Absorbance

Share:

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
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), ...,
  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), ...,
  idx = !is.null(names(spct)))

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 use hinges to reduce interpolation errors

...

other arguments (possibly ignored)

idx

logical whether to add a column with the names of the elements of spct

Methods (by class)

  • default: Default for generic function

  • filter_spct: Specialization for filter spectra

  • object_spct: Specialization for object spectra

  • filter_mspct: Calculates absorbance from a filter_mspct

  • object_mspct: Calculates absorbance 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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
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")

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.