q_fluence {photobiology}

Photon fluence

Description

Photon irradiance (i.e. quantum irradiance) for one or more waveband of a light source spectrum.

Usage

q_fluence(
  spct,
  w.band,
  exposure.time,
  scale.factor,
  wb.trim,
  use.cached.mult,
  use.hinges,
  allow.scaled,
  ...
)

## Default S3 method:
q_fluence(
  spct,
  w.band,
  exposure.time,
  scale.factor,
  wb.trim,
  use.cached.mult,
  use.hinges,
  allow.scaled,
  ...
)

## S3 method for class 'source_spct'
q_fluence(
  spct,
  w.band = NULL,
  exposure.time,
  scale.factor = 1,
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.cached.mult = getOption("photobiology.use.cached.mult", default = FALSE),
  use.hinges = NULL,
  allow.scaled = FALSE,
  naming = "default",
  ...
)

## S3 method for class 'source_mspct'
q_fluence(
  spct,
  w.band = NULL,
  exposure.time,
  scale.factor = 1,
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.cached.mult = getOption("photobiology.use.cached.mult", default = FALSE),
  use.hinges = NULL,
  allow.scaled = FALSE,
  naming = "default",
  ...,
  attr2tb = NULL,
  idx = "spct.idx",
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

spct

an R object.

w.band

a list of waveband objects or a waveband object

exposure.time

lubridate::duration object.

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.

allow.scaled

logical indicating whether scaled or normalized spectra as argument to spct are flagged as an error.

...

other arguments (possibly ignored).

naming

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

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.

Value

One numeric value for each waveband with no change in scale factor, with name attribute set to the name of each waveband unless a named list is supplied in which case the names of the list elements are used. The exposure.time is copied from the spectrum object to the output as an attribute. Units are as follows: moles of photons per exposure.

Methods (by class)

• q_fluence(default): Default for generic function

• q_fluence(source_spct): Calculate photon fluence from a source_spct object and the duration of the exposure

• q_fluence(source_mspct): Calculates photon (quantum) fluence from a source_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 irradiance functions: e_fluence(), e_irrad(), fluence(), irrad(), q_irrad()

Examples

library(lubridate)
q_fluence(sun.spct,
          w.band = waveband(c(400,700)),
          exposure.time = lubridate::duration(3, "minutes") )