prospectr (version 0.1.3)

gapDer: Gap-Segment Derivative

Description

Gap-Segment derivatives of a data matrix, data.frame or vector

Usage

gapDer(X, m = 1, w = 1, s = 1, delta.wav)

Arguments

X

numeric matrix , data.frame or vector to transform

m

order of the derivative, between 1 and 4 (default = 1)

w

filter length (should be odd and >=1), i.e. the spacing between points over which the derivative is computed

s

segment size, i.e. the range over which the points are averaged (default = 1, i.e. no smoothing corresponding to 'Norris' Gap Derivative)

delta.wav

sampling interval (or band spacing)

Value

a matrix or vector with the filtered signal(s)

Details

The sampling interval specified with the delta.wav argument is used for scaling and get numerically correct derivatives.

The convolution function is written in C++/Rcpp for faster computations.

References

Hopkins (2002). NIR News 14(5), 10.

See Also

sgolayfilt, savitzkyGolay, movav, binning, continuumRemoval

Examples

data(NIRsoil)
spc <- 1/10^NIRsoil$spc # conversion to reflectance
opar <- par(no.readonly = TRUE)
par(mfrow=c(2,2),mar=c(4,4,2,2))
# plot of the 10 first spectra
matplot(as.numeric(colnames(spc)),t(spc[1:10,]),
        type='l',xlab='',ylab='Reflectance')
mtext('Raw spectra')
der <- gapDer(spc,m=1,w=1,s = 1,delta.wav=2)
matplot(as.numeric(colnames(der)),t(der[1:10,]),
        type='l',xlab='Wavelength /nm',ylab='gap derivative')
mtext('1st derivative spectra')
der <- gapDer(spc,m=1,w=11,s = 1,delta.wav=2)
matplot(as.numeric(colnames(der)),t(der[1:10,]),
        type='l',xlab='Wavelength /nm',ylab='gap derivative')
mtext('1st derivative spectra with a window size = 11 nm')
der <- gapDer(spc,m=1,w=11,s = 10,delta.wav=2)
matplot(as.numeric(colnames(der)),t(der[1:10,]),
        type='l',xlab='Wavelength /nm',ylab='gap derivative')
mtext('1st derivative spectra with a window size = 11 nm, smoothing of 10 nm')
par(opar)