Creates a preprocessing constructor for computing first or second order
derivatives of spectral data. The constructor is intended to be passed to
preprocess_recipe and executed via process.
Three algorithms are supported: Savitzky-Golay ("savitzky-golay"),
Norris-Gap/Gap-Segment ("gap-segment"), and the derivative
pre-treatment from BUCHI NIRWise PLUS software ("nwp").
Usage
prep_derivative(m, w, p, algorithm = c("savitzky-golay", "gap-segment", "nwp"))Arguments
- m
An integer indicating the derivative order. Must be
1(first derivative) or2(second derivative).- w
A positive odd integer indicating the filter window size. For
"gap-segment",windicates the gap size (spacing between points over which the derivative is computed).- p
An integer. For
"savitzky-golay", indicates the polynomial order and must satisfyp < wandp >= m. For"gap-segment"and"nwp", indicates the segment or smoothing window size and must be a positive odd integer.- algorithm
A character string specifying the algorithm. One of
"savitzky-golay"(default),"gap-segment", or"nwp". See Details.
Value
An object of class preprocessing to be used in
preprocess_recipe and executed by process.
The object is a list containing the method name, all parameters, and
(for algorithm = "nwp") the NIRWise PLUS half-window values
(half_w, half_s) required for device file serialization.
Details
Savitzky-Golay ("savitzky-golay"): fits a polynomial of
order p within a moving window of size w and differentiates
analytically. Implemented via savitzkyGolay.
Gap-Segment ("gap-segment"): computes the derivative over a
gap of w points, with optional averaging over a segment of p
points. When p = 1 this reduces to the standard Norris-Gap
derivative. Implemented via gapDer.
NWP ("nwp"): reproduces the "DG" derivative pre-treatment
from BUCHI NIRWise PLUS calibration software. A moving average of window
p is applied first (pre-smoothing), followed by differentiation.
For first order, a gap derivative with gap w is used. For second
order, a centered second difference with spacing half_w is computed:
\[d^2x_i = \frac{2x_i - (x_{i+h} + x_{i-h})}{2h}\]
where \(h = half_w\). Edge columns affected by the window are removed from the output.
For the "nwp" algorithm, the NIRWise PLUS half-window conventions are:
\[half_w = (w + 1) / 2\]
\[half_s = (p - 1) / 2\]
These are stored internally for device file serialization and are not
user-facing parameters.
Examples
data("NIRcannabis")
X <- NIRcannabis$spc
# Savitzky-Golay first derivative, window 11, polynomial order 3
sg <- prep_derivative(m = 1, w = 11, p = 3, algorithm = "savitzky-golay")
# Gap-Segment second derivative, gap 9, segment 3
gs <- prep_derivative(m = 2, w = 9, p = 3, algorithm = "gap-segment")
# NWP first derivative, window 5, pre-smoothing 11
nwp <- prep_derivative(m = 1, w = 5, p = 11, algorithm = "nwp")
# Apply via preprocess_recipe
recipe <- preprocess_recipe(sg, device = "unspecified")
X_der <- process(X, recipe)