eq_ratio {photobiology}

Energy:photon ratio

Description

This function returns the energy to mole of photons ratio for each waveband and a light source spectrum.

Usage

eq_ratio(spct, w.band, scale.factor, wb.trim, use.cached.mult, use.hinges, ...)

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

## S3 method for class 'source_spct'
eq_ratio(
  spct,
  w.band = NULL,
  scale.factor = 1,
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.cached.mult = FALSE,
  use.hinges = NULL,
  naming = "short",
  name.tag = ifelse(naming != "none", "[e:q]", ""),
  ...
)

## S3 method for class 'source_mspct'
eq_ratio(
  spct,
  w.band = NULL,
  scale.factor = 1,
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.cached.mult = FALSE,
  use.hinges = NULL,
  naming = "short",
  name.tag = ifelse(naming != "none", "[e:q]", ""),
  ...,
  attr2tb = NULL,
  idx = "spct.idx",
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

spct

source_spct.

w.band

waveband or list of waveband objects.

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 Flag telling 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 used by derived methods).

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

The ratio is based on one photon irradiance and one energy irradiance, both computed for the same waveband.

\frac{I(s, wb)}{Q(s, wb)}

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.#' @return Computed values are ratios between energy irradiance and photon irradiance for a given waveband. A named numeric vector in the case of methods for individual spectra, with one value for each waveband passed to parameter w.band. A data.frame in the case of collections of spectra, containing one column for each waveband object, an index column with the names of the spectra, and optionally additional columns with metadata values retrieved from the attributes of the member spectra.

By default values are only integrated, but depending on the argument passed to parameter quantity they can be re-expressed as relative fractions or percentages. In the case of vector output, names attribute is set to the name of the corresponding waveband unless a named list is supplied in which case the names of the list members are used, with "[e:q]" prepended. Units [J mol-1].

Value

Computed values are ratios between energy irradiance and photon irradiance for a given waveband. A named numeric vector in the case of methods for individual spectra, with one value for each waveband passed to parameter w.band. A data.frame in the case of multiple spectra, containing one column with ratios for each waveband object, an index column with the names of the spectra, and optionally additional columns with metadata values retrieved from the attributes of the member spectra.

By default values are only integrated, but depending on the argument passed to parameter quantity they are expressed as relative fractions or percentages. In the case of vector output, names attribute is set to the name of the corresponding waveband unless a named list is supplied in which case the names of the list members are used, with "[e:q]" prepended. Units [mol J-1].

Methods (by class)

• eq_ratio(default): Default for generic function

• eq_ratio(source_spct): Method for source_spct objects

• eq_ratio(source_mspct): Calculates energy:photon from a source_mspct object.

Performance

As this method accepts spectra as its input, it computes irradiances before computing the ratios. If you need to compute both ratios and irradiances from several hundreds or thousands of spectra, computing the ratios from previously computed irradiances avoids their repeated computation. A less dramatic, but still important, increase in performance is available when computing in the same function call ratios that share the same denominator.

See Also

Other photon and energy ratio functions: e_fraction(), e_ratio(), q_fraction(), q_ratio(), qe_ratio()

Examples

eq_ratio(sun.spct,
         waveband(c(400,700), wb.name = "White")) # J mol-1
eq_ratio(sun.spct,
         waveband(c(400,700), wb.name = "White"),
         scale.factor = 1e-6) # J umol-1