R: Convert transmittance into absorbance.

T2A {photobiology}

R Documentation

Convert transmittance into absorbance.

Description

Function that converts transmittance (fraction) into \log_{10}-based absorbance (a.u.).

Usage

T2A(x, action, byref, clean, ...)

## Default S3 method:
T2A(x, action = NULL, byref = FALSE, ...)

## S3 method for class 'numeric'
T2A(x, action = NULL, byref = FALSE, clean = TRUE, ...)

## S3 method for class 'filter_spct'
T2A(x, action = "add", byref = FALSE, clean = TRUE, strict.A = FALSE, ...)

## S3 method for class 'filter_mspct'
T2A(
  x,
  action = "add",
  byref = FALSE,
  clean = TRUE,
  strict.A = TRUE,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

`x`	an R object.
`action`	character Allowed values `"replace"` and `"add"`.
`byref`	logical indicating if new object will be created by reference or by copy of `x`.
`clean`	logical replace off-boundary values before conversion
`...`	not used in current version
`strict.A`	logical Attempt to compute a true internal absorbance even if `"total"` transmittance is stored in `x`.
`.parallel`	if `TRUE`, apply function in parallel, using parallel backend provided by foreach
`.paropts`	a list of additional options passed into the foreach function when parallel computation is enabled. This is important if (for example) your code relies on external data or packages: use the .export and .packages arguments to supply them so that all cluster nodes have the correct environment set up for computing.

Details

Absorbance, A, is frequently used in chemistry as it is linearly related to the concentration of a solute dissolved in a solvent.

A = -\log_{10} \tau

where, A absorbance and \tau is internal transmittance. By default, if total transmittance, T, is stored in x, the returned value computed as

A = -\log_{10} T

is not strictly absorbance. In this case and in cases when the measured light attenuation is the result of scattering, or when part of measured light is re-emitted after absorption the use of attenuance is the IUPAC-recommended name for this quantity.

If strict.A = TRUE is passed in the call and total transmittance, T, and total reflectance, \rho, are both available, absorbance is computed as:

A = -\log_{10} (T - \rho) / (1 - \rho)

where \rho can be either spectral total reflectance stored in x as data or a single approximate Rfr.constant value stored as part of the metadata.

Value

A copy of x with a column A added and other columns possibly deleted except for w.length. If action = "replace", in all cases, the additional columns are removed, even if no column needs to be added.

Methods (by class)

T2A(default): Default method for generic function
T2A(numeric): Method for numeric vectors
T2A(filter_spct): Method for filter spectra
T2A(filter_mspct): Method for collections of filter spectra

Note

The default A.strict = FALSE ensures indentical behaviour as in 'photobiology' (<= 0.11.0).