("amplitude") or an energy ("energy") correction to each FT window. This argument is useful only when one wish to obtain absolute values that is when norm=FALSE. By default no correction is applied ("none").

fftw

if TRUE calls the function FFT of the library fftw. See Notes.

dB

a character string specifying the type dB to return: "max0" (default) for a maximum dB value at 0, "A", "B", "C", "D", and "ITU" for common dB weights. If set to NULL, then a linear scale is used.

dBref

a dB reference value. NULL by default but should be set to 2*10e-5 for a 20 microPa reference.

plot

logical, if TRUE plots the spectrogram (by default TRUE).

flog

a logical to plot the frequency on a logarithmic scale.

grid

logical, if TRUE plots a y-axis grid (by default TRUE).

osc

logical, if TRUE plots an oscillogram beneath the spectrogram (by default FALSE).

scale

logical, if TRUE plots a dB colour scale on the right side of the spectrogram (by default TRUE).

cont

logical, if TRUE overplots contour lines on the spectrogram (by default FALSE).

collevels

a set of levels which are used to partition the amplitude range of the spectrogram (in dB).

palette

a color palette function to be used to assign colors in the plot, see Details.

contlevels

a set of levels which are used to partition the amplitude range for contour overplot (in dB).

colcont

colour for cont plotting.

colbg

background colour.

colgrid

colour for grid plotting.

colaxis

color of the axes.

collab

color of the labels.

cexlab

size of the labels.

cexaxis

size of the axes.

tlab

label of the time axis.

flab

label of the frequency axis.

alab

label of the amplitude axis.

scalelab

amplitude scale label.

main

label of the main title.

scalefontlab

font of the amplitude scale label.

scalecexlab

cex of the amplitude scale label.

axisX

logical, if TRUE plots time X-axis (by default TRUE).

axisY

logical, if TRUE plots frequency Y-axis (by default TRUE).

tlim

modifications of the time X-axis limits.

trel

time X-axis with a relative scale when tlim is not null, i.e. relative to wave.

flim

modifications of the frequency Y-axis limits (in kHz).

flimd

dynamic modifications of the frequency Y-axis limits. New wl and ovlp arguments are applied to increase time/frequency resolution.

widths

a vector of length 2 to control the relative widths of columns on the device when scale is TRUE.

heights

a vector of length 2 to control the relative heights of rows on the device when osc is TRUE.

oma

a vector of length 4 to control the size of outer margins when either scale or osc is TRUE.

listen

if TRUE the sound is played back (by default FALSE).

...

other contour and oscillo graphical parameters.

Details

Following Heisenberg uncertainty principle, the short-term Fourier transform cannot be precised in both time and frequency. The temporal and frequency precisions of the function are actually dependent of the wl value. Choosing a high wl value will increase the frequency resolution but reduce the temporal one, and vice versa. The frequency precision is obtained by calculating the ratio f/wl, and the temporal precision is obtained by calculating the reverse ratio wl/f. This problem can be reduced in some way with zp that adds 0 values on both sides of the analysis window. This increases frequency resolution without altering time resolution.
Any colour palette can be used. In particular, it is possible to use other palettes coming with seewave: temp.colors, reverse.gray.colors.1, reverse.gray.colors.2, reverse.heat.colors, reverse.terrain.colors, reverse.topo.colors, reverse.cm.colors corresponding to the reverse of heat.colors, terrain.colors, topo.colors, cm.colors.
Use locator to identify points. The noise reduction using the argument noisereduction is an image filter, not a signal filter. The principle consists in subtracting each spectrogram row or column by its median. Noise reduction alters energy conservation, it should then be used for visual display only.

Value

This function returns a list of three items:

time

a numeric vector corresponding to the time axis.

freq

a numeric vector corresponding to the frequency axis.

amp

a numeric or a complex matrix corresponding to the amplitude values. Each column is a Fourier transform of length wl/2.

Note

The argument fftw can be used to try to speed up process time. When set to TRUE, the Fourier transform is computed through the function FFT of the package fftw. This pacakge is a wrapper around the fastest Fourier transform of the free C subroutine library FFTW (http://www.fftw.org/). FFT should be then installed on your OS.

Note

This function is based on fft, contour and filled.contour

Author(s)

Jerome Sueur and Caroline Simonis.

References

Hopp, S. L., Owren, M. J. and Evans, C. S. (Eds) 1998. Animal acoustic communication. Springer, Berlin, Heidelberg.

See Also

ggspectro, spectro3D, lts, dynspec, wf, oscillo, dBscale, fft.

Examples

## Not run: 
data(tico)
data(pellucens)
# simple plots
spectro(tico,f=22050)
spectro(tico,f=22050,osc=TRUE)
spectro(tico,f=22050,scale=FALSE)
spectro(tico,f=22050,osc=TRUE,scale=FALSE)
# change the dB scale by setting a different dB reference value (20microPa)
spectro(tico,f=22050, dBref=2*10e-5)
# unnormalised spectrogram with a linear amplitude scale
spectro(tico, dB=NULL, norm=FALSE, scale=FALSE)
# manipulating wl
op<-par(mfrow=c(2,2))
spectro(tico,f=22050,wl=256,scale=FALSE)
title("wl = 256")
spectro(tico,f=22050,wl=512,scale=FALSE)
title("wl = 512")
spectro(tico,f=22050,wl=1024,scale=FALSE)
title("wl = 1024")
spectro(tico,f=22050,wl=4096,scale=FALSE)
title("wl = 4096")
par(op)
# vertical zoom using flim
spectro(tico,f=22050, flim=c(2,6))
spectro(tico,f=22050, flimd=c(2,6))
# a full plot
pellu2<-cutw(pellucens,f=22050,from=1,plot=FALSE)
spectro(pellu2,f=22050,ovlp=85,zp=16,osc=TRUE,
    cont=TRUE,contlevels=seq(-30,0,20),colcont="red",
    lwd=1.5,lty=2,palette=reverse.terrain.colors)
# black and white spectrogram 
spectro(pellu2,f=22050,ovlp=85,zp=16,
    palette=reverse.gray.colors.1)
# colour modifications
data(sheep)
spectro(sheep,f=8000,palette=temp.colors,collevels=seq(-115,0,1))
spectro(pellu2,f=22050,ovlp=85,zp=16,
palette=reverse.cm.colors,osc=TRUE,colwave="orchid1") 
spectro(pellu2,f=22050,ovlp=85,zp=16,osc=TRUE,palette=reverse.heat.colors,
colbg="black",colgrid="white", colwave="white",colaxis="white",collab="white")

## End(Not run)

3D-spectrogram of a time wave

Description

This function returns a three-dimension spectrographic representation of a time wave. The function corresponds to short-term Fourier transform.

