spectro | R Documentation |

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.

```
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,
...)
```

`wave` |
an R object. |

`f` |
sampling frequency of |

`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 |

`zp` |
zero-padding (even number of points), see |

`ovlp` |
overlap between two successive windows (in %). |

`noisereduction` |
a numeric vector of length 1, if |

`fastdisp` |
faster graphic display for long |

`complex` |
if |

`norm` |
if |

`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 |

`fftw` |
if |

`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 |

`dBref` |
a dB reference value. |

`plot` |
logical, if |

`flog` |
a logical to plot the frequency on a logarithmic scale. |

`grid` |
logical, if |

`osc` |
logical, if |

`scale` |
logical, if |

`cont` |
logical, if |

`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 |

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

`colcont` |
colour for |

`colbg` |
background colour. |

`colgrid` |
colour for |

`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 |

`axisY` |
logical, if |

`tlim` |
modifications of the time X-axis limits. |

`trel` |
time X-axis with a relative scale when |

`flim` |
modifications of the frequency Y-axis limits (in kHz). |

`flimd` |
dynamic modifications of the frequency Y-axis limits. New |

`widths` |
a vector of length 2 to control the relative widths of columns on
the device when |

`heights` |
a vector of length 2 to control the relative heights of rows on
the device when |

`oma` |
a vector of length 4 to control the size of outer margins
when either |

`listen` |
if |

`...` |
other |

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.

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 |

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.

This function is based on `fft`

, `contour`

and
`filled.contour`

Jerome Sueur and Caroline Simonis.

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

`ggspectro`

, `spectro3D`

,
`lts`

, `dynspec`

, `wf`

,
`oscillo`

, `dBscale`

, `fft`

.

```
## 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)
```

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