absorbance: Absorbance

Description Usage Arguments Value Methods (by class) Note Examples

View source: R/spct.absorbance.R

Description

Function to calculate the mean, total, or other summary of absorbance for spectral data stored in a filter_spct or in an object_spct.

Usage

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

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

## S3 method for class 'filter_spct'
absorbance(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'
absorbance(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'
absorbance(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'
absorbance(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 indicating 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)

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

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absorbance(polyester.spct, new_waveband(400,700))
absorbance(yellow_gel.spct, new_waveband(400,700))
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3))
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3),
        quantity = "average")
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3),
        quantity = "total")
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3),
        quantity = "relative")
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3),
        quantity = "relative.pc")
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3),
        quantity = "contribution")
absorbance(yellow_gel.spct, split_bands(c(400,700), length.out = 3),
        quantity = "contribution.pc")

photobiology documentation built on April 3, 2018, 1:06 a.m.