Usage

spectro3D(wave, f, channel = 1, wl = 512, wn = "hanning", zp = 0,
ovlp = 0, noisereduction = FALSE, norm = TRUE, correction = "none", fftw = FALSE,
dB = "max0", dBref = NULL, plot = TRUE,
magt = 10, magf = 10, maga = 2,
palette = reverse.terrain.colors)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

length of the window for the analysis (even number of points).

wn

window name, see ftwindow (by default "hanning").

zp

zero-padding (even number of points), see Details.

ovlp

overlap between two successive windows (in % ).

noisereduction

a logical, if TRUE a noise reduction is applied.

norm

if TRUE the STFT is normalised (i. e. scaled) by its maximum.

correction

a character vector of length 1 to apply an amplitude ("amplitude") or an energy ("energy") correction to the FT window. This argument is useful only when one wish to obtain absolute values that is when norm=FALSE, scaled=FALSE, and PMF=FALSE. By default no correction is applied ("none").

fftw

if TRUE calls the function FFT of the library fftw. See Notes of the spectro.

dB

a character string specifying the type dB to return: "max0" for a maximum dB value at 0, "A", "B", "C", "D", and "ITU" for common dB weights.

dBref

a dB reference value when dB is TRUE. NULL by default but should be set to 2*10e-5 for a 20 microPa reference.

plot

logical, if TRUE plots the spectrogram (by default TRUE).

magt

magnification of the time axis.

magf

magnification of the frequency axis.

maga

magnification of the amplitude axis.

palette

a color palette function to be used to assign colors in the plot, see Details.

Details

Following Heisenberg uncertainty principle, the short-term Fourier transform cannot be precised in both time and frequency. The temporal and frequency precisions of the function are actually dependent of the wl value. Choosing a high wl value will increase the frequency resolution but reduce the temporal one, and vice versa. The frequency precision is obtained by calculating the ratio f/wl, and the temporal precision is obtained by calculating the reverse ratio wl/f. This problem can be reduced in some way with zp that adds 0 values on both sides of the analysis window. This increases frequency resolution without altering time resolution.
Any colour palette can be used. In particular, it is possible to use other palettes coming with seewave: reverse.gray.colors.1, reverse.gray.colors.2, spectro.colors, temp.colors, reverse.heat.colors, reverse.cm.colors, reverse.topo.colors, corresponding to the reverse of heat.colors,topo.colors, cm.colors.
Use magt, magf and maga to resize the plot.

Value

This function returns a list of three items:

time

a numeric vector corresponding to the time axis.

freq

a numeric vector corresponding to the frequency axis.

amp

a numeric matrix corresponding to the amplitude values. Each column is a Fourier transform of length wl/2.

Note

This function requires rgl and is based on fft. See examples of spectro for analysis arguments (wl,zp, ovlp).

Author(s)

Jerome Sueur [email protected] and Caroline Simonis [email protected].

See Also

spectro, ggspectro, lts, dynspec, wf, fft.

Examples

## Not run: 
require(rgl)
data(tico)
spectro3D(tico,f=22050,wl=512,ovlp=75,zp=16,maga=4,palette=reverse.terrain.colors)
# linear amplitude scale without a normisation of the STFT matrix
# time and frequency scales need to be dramatically amplified
spectro3D(tico, norm=FALSE, dB=NULL, magt=100000, magf=100000)

## End(Not run)

Frequency square filter

Description

This function prepares the amplitude profile of a square frequency filter.

Usage

squarefilter(f, from = NULL, to = NULL, bandpass = TRUE, wl = 1024)

Arguments

f

a numeric vector of length 1 for the sampling frequency of the object to be filtered (in Hz).

from

a numeric vector for the start frequencies (in Hz) where to apply the filter.

to

a numeric vector of the end frequencies (in Hz) where to apply the filter.

bandpass

if TRUE a band-pass filter is prepared between start and end frequencies (arguments from and to), if FALSE a bandstop filter is prepared.

wl

window length of the impulse filter (even number of points).

Value

The function returns a two-column matrix, the first column is the frequency in kHz and the second column is the amplitude of the filter (frequency response of the filter).

Note

This function can be used to prepare bandpass or bandstop filters to be used with fir and ffilter. See examples.

Author(s)

Laurent Lellouch

See Also

fir, drawfilter, ffilter, combfilter, bwfilter

Examples

f <- 44100
a <- noisew(f = f, d = 1)
p <- squarefilter(f, from = c(100, 1000, 4000), to = c(500, 3000, 8000))
plot(p, type="l")
h <- fir(a, f = f, custom = p, wl = 1024, output = 'Wave')
spectro(h)

Symbol analysis of a numeric (time) series

Description

This function analyses one or two sequences of symbols from numeric (time) series.

Usage

symba(x, y = NULL, symb = 5, collapse = TRUE, entropy = "abs",
plot = FALSE, type = "l", lty1 = 1, lty2 = 2, col1 = 2, col2 = 4,
cex1 = 0.75, cex2= 0.75, xlab = "index", ylab = "Amplitude", legend=TRUE, ...)

Arguments

x

a first R object.

y

a second R object

symb

the number of symbols used for the discretisation, can be set to 3 or 5 only.

collapse

logical, if TRUE, the symbols are pasted in a character string of length 1.

entropy

either "abs" for an absolute value or "rel" for a relative value, i. e. between 0 and 1.

plot

logical, if TRUE plots the series x (and y) and the respective symbols.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

lty1

line type of the object x if type="l".

lty2

line type of the object y if type="l".

col1

colour of the object x.

col2

colour of the object y.

cex1

character size of x symbols.

cex2

character size of y symbols.

xlab

title of the x axis.

ylab

title of the y axis.

legend

logical, if TRUE and if y is not NULL adds a legend to the plot.

...

other plot graphical parameters.

Details

The analysis consists in transforming the series into a sequence of symbols (see the function discrets) and in computing the absolute frequency of each symbol within the sequence.
The entropy (H) is then calculated using the symbol frequencies. Using the argument entropy, the entropy can be expressed along an absolute scale or as a relative value varying between 0 and 1.
If two numeric (time) series are provided (x and y) the absolute symbol frequencies and entropy of each series is returned. Besides the mutual information (I) is estimated according to:

I=Hx+HyHxyI = H_{x} + H_{y} - H{xy}

with Hx the entropy of x symbol series, Hy the entropy of y symbol series, and Hxy$ the joint entropy of x and y symbol series.

Value

If y is NULL a list of three items is returned (s1, freq1, h1).
If y is not NULL, a list of 6 items is returned (s1, freq1, h1, s2, freq2, h2, I):

s1

the sequence of symbols of x,

freq1

the relative frequency of each x symbol,

h1

the entropy of x symbol sequence,

s2

the sequence of symbols of y,

freq2

the relative frequency of each y symbol,

h2

the entropy of y symbol sequence,

I

the mutual information between x and y.

