Internal Standard Normalization Recipe Step

step_line_ratio() creates a specification of a recipe step that divides each spectrum by the intensity of a reference emission line, such as a line of a matrix element of constant concentration (internal standard). This compensates for shot-to-shot changes of the ablated mass and of the plasma conditions.

Usage

step_line_ratio(
  recipe,
  ...,
  reference,
  window = 0.1,
  method = "area",
  baseline = FALSE,
  role = NA,
  trained = FALSE,
  columns = NULL,
  channels = NULL,
  skip = FALSE,
  id = recipes::rand_id("line_ratio")
)

Arguments

recipe: A recipe object. The step will be added to the sequence of operations for this recipe.
...: One or more selector functions to choose the predictors (for example, the spectral channels). See recipes::selections().
reference: The wavelength(s) of the reference line(s), in nm.
window: The half-width of the window around each reference wavelength, in nm. Default is 0.1.
method: The intensity of the reference line: "area" (default) or "height".
baseline: A logical: subtract a linear baseline under the reference line (FALSE, default).
role: Not used by this step, since no new variables are created.
trained: A logical indicating whether the step has been trained.
columns: The names of the selected columns, stored once the step has been trained.
channels: The channels of each reference window, found when the recipe is prepped. Not to be set by the user.
skip: A logical. Should the step be skipped when the recipe is baked by recipes::bake()? Keep the default FALSE, so that new data are corrected with the same filter as the training data.
id: A character string that is unique to this step.

Value

An updated version of recipe with the new step added to the sequence of existing steps.

Details

The selected columns form one spectrum per row, and their names must be their wavelengths (in nm). The intensity of the reference line is measured in each spectrum over the channels within window nm of reference:

method = "area" (default): the integrated intensity (trapezoidal rule), more robust to noise and to small wavelength shifts;
method = "height": the maximum intensity.

With baseline = TRUE, a straight line through the intensities at both ends of the window is subtracted first, so that the continuum under the line does not contribute. When several reference wavelengths are given, their intensities are summed.

Nothing is estimated from the training data: the channels of the window are found when the recipe is prepped, and each spectrum is normalized independently when it is baked. The selected columns are replaced by the normalized values. Spectra whose reference intensity is not positive are set to NA, with a warning. tidy() returns the reference wavelengths, the window, the method and id.

Choose a line that is well resolved, not self-absorbed and not saturated (see saturation_summary() and self_absorption()), and from an upper level close to that of the analyte lines, so that the ratio depends little on the plasma temperature.

References

Body, D., Chadwick, B.L., (2001). Optimization of the spectral data processing in a LIBS simultaneous elemental analysis system. Spectrochimica Acta Part B, 56(6):725-736.

Author

Christian L. Goueguel

Examples

if (rlang::is_installed("recipes")) {
  data(forageLIBS)
  # normalize to the C I 247.86 nm line of the organic matrix
  rec <- recipes::recipe(~ ., data = forageLIBS[-(1:14)]) |>
    step_line_ratio(recipes::all_numeric(), reference = 247.856, window = 0.15) |>
    recipes::prep()
  recipes::tidy(rec, number = 1)
}
#> # A tibble: 1 × 5
#>   reference window method baseline id              
#>       <dbl>  <dbl> <chr>  <lgl>    <chr>           
#> 1      248.   0.15 area   FALSE    line_ratio_PLUtB