R: Absorptance

absorptance {photobiology} | R Documentation

## Absorptance

### Description

Function to calculate the mean, total, or other summary of absorptance for spectral data stored in a `filter_spct` or in an `object_spct`. Absorptance is a different quantity than absorbance.

### Usage

    absorptance(spct, w.band, quantity, wb.trim, use.hinges, ...)

    ## Default S3 method:
    absorptance(spct, w.band, quantity, wb.trim, use.hinges, ...)

    ## S3 method for class 'filter_spct'
    absorptance(spct, w.band = NULL, quantity = "average",
      wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
      use.hinges = getOption("photobiology.use.hinges", default = NULL), ...)

    ## S3 method for class 'object_spct'
    absorptance(spct, w.band = NULL, quantity = "average",
      wb.trim = getOption("photobiology.waveband.trim", default = TRUE),
      use.hinges = getOption("photobiology.use.hinges", default = NULL), ...)

    ## S3 method for class 'filter_mspct'
    absorptance(spct, w.band = NULL,
      quantity = "average", wb.trim = getOption("photobiology.waveband.trim",
      default = TRUE), use.hinges = getOption("photobiology.use.hinges", default =
      NULL), ..., attr2tb = NULL, idx = !is.null(names(spct)))

    ## S3 method for class 'object_mspct'
    absorptance(spct, w.band = NULL,
      quantity = "average", wb.trim = getOption("photobiology.waveband.trim",
      default = TRUE), use.hinges = getOption("photobiology.use.hinges", default =
      NULL), ..., attr2tb = NULL, idx = !is.null(names(spct)),
      .parallel = FALSE, .paropts = NULL)

### Arguments

`spct` | an R object.
`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.
`quantity` | character string One of "average" or "mean", "total", "contribution", "contribution.pc", "relative" or "relative.pc".
`wb.trim` | logical Flag if wavebands crossing spectral data boundaries are trimmed or ignored.
`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).
`attr2tb` | character vector, see `add_attr2tb` for the syntax for `attr2tb` passed as is to formal parameter `col.names`.
`idx` | logical whether to add a column with the names of the elements of spct
`.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.

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)

- `default`: Default for generic function

- `filter_spct`: Specialization for filter spectra

- `object_spct`: Specialization for object spectra

- `filter_mspct`: Calculates absorptance from a `filter_mspct`

- `object_mspct`: Calculates absorptance from a `object_mspct`

### Note

The `use.hinges` parameter 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.

### Examples

    absorptance(black_body.spct, new_waveband(400,500))
    absorptance(white_body.spct, new_waveband(300,400))
    absorptance(black_body.spct, split_bands(c(400,700), length.out = 3))
    absorptance(black_body.spct, split_bands(c(400,700), length.out = 3),
            quantity = "average")
    absorptance(black_body.spct, split_bands(c(400,700), length.out = 3),
            quantity = "total")
    absorptance(black_body.spct, split_bands(c(400,700), length.out = 3),
            quantity = "relative")
    absorptance(black_body.spct, split_bands(c(400,700), length.out = 3),
            quantity = "relative.pc")
    absorptance(black_body.spct, split_bands(c(400,700), length.out = 3),
            quantity = "contribution")
    absorptance(black_body.spct, split_bands(c(400,700), length.out = 3),
            quantity = "contribution.pc")

[Package photobiology version 0.9.21 Index]