Note

It might be useful to round the values of the input series (see examples).
The mutual information (I) should increase with the similarity between the series to compare (x and y).

Author(s)

Jerome Sueur [email protected]

References

Cazelles, B. 2004 Symbolic dynamics for identifying similarity between rhythms of ecological time series. Ecology Letters, 7: 755-763.

See Also

discrets, SAX

Examples

# analysis of a frequency spectrum
data(tico)
spec1<-spec(tico,f=22050,at=0.2,plot=FALSE)
symba(spec1[,2],plot=TRUE)
# it might be better to round the values
symba(round(spec1[,2],2),plot=TRUE)
# in that case the symbol entropy is close to the spectral entropy
symba(round(spec1[,2],2),entrop="rel")$h1
sh(spec1)
# to compare two frequency spectra
spec2<-spec(tico,f=22050,wl=512,at=1.1,plot=FALSE)
symba(round(spec1[,2],2),round(spec2[,2],2),plot=TRUE)

Synthesis of time wave (additive model)

Description

This functions synthesizes pure or harmonic tone sound with amplitude modulation (am) and/or frequency modulation (fm).

Usage

synth(f, d, cf, a = 1, signal = "sine", shape = NULL, p = 0,
am = c(0, 0, 0), fm = c(0, 0, 0, 0, 0), harmonics = 1, 
plot = FALSE, listen = FALSE, output = "matrix",...)

Arguments

f

sampling frequency (in Hz).

d

duration (in s).

cf

carrier frequency (in Hz).

a

amplitude (linear scale, relative when adding different waves).

signal

a character vector specifying the shape of the signal, see details.

shape

modification of the whole amplitude shape of the wave, see details.

p

initial phase (in radians).

am

a numeric vector of length 3 describing amplitude modulation parameters, see details.

fm

a numeric vector of length 5 describing frequency modulation parameters, see details.

harmonics

a numeric specifying the number and the relative amplitude of harmonics, see details.

plot

if TRUE returns the spectrogram of the synthezised sound (by default FALSE).

listen

if TRUE the new sound is played back.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other spectro graphical parameters.

Details

  • signal is a character vector of length 1 that specifies the function used to synthesize the signal. There are three options:

    1. "sine": for a sinus function,

    2. "tria": for a triangle function,

    3. "square": for a square function,

    4. "saw": for a square function.

  • shape is a character vector of length 1 that allows to modify the whole amplitude shape of the wave. There are four options:

    1. "incr": linear increase

    2. "decr": linear decrease

    3. "sine": sinusoid-like shape

    4. "tria": triangular shape

  • am is a numeric vector of length 3 including:

    1. the amplitude modulation depth (in %)

    2. the frequency of the amplitude modulation (in Hz),

    3. the phase of the amplitude modulation (in radian).

  • fm is a numeric vector of length 5 including:

    1. the maximum excursion of a sinusoidal frequency modulation (in Hz),

    2. the frequency of a sinusoidal frequency modulation (in Hz),

    3. the maximum excursion of a linear frequency modulation (in Hz).

    4. the phase of the frequency modulation (in radian).

    5. the maximum excursion of an exponential frequency modulation (in Hz).

  • harmonics is a numeric vector that controls the number and the relative amplitude of harmonics synthesized.
    By default harmonics = 1 meaning that a pure tone made of a single harmonic (fundamental) will be produced.
    To produce harmonics, the length of harmonics has to be greater than 1. The length of harmonics will set the number of harmonics, including the first one (fundamental). The value of each element of harmonics specify the relative ampltiude of each harmonic. The first value must equal to 1.
    Here are some examples:

    • harmonics = c(1, 0.5, 0.25) will produce a sound with three harmonics (fundamental + 2 harmonics), the second harmonic having an amplitude half the fundamental ampltiude and the second harmonic an amplitude a quarter of the fundamental amplitude.

    • harmonics = c(1, 0, 0.25) will produce a sound with two harmonics (fundamental + 1 harmonic) the second harmonic having a null relative amplitude.

    • harmonics = rep(1,4) will produce a sound with four harmonics (fundamental + 3 harmonics) of equal amplitude.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jerome Sueur and Laurent Lellouch.

References

Hartmann, W. M. 1998 Signals, sound and sensation. New York: Springer.

See Also

synth2, noisew, pulse, echo

Examples

## You can use plot=TRUE and spectro() options
## to directly 'see' the new-built sounds
f <- 8000 # sampling frequency
d <- 1    # duration (1 s)
cf <- 440 # carrier frequecy (440 Hz, i.e. flat A tone)
# pure sinusoidal tone
s <- synth(f=f,d=d,cf=cf)
# pure triangular tone
s <- synth(f=f,d=d,cf=cf, signal="tria")
# pure tone with triangle overall shape
s <- synth(f=f,d=d,cf=cf,shape="tria")
# pure tones with am
s <- synth(f=f,d=d,cf=cf,am=c(50,10))
# pure tones with am
# and phase shift of pi radian (180 degrees)
s <- synth(f=f,d=d,cf=cf,am=c(50,10,pi))
# pure tone with +1000 Hz linear fm 
s <- synth(f=f,d=d,cf=cf,fm=c(0,0,1000,0,0))
# pure tone with sinusoidal fm
# (maximum excursion of 250 Hz, frequency of 10 Hz)
s <- synth(f=f,d=d,cf=cf,fm=c(250,10,0,0,0))
# pure tone with sinusoidal fm
# (maximum excursion of 250 Hz, frequency of 10 Hz,
# phase shift of pi radian (180 degrees))
s <- synth(f=f,d=d,cf=cf,fm=c(250,10,0, pi,0))
# pure tone with sinusoidal am
# (maximum excursion of 250 Hz, frequency of 10 Hz)
# and linear fm (maximum excursion of 500 Hz)
s <- synth(f=f,d=d,cf=cf,fm=c(250,10,500,0,0))
# the same with am
s <- synth(f=f,d=d,cf=cf,am=c(50,10), fm=c(250,10,250,0,0))
# the same with am and a triangular overall shape 
s <- synth(f=f,d=d,cf=cf,shape="tria",am=c(50,10), fm=c(250,10,250,0,0))
# an harmonic sound
s <- synth(f=f,d=d,cf=cf, harmonics=c(1, 0.5, 0.25))
# a clarinet-like sound
clarinet <- c(1, 0, 0.5, 0, 0.14, 0, 0.5, 0, 0.12, 0, 0.17)
s <- synth(f=f, d=d, cf = 235.5, harmonics=clarinet)
# inharmonic FM sound built 'manually'
fm <- c(250,5,0,0,0)
F1<-synth(f=f,d=d,cf=cf,fm=fm)
F2<-synth(f=f,d=d,a=0.8,cf=cf*2,fm=fm)
F3<-synth(f=f,d=d,a=0.6,cf=cf*3.5,fm=fm)
F4<-synth(f=f,d=d,a=0.4,cf=cf*6,fm=fm)
final1<-F1+F2+F3+F4
spectro(final1,f=f,wl=512,ovlp=75,scale=FALSE)

Synthesis of time wave (tonal model)

Description

This functions synthesizes pure tone sound based on an amplitude envelope and an instantaneous frequency contour. The function can also be used to modify a reference sound.

