process_spec {OpenSpecy}

Process Spectra

Description

process_spec() is a monolithic wrapper function for all spectral processing steps.

Usage

process_spec(x, ...)

## Default S3 method:
process_spec(x, ...)

## S3 method for class 'OpenSpecy'
process_spec(
  x,
  active = TRUE,
  adj_intens = FALSE,
  adj_intens_args = list(type = "none"),
  conform_spec = TRUE,
  conform_spec_args = list(range = NULL, res = 5, type = "interp"),
  restrict_range = FALSE,
  restrict_range_args = list(min = 0, max = 6000),
  flatten_range = FALSE,
  flatten_range_args = list(min = 2200, max = 2420),
  subtr_baseline = FALSE,
  subtr_baseline_args = list(type = "polynomial", degree = 8, raw = FALSE, baseline =
    NULL),
  smooth_intens = TRUE,
  smooth_intens_args = list(polynomial = 3, window = 11, derivative = 1, abs = TRUE),
  make_rel = TRUE,
  make_rel_args = list(na.rm = TRUE),
  ...
)

Arguments

x

an OpenSpecy object.

active

logical; indicating whether to perform processing. If TRUE, the processing steps will be applied. If FALSE, the original data will be returned.

adj_intens

logical; describing whether to adjust the intensity units.

adj_intens_args

named list of arguments passed to smooth_intens().

conform_spec

logical; whether to conform the spectra to a new wavenumber range and resolution.

conform_spec_args

named list of arguments passed to conform_spec().

restrict_range

logical; indicating whether to restrict the wavenumber range of the spectra.

restrict_range_args

named list of arguments passed to restrict_range().

flatten_range

logical; indicating whether to flatten the range around the carbon dioxide region.

flatten_range_args

named list of arguments passed to flatten_range().

subtr_baseline

logical; indicating whether to subtract the baseline from the spectra.

subtr_baseline_args

named list of arguments passed to subtr_baseline().

smooth_intens

logical; indicating whether to apply a smoothing filter to the spectra.

smooth_intens_args

named list of arguments passed to smooth_intens().

make_rel

logical; if TRUE spectra are automatically normalized with make_rel().

make_rel_args

named list of arguments passed to make_rel().

na.rm

Whether to allow NA or set all NA values to

...

further arguments passed to subfunctions.

Value

process_spec() returns an OpenSpecy object with processed spectra based on the specified parameters.

Examples

data("raman_hdpe")
plot(raman_hdpe)

# Process spectra with range restriction and baseline subtraction
process_spec(raman_hdpe,
             restrict_range = TRUE,
             restrict_range_args = list(min = 500, max = 3000),
             subtr_baseline = TRUE,
             subtr_baseline_args = list(type = "polynomial",
                                        polynomial = 8)) |>
  lines(col = "darkred")

# Process spectra with smoothing and derivative
process_spec(raman_hdpe,
             smooth_intens = TRUE,
             smooth_intens_args = list(
               polynomial = 3,
               window = 11,
               derivative = 1
               )
             ) |>
  lines(col = "darkgreen")