prospectr (version 0.2.0)

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

a numeric matrix , data.frame or vector to transform.

m

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

w

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

s

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

delta.wav

the 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

savitzkyGolay, movav, binning, continuumRemoval

Examples

# NOT RUN {
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)
# }