R: Integrated response

response {photobiology}

R Documentation

Integrated response

Description

Calculate average photon- or energy-based photo-response.

Usage

response(
  spct,
  w.band,
  unit.out,
  quantity,
  time.unit,
  scale.factor,
  wb.trim,
  use.hinges,
  ...
)

## Default S3 method:
response(
  spct,
  w.band,
  unit.out,
  quantity,
  time.unit,
  scale.factor,
  wb.trim,
  use.hinges,
  ...
)

## S3 method for class 'response_spct'
response(
  spct,
  w.band = NULL,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  quantity = "total",
  time.unit = NULL,
  scale.factor = 1,
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.hinges = getOption("photobiology.use.hinges", default = NULL),
  naming = "default",
  ...
)

## S3 method for class 'response_mspct'
response(
  spct,
  w.band = NULL,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  quantity = "total",
  time.unit = NULL,
  scale.factor = 1,
  wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
  use.hinges = getOption("photobiology.use.hinges", default = NULL),
  naming = "default",
  ...,
  attr2tb = NULL,
  idx = "spct.idx",
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

`spct`	an R object of class "generic_spct".
`w.band`	waveband or list of waveband objects or a numeric vector of length two. The waveband(s) determine the region(s) of the spectrum that are summarized. If a numeric range is supplied a waveband object is constructed on the fly from it.
`unit.out`	character Allowed values `"energy"`, and `"photon"`, or its alias `"quantum"`.
`quantity`	character string One of `"average"` or `"mean"`, `"total"`, `"contribution"`, `"contribution.pc"`, `"relative"` or `"relative.pc"`.
`time.unit`	character or 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.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.
`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

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.

Whether returned values are expressed in energy-based or photon-based units depends on unit.out. 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.

Methods (by class)

response(default): Default for generic function
response(response_spct): Method for response spectra.
response(response_mspct): Calculates response from a response_mspct

Note

The parameter use.hinges controls speed optimization. The defaults should be suitable in most cases. Only the range of wavelengths in the wavebands is used and all BSWFs are ignored.