Detrending constructor for spectral preprocessing

Creates a preprocessing constructor for detrending spectral data. The constructor is intended to be passed to preprocess_recipe and executed via process.

Usage

prep_detrend(p = 2)

Arguments

p: A positive integer specifying the polynomial order used for fitting. Must be >= 1. Default is 2.

Value

An object of class preprocessing to be used in preprocess_recipe and executed by process.

Details

For each spectrum, a polynomial of order p is fitted using the column wavelengths as the explanatory variable (or integer indices if column names are not numeric). The residuals from this fit are returned as the detrended spectrum, removing wavelength-dependent baseline effects.

This constructor always performs pure polynomial detrending without a prior SNV transformation. Users who want the full Barnes et al. (1989) procedure (SNV followed by detrending) should chain prep_snv before prep_detrend in their recipe.

The computation is delegated to detrend with snv = FALSE.

References

Barnes RJ, Dhanoa MS, Lister SJ. 1989. Standard normal variate transformation and de-trending of near-infrared diffuse reflectance spectra. Applied Spectroscopy, 43(5): 772-777.

Author

Leonardo Ramirez-Lopez

Examples

data("NIRcannabis")
X <- NIRcannabis$spc

# Pure polynomial detrend
dt <- prep_detrend(p = 2)
recipe <- preprocess_recipe(dt, device = "unspecified")
X_dt <- process(X, recipe)

# Barnes et al. (1989): SNV followed by detrend
recipe_barnes <- preprocess_recipe(
  prep_snv(), prep_detrend(p = 2),
  device = "unspecified"
)
X_barnes <- process(X, recipe_barnes)