Usage

synth2(env = NULL, ifreq, f, plot = FALSE, listen = FALSE, output = "matrix", ...)

Arguments

env

a numeric vector describing the amplitude envelope (i.e. the amplitude modulation). By default NULL, generating a squared enveloppe.

ifreq

a numeric vector describing the instantaneous frequency (in Hz).

f

a numeric vector for the sampling frequency (in Hz)

plot

if TRUE returns the spectrogram of the synthezised sound (by default FALSE).

listen

if TRUE the new sound is played back.

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other spectro graphical parameters.

Details

env and ifreq must have exactly the same length.
The amplitude envelope can be obtained with the Hilbert envelope (function env) and the instantaneous frequency can be obtained with the Hilbert transform (function ifreq). This opens a great variety of signal modidications as shown in the example section.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Author(s)

Jérôme Sueur and Laurent Lellouch

References

Beeman, K. 1998 Digital signal analysis, editing and synthesis, in Animal acoustic communication edited by Hopp SL, Owren MJ, Evans CS, Springer, 59-103.

See Also

synth2, noisew, pulse, echo

Examples

## You can use plot=TRUE and spectro() options
## to directly 'see' the new-built sounds
## MODIFICATION OF A REFERENCE SIGNAL
data(tico)
env.tico <- env(tico, f=22050, plot=FALSE)
ifreq.tico <- ifreq(tico, f=22050, plot=FALSE)$f[,2]
# recover the original signal
s <- synth2(env=env.tico, ifreq=ifreq.tico*1000, f=22050)
# original signal with instantaneous frequency reversed
s <- synth2(env=env.tico, ifreq=rev(ifreq.tico)*1000, f=22050)
# original signal with a +1000 Hz linear frequency shift
s <- synth2(env=env.tico, ifreq=ifreq.tico*1000+1000, f=22050)
# original signal with instantaneous frequency multiplied by 2
s <- synth2(env=env.tico, ifreq=ifreq.tico*1000*2, f=22050)
# original signal with a linear  instantaneous frequency at 2000 Hz
s <- synth2(env=env.tico, ifreq=rep(2000, times=length(tico@left)), f=22050)

## DE NOVO SYNTHESIS
# instantaneous frequency increasing by step of 500 Hz
s <- synth2(ifreq=rep(c(500,1000,1500,2000,2500,3000,3500,4000), each=2000), f=16000)
# square function of the instantaenous frequency
s <- synth2(ifreq=500+seq(-50,50, length.out=8000)^2, f=8000)
# linear increase of the amplitude envelope
s <- synth2(env=seq(0,1,length=8000), ifreq=rep(2000,8000), f=8000)
# square-root increase of the amplitude envelope
s <- synth2(env=sqrt(seq(0,1,length=8000)), ifreq=rep(2000,8000), f=8000)
# square-root increase and decrease of the amplitude envelope
s <- synth2(env=c(sqrt(seq(0,1,length=4000)), sqrt(seq(1,0,length=4000))),
    ifreq=rep(2000,8000), f=8000)
# amplitude envelope and instantaneous frequency following a normal density shape
norm <- rep(dnorm(-4000:3999, sd=1000), 2)
s <- synth2(env=norm, ifreq=500+(norm/max(norm))*1000, f=8000)

normalized Time and Frequency Second Derivative

Description

This function computes the normalized Time and Frequency Second Derivative as described by Aumond et al. (2017).

Usage

TFSD(wave, f, channel = 1, ovlp = 0,  wn = "hamming", flim = c(2,6), nbwindows = 1)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

ovlp

overlap between two successive windows (in %).

wn

window name, see ftwindow (by default "hanning").

flim

a numeric vector of length 2 to select a frequency band (in kHz). Cannot be NULL.

nbwindows

a numeric vector of length 1 specifying the number of windows (by default 1, ie a single window including the complete wave object.

Details

The TFSD aims at estimating the time of presence of avian or human vocalizations within a sound environment. It calculates the variation in time and frequency of a signal around frequencies of interest, normalized by the spectral time variation of a signal as a whole.

Warning, this index was initially developed to work from a third octave spectrogram with a time sampling of 125 ms.

TFSD is computed according to formulation in reference.

The higher the TFSD varies between 0 and 1, the greater the temporal presence of avian or human vocalizations. With the default configuration, a TFSD > 0.3 indicates a very important presence time of the vocalizations in the signal. The TFSD is always greater than 0.

Value

A numeric vector of length nbwindows giving the TFSD values.

Author(s)

Pierre Aumond, Guillaume Corbeau

References

Aumond, P., Can, A., De Coensel, B., Botteldooren, D., Ribeiro, C., & Lavandier, C. (2017). Modeling soundscape pleasantness using perceptual assessments and acoustic measurements along paths in urban context. Acta Acustica united with Acustica, 12, 50-67.

Gontier, F., Lavandier, C., Aumond, P., Lagrange, M., & Petiot, J. F. (2019). Estimation of the perceived time of presence of sources in urban acoustic environments using deep learning techniques. Acta Acustica united with Acustica, 105(6), 1053-1066.

See Also

ACI, NDSI

Examples

## Note that 'tico' is not a soundscape recording...
data(tico)
TFSD(tico)
## dividing the sound sample into 4 windows of equal duration
TFSD(tico, nbwindows=4)
## selection of a frequency band
TFSD(tico, flim=c(2,6))

Temporal entropy

Description

Compute the entropy of a temporal envelope.

Usage

th(env, breaks)

Arguments

env

a data set resulting of an envelope obtained using env

breaks

'breaks' argument of hist to compute the entropy on the distribution obtained with an histogram.

Details

Temporal entropy is calculated according to:

S=i=1Nyilog2(yi)log2(N)S = -\frac{\sum_{i = 1}^{N} y_i log_2(y_i)}{log_2(N)}

with:
y = relative amplitude of the i envelope point,
and

i=1Nyi=1\sum_{i = 1}^{N} y_i = 1


and N = number of envelope points.

