R: Kolmogorov-Smirnov distance

ks.dist {seewave}

R Documentation

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

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)

[Package seewave version 2.1.6 Index]