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Adjust spectral intensities to standard absorbance units.

Source: R/adj_intens.R
adj_intens.Rd

Converts reflectance or transmittance intensity units to absorbance units and adjust log or exp transformed units.

Usage

adj_intens(x, ...)

# Default S3 method
adj_intens(x, type = "none", make_rel = TRUE, log_exp = "none", ...)

# S3 method for class 'OpenSpecy'
adj_intens(x, type = "none", make_rel = TRUE, log_exp = "none", ...)

Arguments

x

a list object of class OpenSpecy.

type

a character string specifying whether the input spectrum is in absorbance units ("none", default) or needs additional conversion from "reflectance" or "transmittance" data.

make_rel

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

log_exp

a character string specifying whether the input needs to be log transformed "log", exp transformed "exp", or not ("none", default).

...

further arguments passed to submethods; this is to adj_neg() for adj_intens() and to conform_res() for conform_intens().

Value

adj_intens() returns a data frame containing two columns named "wavenumber" and "intensity".

Details

Many of the Open Specy functions will assume that the spectrum is in absorbance units. For example, see subtr_baseline(). To run those functions properly, you will need to first convert any spectra from transmittance or reflectance to absorbance using this function. The transmittance adjustment uses the \(log(1 / T)\) calculation which does not correct for system and particle characteristics. The reflectance adjustment uses the Kubelka-Munk equation \((1 - R)^2 / 2R\). We assume that the reflectance intensity is a percent from 1-100 and first correct the intensity by dividing by 100 so that it fits the form expected by the equation.

See also

subtr_baseline() for spectral background correction.

Author

Win Cowger, Zacharias Steinmetz

Examples

data("raman_hdpe")

adj_intens(raman_hdpe)
#>      wavenumber  intensity
#>           <num>      <num>
#>   1:    301.040 0.00000000
#>   2:    304.632 0.03037975
#>   3:    308.221 0.02784810
#>   4:    311.810 0.02405063
#>   5:    315.398 0.02531646
#>  ---                      
#> 960:   3187.990 0.05696203
#> 961:   3190.520 0.05696203
#> 962:   3193.060 0.06202532
#> 963:   3195.590 0.06202532
#> 964:   3198.120 0.05189873
#> 
#> $metadata
#>        x     y  user_name spectrum_type spectrum_identity      organization
#>    <int> <int>     <char>        <char>            <char>            <char>
#> 1:     1     1 Win Cowger         Raman              HDPE Horiba Scientific
#>     license                                                        session_id
#>      <char>                                                            <char>
#> 1: CC BY-NC 5728ddde4f649fd71f6f487fc5ad8d80/dc85257201307a131e71d9ec24aaccbf
#>                             file_id
#>                              <char>
#> 1: cb06ce2846b119d932fb6696479a445b