T2Afr: Convert transmittance into absorptance.
In aphalo/photobiology: Photobiological Calculations

T2Afr

R Documentation

Convert transmittance into absorptance.

Description

Function that converts transmittance (fraction) into absorptance (fraction). If reflectance (fraction) is available, it also allows conversions between internal and total absorptance.

Usage

T2Afr(x, action, byref, clean, ...)

## Default S3 method:
T2Afr(x, action = NULL, byref = FALSE, clean = FALSE, ...)

## S3 method for class 'numeric'
T2Afr(x, action = NULL, byref = FALSE, clean = FALSE, Rfr = NA_real_, ...)

## S3 method for class 'filter_spct'
T2Afr(x, action = "add", byref = FALSE, clean = FALSE, ...)

## S3 method for class 'object_spct'
T2Afr(x, action = "add", byref = FALSE, clean = FALSE, ...)

## S3 method for class 'filter_mspct'
T2Afr(
  x,
  action = "add",
  byref = FALSE,
  clean = FALSE,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'object_mspct'
T2Afr(
  x,
  action = "add",
  byref = FALSE,
  clean = FALSE,
  ...,
  .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.
`Rfr`	numeric vector. Spectral reflectance o reflectance factor. Set to zero if `x` is internal reflectance,
`.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

Absorptance, internal transmittance and total reflectance when expressed as fractions, add up to one:

1 = \alpha + \tau + \rho

where, \alpha is absorptance, \tau is internal transmittance and \rho is total reflectance. If any two of these quantities are known, the third one can be computed from them.

On the other hand:

1 = \alpha\prime + T

where, \alpha\prime = \alpha + \rho, measured together. In this case, there is not enough information available to compute \alpha.

Thus, method T2Afr() computes either \alpha or \alpha\prime, depending on whether \tau or T are contained in the argument passed to x, but neither of them when only \tau is known. To know which quantity has been computed, use getTfrType() to query whether the computations were based on \tau or T.

The R names used are: Tfr for \tau and T are Tfr, Afr for \alpha and \alpha\prime, and Rfr for rho. The distinction between \tau and T and between \alpha and \alpha\prime is made based on metadata attributes.

Value

A copy of x with a column Afr added and other columns possibly deleted except for w.length. If action = "replace", in all cases, the redundant columns are removed, even when column Afr was present in the argument passed to x.