Value

A single value varying between 0 and 1 is returned. The value has no unit.

Note

The temporal entropy of a noisy signal with many amplitude modulations will tend towards 1 whereas the temporal entropy of quiet signal will tend towards 0.
Note, however, that a sustained sound with an almost flat envelope will also show a very high temporal entropy except if you compute the entropy on the distribution obtained with the histogram. See examples.

Author(s)

Jerome Sueur, George Zhan for the idea and implementation of the argument breaks.

See Also

sh, csh, H

Examples

# Temporal entropy of a cicada song
data(orni)
envorni<-env(orni,f=22050,plot=FALSE)
th(envorni)
# Smoothing the envelope might slightly change the result.
envorniS<-env(orni,f=22050,smooth=c(50,0),plot=FALSE)
th(envorniS)
# If we mute a part of the cicada song, the temporal entropy decreases
orni2<-mutew(orni,f=22050,from=0.3,to=0.55,plot=FALSE)
envorni2<-env(orni2,f=22050,plot=FALSE)
th(envorni2)
# The temporal entropy of noise tends towards 1
a<-noisew(d=1,f=8000)
enva<-env(a,f=8000,plot=FALSE)
th(enva)
# But be aware that the temporal entropy
# of a sustained sound also tends towards 1
b<-synth(f=8000,d=1,cf=2000,plot=FALSE)
envb<-env(b,f=8000,plot=FALSE)
th(envb)
# except if you use the distribution of the histogram
th(envb, breaks="Sturges")

Song of the bird Zonotrichia capensis

Description

Recording of a song emitted by a male of the neotropical sparrow Zonotrichia capensis.

Usage

data(tico)

Format

A Wave object.

Details

Duration = 1.795 s. Sampling frequency = 22050 hz.

Source

Recording by Thierry Aubin.

Examples

data(tico)
oscillo(tico,f=22050)

Time lapse

Description

Append successive input sounds into a single output sound

Usage

timelapse(dir, from = 1, to = Inf,
units = c("samples", "seconds", "minutes", "hours"), verbose = TRUE)

Arguments

dir

a character vector, the path to the directory where the .wav files are stored or directly the names of the .wav files to be appended.

from

where to start reading the input files, in units. See readWave of the package tuneR.

to

where to stop reading, in units. See readWave of the package tuneR.

units

time units in which from and to is given, the default is "samples", but can be set to time intervals such as "seconds". See readWave of the package tuneR.

verbose

a logical, if TRUE (default) the file number and name processed are displayed in the console.

Details

The function takes the .wav files which names are provided in the argument dir and append (paste) them successively so that a single object is obtained. This can be used to produce sound time lapse based on a series of ordered files as those produced by an automatic recorder (e.g. SongMeter of the society 'Wildlife Acoustics').
Only a section of each file can be extracted by using the arguments from and to. The function is based on readWave and bind of the package tuneR.

Value

A Wave object, a class defined in the package tuneR.

Note

The characteristics (sampling rate, number of bits, stereo/mono) of the output object are those of the .wav file.
The files should be alphabatically ordered according to time to ensure a proper time lapse.
You should use either savewav or writeWave to save the results as a .wav file.

Author(s)

Jérôme Sueur

See Also

pastew

Examples

## Not run: 
## if 'dir' contains a set of files recorded with a Wildlife Acoustics
# songmeter recorder then a direct way to obtain
# the spectrogram of all .wav files is
dir <- "pathway-to-directory-containing-wav-files"
res <- timelapse(dir)
# to extract a selection of each file (here a section starting
# at 10 s and ending at 12 s)
res <- timelapse(dir, from=10, to=12, unit="seconds")

## End(Not run)

Time measurements of a time wave

Description

This function computes and shows the duration of signal periods, pause periods and their ratio.

Usage

timer(wave, f, channel = 1, threshold = 5, dmin = NULL, envt="abs",
power = 1, msmooth = NULL, ksmooth = NULL,
ssmooth = NULL, asmooth=NULL, tlim = NULL, plot = TRUE, plotthreshold = TRUE,
col = "black", colval = "red", 
xlab = "Time (s)", ylab = "Amplitude", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

threshold

amplitude threshold for signal detection (in %), or alternatively a function to be applied on the waveform scaled between 0 and 1. See examples.

dmin

time threshold (minimum duration) for signal detection (in s).

envt

the type of envelope to be used: either "abs" for absolute amplitude envelope or "hil" for Hilbert amplitude envelope. See env.

power

a power factor applied to the amplitude envelope. Increasing power will reduce low amplitude modulations and increase high amplide modulations. This can be used to reduce background noise (by default equals to 1, i.e. no change.

msmooth

a vector of length 2 to smooth the amplitude envelope with a mean sliding window. The first component is the window length (in number of points). The second component is the overlap between successive windows (in %). See env.

ksmooth

kernel smooth for the amplitude enveloppe via kernel. See env.

ssmooth

sum smooth for the amplitude enveloppe. See env.

asmooth

autocorrelation smooth for the amplitude enveloppe. See env.

tlim

modifications of the time X-axis limits.

plot

logical, if TRUE plots the envelope and the measurements (by default TRUE).

plotthreshold

logical, if TRUE plots the threshold as an horizontal line on the graph (by default TRUE).

col

colour of the envelope.

colval

colour of plotted measurements.

xlab

title of the x-axis.

ylab

title of the y-axis.

...

other plot graphical parameters.

Value

A list containing seven items:

s

duration of signal period(s) in seconds

p

duration of pause period(s) in seconds

r

ratio between the signal and silence periods(s)

positions

a list containing four elements:

s.start

start position(s) of signal period(s)

s.end

end position(s) of signal period(s)

first

whether the first event detected is a pause or a signal

Warning

Setting to high values to msmooth or ssmooth might return inaccurate results. Double check your results if so.

Author(s)

Jerome Sueur

See Also

env, cutw, pastew.


Teager-Kaiser energy tracking operator

Description

This function computes the Teager-Kaiser energy operator.

Usage

TKEO(wave, f, channel = 1, m = 1, M = 1, plot = TRUE,
xlab = "Time (s)", ylab = "Energy",
type = "l", bty = "l", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

m

a numeric vector of length 1 for the exponent parameter. See details.

M

a numeric vector of length 1 for the lag parameter. See details.

plot

logical, if TRUE returns a plot of the TK energy along time (by default TRUE).

xlab

Label of time x-axis.

ylab

Label of energy y-axis.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

bty

the type of box to be drawn around the energy plot.

...

other plot graphical parameters.

