Tfr_fraction {photobiology}

transmittance:transmittance fraction

Description

This function returns the transmittance fraction for a given pair of wavebands of a filter spectrum.

Usage

Tfr_fraction(
  spct,
  w.band.num,
  w.band.denom,
  scale.factor,
  wb.trim,
  use.cached.mult,
  use.hinges,
  ...
)

## Default S3 method:
Tfr_fraction(
  spct,
  w.band.num,
  w.band.denom,
  scale.factor,
  wb.trim,
  use.cached.mult,
  use.hinges,
  ...
)

## S3 method for class 'filter_spct'
Tfr_fraction(
  spct,
  w.band.num = NULL,
  w.band.denom = NULL,
  scale.factor = 1,
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.cached.mult = FALSE,
  use.hinges = NULL,
  quantity = "mean",
  naming = "short",
  name.tag = NULL,
  ...
)

## S3 method for class 'filter_mspct'
Tfr_fraction(
  spct,
  w.band.num = NULL,
  w.band.denom = NULL,
  scale.factor = 1,
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.cached.mult = FALSE,
  use.hinges = NULL,
  quantity = "mean",
  naming = "short",
  name.tag = NULL,
  ...,
  attr2tb = NULL,
  idx = "spct.idx",
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

spct

an object of class "filter_spct".

w.band.num

waveband object or a list of waveband objects used to compute the numerator(s) and denominator(s) of the fraction(s).

w.band.denom

waveband object or a list of waveband objects used to compute the denominator(s) of the fraction(s).

scale.factor

numeric vector of length 1, or length equal to that of w.band. Numeric multiplier applied to returned values.

wb.trim

logical if TRUE wavebands crossing spectral data boundaries are trimmed, if FALSE, they are discarded

use.cached.mult

logical indicating whether multiplier values should be cached between calls

use.hinges

logical Flag indicating whether to insert "hinges" into the spectral data before integration so as to reduce interpolation errors at the boundaries of the wavebands.

...

other arguments (possibly ignored)

quantity

character One of "total", "average" or "mean".

naming

character one of "long", "default", "short" or "none". Used to select the type of names to assign to returned value.

name.tag

character Used to tag the name of the returned values.

attr2tb

character vector, see add_attr2tb for the syntax for attr2tb passed as is to formal parameter col.names.

idx

character Name of the column with the names of the members of the collection of spectra.

.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

With the default quantity = "mean" or quantity = "average" the ratio is based on two mean spectral transmittance, one computed for each waveband.

\frac{\overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{num})}{\overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{denom}) + \overline{\mathrm{Tfr}_\lambda}(s, wb_\mathrm{num})}

If the argument is set to quantity = "total" the fraction is based on two integrated transmittance, one computed for each waveband.

\frac{\mathrm{Tfr}(s, wb_\mathrm{num})}{\mathrm{Tfr}(s, wb_\mathrm{denom}) + \mathrm{Tfr}(s, wb_\mathrm{num})}

Only if the wavelength expanse of the two wavebands is the same, these two ratios are numerically identical.

Value

In the case of methods for individual spectra, a numeric vector with name attribute set. The name is based on the name of the wavebands unless a named list of wavebands is supplied in which case the names of the list elements are used. "[Tfr:Tfr]" is appended if quantity = "total" and "[Tfr(wl):Tfr(wl)]" if quantity = "mean" or quantity = "average".

A data.frame is returned in the case of collections of spectra, containing one column for each fraction definition, an index column with the names of the spectra, and optionally additional columns with metadata values retrieved from the attributes of the member spectra.

Fraction definitions are "assembled" from the arguments passed to w.band.num and w.band.denom. If both arguments are lists of waveband definitions, with an equal number of members, then the wavebands are paired to obtain as many fractions as the number of wavebands in each list. Recycling for wavebands takes place when the number of denominator and numerator wavebands differ.

Methods (by class)

• Tfr_fraction(default): Default for generic function

• Tfr_fraction(filter_spct): Method for filter_spct objects

• Tfr_fraction(filter_mspct): Calculates Tfr:Tfr from a filter_mspct object.

Note

The last two parameters control speed optimizations. The defaults should be suitable in most cases. If you will use repeatedly the same SWFs on many spectra measured at exactly the same wavelengths you may obtain some speed up by setting use.cached.mult=TRUE. However, be aware that you are responsible for ensuring that the wavelengths are the same in each call, as the only test done is for the length of the w.length vector.

See Also

Other transmittance ratio functions: Tfr_normdiff(), Tfr_ratio()

Examples

Tfr_fraction(Ler_leaf_rflt.spct,
             waveband(c(400,500), wb.name = "Blue"),
             waveband(c(600,700), wb.name = "Red"))
Tfr_fraction(Ler_leaf_rflt.spct,
             waveband(c(400,500), wb.name = "Blue"),
             waveband(c(600,700), wb.name = "Red"),
             quantity = "total")
Tfr_fraction(Ler_leaf_rflt.spct,
             waveband(c(400,500), wb.name = "Blue"),
             waveband(c(600,700), wb.name = "Red"),
             quantity = "mean")