The pipeline is defined as a character vector of step names:
"ABSORBANCE": convert reflectance → absorbance (−ln R)
"SG_SMOOTH(m,p)": Savitzky-Golay smooth (derivative = 0)
"SG_DERIV(m,p,d)": Savitzky-Golay derivative (d ≥ 1)
"SG(m,p,d)": legacy single-step SG (backward compatible)
"SNV": Standard Normal Variate
Usage
apply_pipeline(M, steps, absorbance_base10 = FALSE)
Arguments
- M
Numeric matrix (rows = samples, cols = wavelengths/wavenumbers)
- steps
Character vector of preprocessing step strings
- absorbance_base10
Logical; use base-10 log for absorbance conversion
Value
Preprocessed matrix
Details
The recommended two-step pipeline for OSSL VisNIR data is:
c("ABSORBANCE", "SG_SMOOTH(11,2)", "SG_DERIV(11,2,1)")
For MIR data (already in absorbance):
c("SG_SMOOTH(11,2)", "SG_DERIV(11,2,1)")