Details

The discrete version of the Teager-Kaiser operator is computed according to:

yn=xn2/m(xnM×xn+M)1/my_{n} = x_{n}^{2/m} - (x_{n-M} \times x_{n+M})^{1/m}

,
with m the exponent parameter and M the lag parameter which both are usually equal to 1 for a conventional operator.
The Teaser-Kaiser operator can be used to track amplitude modulations (AM) and/or frequency modulations (FM).
See examples.

Value

This function returns a two-column matrix, the first column is time and the second column includes the successive energy values.
m/2 NA values are added at the start and end of the vector.

Author(s)

Jerome Sueur

References

Kvedalen, E. (2003). Signal processing using the Teager Energy Operator and other nonlinear operators. University of Oslo, Department of Informatics, PhD Thesis, x + 100 p.

See Also

env, ifreq.

Examples

op <- par(mfrow=c(2,1))

## sinusoid AM 
s1 <- synth(f=8000, d=0.1, cf=200, am=c(100,10), output="Wave") 
oscillo(s1)
TKEO(s1)
## linear AM decrease
s2 <- synth(f=8000, d=0.1, cf=200, shape="decr", output="Wave") 
oscillo(s2)
TKEO(s2)
## sinusoid FM
s3 <- synth(f=8000, d=0.1, cf=200, fm=c(150,50,0,0,0), output="Wave") 
oscillo(s3)
TKEO(s3)
## linear FM increase
s4 <- synth(f=8000, d=0.1, cf=200, fm=c(0,0,600,0,0), output="Wave") 
oscillo(s4)
TKEO(s4)
## AM and FM
s5 <- synth(f=8000, d=0.1, cf=200, am=c(100,10), fm=c(150,50,0,0,0), output="Wave")
oscillo(s5)
TKEO(s5)
par(op)

WAve length and SPeed of sound

Description

This function returns the wavelength and the speed of sound of a given frequency in air, fresh-water or sea-water.

Usage

wasp(f, t = 20, c = NULL, s = NULL, d = NULL, medium = "air")

Arguments

f

frequency (Hz).

t

temperature (degree Celsius).

c

celerity (m/s) if a wavelength is to be found at a particular speed of sound.

s

salinity (parts per thousand) when medium is "sea".

d

depth (m) when medium is "sea".

medium

medium for sound propagation, either "air", "fresh" for fresh, or pure, water, "sea" for sea water.

Details

Speed of sound in air is computed according to:

c=331.4+0.6×tc = 331.4 + 0.6\times{t}

Speed of sound in fresh-water is computed according to Marczak equation:

c=1.402385.103+5.038813×t5.799136.102×t2c = 1.402385.10^{3} + 5.038813\times{t} - 5.799136.10^{-2}\times{t^{2}}

+3.287156.104×t31.398845.106×t4+ 3.287156.10^{-4}\times{t^{3}} - 1.398845.10^{-6}\times{t^{4}}

+2.787860.109×t5+ 2.787860.10^{-9}\times{t^{5}}

with t = temperature in degrees Celsius; range of validity: 0-95 degrees Celcius at atmospheric pressure.

Speed of sound in sea-water is computed according to Mackenzie equation:

c=1448.96+4.591×t5.304.102×t2c = 1448.96 + 4.591\times{t}- 5.304.10^{-2}\times{t^{2}}

+2.374.104×t3+1.34×(s35)+1.63.102×d+ 2.374.10^{-4}\times{t^{3}} + 1.34\times{(s-35)} + 1.63.10^{-2}\times{d}

+1.675.107×d21.025.102×t×(s35)+ 1.675.10^{-7}\times{d^{2}} - 1.025.10^{-2}\times{t}\times{(s-35)}

7.139.1013×t×d3- 7.139.10^{-13}\times{t}\times{d^3}

with t = temperature in degrees Celsius; s = salinity in parts per thousand; d = depth in meters; range of validity: temperature 2 to 30 degrees Celcius, salinity 25 to 40 parts per thousand, depth 0 to 8000 m.

Wavelength is obtained following:

λ=cf\lambda = \frac{c}{f}

with c = speed of sound in meters/second; f = frequency in Hertz.

Value

A list of two values is returned:

l

wavelength in meters

c

speed of sound in meters/second.

Author(s)

Jerome Sueur [email protected]

References

http://resource.npl.co.uk

Examples

# wavelength (m) of a 2000 Hz air-borne sound at 20 degrees Celsius
wasp(f=2000)$l
# [1] 0.1717

# sound speed in sea at 0 and -500 m
# for a respective temperature of 22 degrees Celcius and 11 degrees Celcius
wasp(f=1000,s=30,d=c(0,500),t=c(22,11),medium="sea")$c
# [1] 1521.246 1495.414

# wavelength (m) of a 1000 Hz sound in a medium unspecified where c = 1497 m/s
wasp(f=1000,c=1497)$l
# [1] 1.497

# variation of wavelength according to frequency and air temperature
op<-par(bg="lightgrey")
a<-seq(1000,20000,by=100) ; na<-length(a)
b<-seq(-20,40,by=10) ; nb<-length(b)
res<-matrix(numeric(na*nb),nrow=na)
for(i in 1:nb) res[,i]<-wasp(a,t=b[i])$l
matplot(x=a,y=res,type="l",lty=1,col= spectro.colors(nb),
  xlab="Frequency (Hz)",ylab="Wavelength (m)")
title("Wavelength of air-borne sound at different temperatures (deg. C)")
legend(x=15000,y=0.3,c("-20","-10","0","10","20","30","40"),
  lty=1,col= spectro.colors(nb),bg="grey")
par(op)

Convert wave amplitude to instantaneous sound pressure level (dB SPL)

Description

This function applies an absolute dB SPL scale to the amplitude of a time wave based on the properties of the recording chain, if known.

Usage

wav2dBSPL(wave, f, channel = 1, gain, sensitivity = -35, Vadc = 2, pref = 2 * 10^-5)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

gain

total gain applied to the sound (preamplifer + amplifier), in dB.

sensitivity

sensitivity of the microphone, in dB/V (by default - 35 dB/V).

Vadc

maximal voltage (peak to peak) converted by the analog to digital convertor ADC, in V (by default 2 V).

pref

sound pressure reference in the medium, in Pa (by default = 2*10^-5 Pa in air).

Value

A numeric vector of the same legnth as wave containing the sound waveform in dB SPL (Sound Pressure level in dB)

Note

This function can be used to turn a recorder, as a Songmeter or an Audiomoth, in a kind of soundlevel meter.

