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Corrects artifacts in a spectrum based on reference spectra of the artifact compound

Source: R/ir_correct_atmosphere.R
ir_correct_atmosphere.Rd

ir_correct_atmosphere takes two objects of class ir with the same number of spectra in each and corrects the spectra of the first object with the spectra of the second object according to the procedure presented by (Perez-Guaita et al. 2013) .

Usage

ir_correct_atmosphere(
  x,
  ref,
  wn1,
  wn2,
  do_interpolate = FALSE,
  start = NULL,
  dw = 1,
  warn = TRUE
)

Source

Perez-Guaita D, Kuligowski J, Quintás G, Garrigues S, de La Guardia M (2013). “Atmospheric compensation in Fourier transform infrared (FT-IR) spectra of clinical samples.” Applied spectroscopy, 67(11), 1339--1342. doi:10.1366/13-07159 .

Arguments

x

An object of class ir containing the spectra to correct (with intensities representing absorbances).

ref

An object of class ir containing the reference spectra to use for correction (with intensities representing absorbances). ref must have the same number of rows as x, the contained spectra must cover the wavenumber range of all spectra in x, and if do_interpolate = FALSE, all spectra must have identical wavenumber values.

wn1

A numeric value representing the first wavenumber value to use as reference point (Perez-Guaita et al. 2013) . Examples used by Perez-Guaita et al. (2013) are:

H\(_2\)O

3902 cm\(^{-1}\).

CO\(_2\)

2361 cm\(^{-1}\).

wn2

A numeric value representing the second wavenumber value to use as reference point (Perez-Guaita et al. 2013) . Examples used by Perez-Guaita et al. (2013) are:

H\(_2\)O

3912 cm\(^{-1}\).

CO\(_2\)

2349 cm\(^{-1}\).

do_interpolate

A logical value indicating if x and ref should be interpolated prior correction (TRUE) or not (FALSE).

start

See ir_interpolate().

dw

See ir_interpolate().

warn

A logical value indicating whether warnings about mismatching wavenumber values should be displayed (TRUE) or not (FALSE). If set to TRUE and wn1 or wn2 do not exactly match the wavenumber values in x and ref, a warning will be printed to inform about the wavenumber difference between the selected and targeted wavenumber value.

Value

x corrected with the reference spectra in ref.

Note

The function was not tested yet.

Examples

ir_correct_atmosphere(ir_sample_data, ir_sample_data, wn1 = 2361, wn2 = 2349)
#> # A tibble: 58 × 7
#>    id_measurement id_sample sample_type sample_comment             klason_lignin
#>  *          <int> <chr>     <chr>       <chr>                      <units>      
#>  1              1 GN 11-389 needles     Abies Firma Momi fir       0.359944     
#>  2              2 GN 11-400 needles     Cupressocyparis leylandii… 0.339405     
#>  3              3 GN 11-407 needles     Juniperus chinensis Chine… 0.267552     
#>  4              4 GN 11-411 needles     Metasequoia glyptostroboi… 0.350016     
#>  5              5 GN 11-416 needles     Pinus strobus Torulosa     0.331100     
#>  6              6 GN 11-419 needles     Pseudolarix amabili Golde… 0.279360     
#>  7              7 GN 11-422 needles     Sequoia sempervirens Cali… 0.329672     
#>  8              8 GN 11-423 needles     Taxodium distichum Cascad… 0.356950     
#>  9              9 GN 11-428 needles     Thuja occidentalis Easter… 0.369360     
#> 10             10 GN 11-434 needles     Tsuga caroliniana Carolin… 0.289050     
#> # … with 48 more rows, and 2 more variables: holocellulose <units>,
#> #   spectra <list>