photobiology (version 0.11.3)

T2A: Convert transmittance into absorbance.

Description

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

Usage

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

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.

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.

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

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.

See Also

Other quantity conversion functions: A2T(), Afr2T(), T2Afr(), any2T(), as_quantum(), e2q(), e2qmol_multipliers(), e2quantum_multipliers(), q2e()