Author(s)

Sylvain Haupert

See Also

wav2leq

Examples

## note that the original gain, sensitivity and Vadc of tico
## are unknown, this is therefore a kind of 'unreal' example
data(tico)
res <- wav2dBSPL(tico, gain=18)
plot(x=seq(0,duration(tico),length=length(tico@left)), y=res, type="l", xlab="Time (s)",
ylab="dB SPL", las=1)
## dB SPL approximation for the complete sound
meandB(res)

wav-flac file conversion

Description

This function converts .wav files into .flac files and reversely

Usage

wav2flac(file, reverse = FALSE, overwrite = FALSE,
exename = NULL, path2exe = NULL)

Arguments

file

the .wav or .flac file to convert.

reverse

logical, if TRUE converts a .flac file into a .wav file.

overwrite

logical, if TRUE overwrites the file to convert.

exename

a character string specifying the name of the FLAC binary file. If NULL, the dedault name "flac" will be used for Linux OS and "flac.exe" for Windows OS.

path2exe

a character string giving the path to the FLAC binary file. If NULL, the dedault path "c:/Program Files/FLAC/" will be used for Windows OS.

Details

The function runs FLAC. FLAC has then to be installed first, if not the function will not work.

Value

A new file is created.

Note

FLAC must be installed to use this function but not to install the package seewave. Free Lossless Audio Codec (FLAC) is a file format by Josh Coalson for lossless audio data compression. FLAC reduces bandwidth and storage requirements without sacrificing the integrity of the audio source. Audio sources encoded to FLAC are typically reduced in size 40 to 50 percent.

Author(s)

Luis J. Villanueva-Rivera

See Also

savewav

Examples

## Not run: 
# synthesis of a 1kHz sound
a<-synth(d=10,f=8000,cf=1000)
# save it as a .wav file in the default working directory
savewav(a,f=8000)
# compress it to FLAC format and overwrite on the file a.wav
wav2flac("a.wav", overwrite=TRUE)
# back to .wav format
wav2flac("a.flac", reverse=TRUE)
# remove the files
unlink(c("a.wav","a.flac"))

## End(Not run)

Convert wave amplitude to equivalent continuous sound pressure level (Leq)

Description

This function computes the Leq value of a time wave based on the properties of the recording chain, if known.

Usage

wav2leq(wave, f, channel = 1, gain, dt = 1, sensitivity = -35, Vadc = 2, pref = 2 * 10^-5)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

gain

total gain applied to the sound (preamplifer + amplifier), in dB.

dt

integration time step, in s (by default 1 s).

sensitivity

sensitivity of the microphone, in dB/V (by default - 35 dB/V).

Vadc

maximal voltage (peak to peak) converted by the analog to digital convertor ADC, in V (by default 2 V).

pref

sound pressure reference in the medium, in Pa (by default = 2*10^-5 Pa in air).

Value

A numeric vector of length 1 returning the Leq value, in dB.

Note

This function can be used to turn a recorder, as a Songmeter or an Audiomoth, in a kind of soundlevel meter.

Author(s)

Sylvain Haupert

See Also

wav2dBSPL

Examples

data(tico)
## with a 1 s time of integration (that is for the first time window)
wav2leq(tico, gain=18)
## with a 0.5 s time of integration (that is for 3 successive time windows)
wav2leq(tico, dt=0.5, gain=18)
## for the complete sound
wav2leq(tico, dt=duration(tico), gain=18)
## which is equivalent to
meandB(wav2dBSPL(tico, gain=18))

Waterfall display

Description

This function returns a waterfall display of a short-term Fourier transform or of any matrix.

Usage

wf(wave, f, channel = 1, wl = 512, zp = 0, ovlp = 0, fftw= FALSE, dB = "max0",
dBref = NULL, wn = "hanning", x = NULL,
hoff = 1, voff = 1, col = heat.colors,
xlab = "Frequency (kHz)", ylab = "Amplitude (dB)",
xaxis = TRUE, yaxis = TRUE,
density = NULL, border = NULL, lines = FALSE, lwd=NULL, ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

window length for the analysis (even number of points). (by default = 512)

zp

zero-padding (even number of points), see Details.

ovlp

overlap between two successive windows (in %).

fftw

if TRUE calls the function FFT of the library fftw. See Notes of the spectro.

dB

a character string specifying the type dB to return: "max0" for a maximum dB value at 0, "A", "B", "C", "D", and "ITU" for common dB weights.

dBref

a dB reference value when dB is TRUE. NULL by default but should be set to 2*10e-5 for a 20 microPa reference.

wn

window name, see ftwindow (by default "hanning").

x

a matrix if wave is not provided.

hoff

horizontal 'offset' which shifts actual x-values slightly per row for visibility. Fractional parts will be removed.

voff

vertical 'offset' which separates traces.

col

a color or a color palette function to be used to assign colors in the plot

xlab

title of the frequency x-axis.

ylab

title of the amplitude y-axis.

xaxis

a logical, if TRUE adds the frequency x-axis according to f.

yaxis

a logical, if TRUE adds the amplitude y-axis according.

density

argument of polygon: the density of shading lines, in lines per inch. The default value of 'NULL' means that no shading lines are drawn. A zero value of 'density' means no shading nor filling whereas negative values (and 'NA') suppress shading (and so allow color filling).

border

argument of polygon: the color to draw the border. The default, 'NULL', means to use 'par("fg")'. Use 'border = NA' to omit borders.

lines

a logical, if TRUE plots lines instead of surfaces (polygons).

lwd

line width.

...

other graphical arguments to passed to plot

Details

Data input can be either a time wave (wave) or a matrix (x). In that case, if xaxis is set to TRUE the x-axis will follow the row index. To change it, turn xaxis to FALSE and use axis afterwards. See examples.

Note

The function is well adapted to display short-term Fourier transform. However, any matrix can be called using the argument x instead of wave.

Author(s)

Carl G. Witthoft and Jerome Sueur [email protected]

See Also

spectro, spectro3D, dynspec

Examples

data(tico)
wf(tico,f=22050)
# changing the display parameters
jet.colors <- colorRampPalette(c("blue", "green"))
wf(tico,f=22050, hoff=0, voff=2, col=jet.colors, border = NA)
# matrix input instead of a time wave and transparent lines display
m <- numeric()
for(i in seq(-pi,pi,len=40)) {m <- cbind(m,10*(sin(seq(0,2*pi,len=100)+i)))}
wf(x=m, lines=TRUE, col="#0000FF50",xlab="Time", ylab="Amplitude",
main="waterfall display")

Audacity audio markers export

Description

Write audio markers to be imported by Audacity.

Usage

write.audacity(x, filename)

Arguments

x

a data frame with the three or five colums, see details.

filename

name of the .txt file. (by default the name of x).

Details

The input x object should be a data frame with two or three columns depending on whether the markers include frequency limits or not :

  • time limits only:

    1. text label of each marker,

    2. time marker of the beginning of each marker,

    3. time marker of the end of each marker.

  • time and frequency limits:

    1. text label of each marker,

    2. time marker of the beginning of each marker,

    3. time marker of the end of each marker,

    4. lower frequency limit of each marker,

    5. higher frequency limit of each marker.

Value

A .txt file is generated to be imported as a markers in Audacity.

Note

Naming the columns of x is not necessary.

Author(s)

Jerome Sueur

References

Audacity is a free software distributed under the terms of the GNU General Public License.
Web site: https://www.audacityteam.org/

See Also

read.audacity

Examples

## 3 markers, time only
t1 <- c(9.2, 16.2, 24.4)
t2 <- c(11.7, 18.7, 26.9)
label <- c("a", "b", "c")
df <- data.frame(label, t1, t2)
write.audacity(df, filename="test-time.txt")
## 3 markers, time and frequency
t1 <- c(9.4, 15.2, 24.9)
t2 <- c(10.54, 16.6, 26.1)
f1 <- c(1703.4, 3406.8, 1608.8)
f2 <- c(7476.2, 8517.2, 5110.3)
label <- c("a", "b", "c")
dff <- data.frame(label, t1, t2, f1, f2)
write.audacity(dff, filename="test-time-frequency.txt")
## delete files
unlink(c("test-time.txt", "test-time-frequency.txt"))

Zap silence periods of a time wave

Description

This function simply deletes the silence periods of a time wave.

Usage

zapsilw(wave, f, channel = 1, threshold = 5, plot = TRUE, output = "matrix", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

threshold

amplitude threshold (in %) between silence and signal.

plot

logical, if TRUE plots the orginal and the new oscillograms (by default TRUE).

output

character string, the class of the object to return, either "matrix", "Wave", "Sample", "audioSample" or "ts".

...

other oscillo graphical parameters.

Value

If plot is FALSE, a new wave is returned. The class of the returned object is set with the argument output.

Note

Use the argument threshold to set the level of silence. See the examples.

Author(s)

Jerome Sueur

See Also

afilter, oscillo

Examples

data(orni)
zapsilw(orni,f=22050,colwave="red")
# setting the threshold value
zapsilw(orni,f=22050,threshold=1)

Instantaneous frequency of a time wave by zero-crossing

Description

This function measures the period of a full oscillating cycle.

Usage

zc(wave, f, channel = 1,  plot = TRUE, interpol = 1, threshold = NULL,
xlab = "Time (s)", ylab = "Frequency (kHz)", ylim = c(0, f/2000),
warning = TRUE, ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

plot

logical, if TRUE plots the dominant frequency along the time wave(by default TRUE).

interpol

a numeric vector of length 1, interpolation factor.

threshold

amplitude threshold for signal detection (in % ).

xlab

title of the x axis.

ylab

title of the y axis.

ylim

the range of y values.

warning

a logial to specify if warning message should be displayed or not when interpol is > 100.

...

other plot graphical parameters.

Details

If plot is FALSE, zc returns a vector of numeric data with the instantaneous frequency.

Value

If plot is FALSE, zc returns a two-column matrix, the first column corresponding to time in seconds (x-axis) and the second column corresponding to the instantaneous frequency of the time wave in kHz (y-axis).
‘NA’s correspond either to pause periods (e. g. detected applying threshold) or sections of the time wave not crossing the zero line. To remove ‘NA’s with na.omit allows to get only instantaneous frequency values but discards information about pause sections.

Note

interpol adds points to the time wave by linear interpolation (through approx). This increases measurement precision but as well time process. Type argument of plot cannot be set to “l”.

Author(s)

Jerome Sueur [email protected], Caroline Simonis and Thierry Aubin

References

Hopp, S. L., Owren, M. J. and Evans, C. S. (Eds) 1998. Animal acoustic communication. Springer, Berlin, Heidelberg.

See Also

zc, ifreq

Examples

data(pellucens)
pellu1 <- cutw(pellucens,f=22050,from=0,to=1,plot=FALSE)
# without interpolation
zc(pellu1,f=22050,threshold=5,pch=20)
# with interpolation
zc(pellu1,f=22050,threshold=5,interpol=20,pch=20)
# a way to plot with a line and to filter low frequencies
pellu2 <- zc(pellu1,f=22050,threshold=5,interpol=20,plot=FALSE)
pellu3 <- na.omit(pellu2[,2])
pellu4 <- pellu3[pellu3>3]
plot(x=seq(0,nrow(pellu1)/22050,length.out=length(pellu4)),
    y=pellu4,type="l",xlab="Time(s)",ylab="Frequency(kHz)")

Zero-crossing rate

Description

This functions computes the zero-crossing rate of a time function, i. e. the average number the sign of a time wave changes.

Usage

zcr(wave, f, channel = 1, wl = 512, ovlp = 0, plot = TRUE, type = "o", xlab =
"Time (s)", ylab = "Zero crossing rate", ...)

Arguments

wave

an R object.

f

sampling frequency of wave (in Hz). Does not need to be specified if embedded in wave.

channel

channel of the R object, by default left channel (1).

wl

length of the window for the analysis (even number of points, by default = 512). If NULL the zero-crossing rate is computed of the complete signal.

ovlp

overlap between two successive analysis windows (in %) if wl is not NULL.

plot

a logical, if TRUE plots a the zero-crossing rate results along time.

type

if plot is TRUE, type of plot that should be drawn. See plot for details (by default "l" for lines).

xlab

if plot is TRUE, label of the x axis.

ylab

if plot is TRUE, label of the y axis.

...

other plot graphical parameters.

Details

The zero-crossing rate is computed according to:

zcr=12×Nt=0N1sgn[x(t+1)]sgn[x(t)]zcr = \frac{1}{2 \times N} \sum_{t=0}^{N-1} |sgn[x(t+1)] -sgn[x(t)]|

with:
N the length of the signal x
and where:

sgn[x(t)]=1sgn[x(t)] = 1

if

x(t)0x(t) \geq 0

and

sgn[x(t)]=1sgn[x(t)] = -1

if

x(t)<0x(t) < 0

Value

The are two possibilities:

  1. a numeric vector of length 1 if wl is NULL,

  2. a numeric two-column matrix is returned with the first columnn being time (s) and the second colum being the zero-crossing rate (no scale) if wl is not NULL.

Note

The are two possibilities:

  1. if wl is NULL then the zero-crossing rate is computed for the complete signal.

  2. if wl is not NULL the the zero-crossing rate is computed for for a window sliding along the time wave.

The ZCR is supposed to help in detection of voiced/unvoiced sound sections.

Author(s)

Jerome Sueur

References

https://en.wikipedia.org/wiki/Zero-crossing_rate

See Also

zc

Examples

data(tico)
## a single value for the complete signal, no plot
zcr(tico, wl=NULL)
## a series of values computed for a sliding window of 512 samples, plot
zcr(tico)