feemindex: Fluorescence indices and peak values

In albatross: PARAFAC Analysis of Fluorescence Excitation-Emission Matrices

Fluorescence indices and peak values

Description

Calculate fluorescence indices or peak values for individual FEEMs or groups of them.

Usage

  feemindex(x, ...)
  ## S3 method for class 'feem'
feemindex(
    x,
    indices = c(
      "HIX", "BIX", "MFI", "CFI", "YFI", "FrI",
      "A", "B", "C", "M", "P", "T"
    ),
    tolerance = 1, interpolate = FALSE, ...
  )
  ## S3 method for class 'feemcube'
feemindex(x, ..., progress = FALSE)
  ## S3 method for class 'list'
feemindex(x, ..., progress = FALSE)

Arguments

x	A FEEM, a FEEM cube, or a list of feem objects.
indices	Fluorescence indices or peaks to return. By default, all indices and peaks known to the function are returned. See Details for their meaning.
tolerance	A numeric scalar signifying the acceptable emission and excitation wavelength error in nm. For example, if a wavelength of 254 nm is needed to calculate an index, a value at 255 nm can be considered if tolerance >= 1. Defaults to 1 nm. See below for what happens if no matching value is found.
interpolate	A string specifying an interpolation method (“whittaker”, “loess”, “kriging”, “pchip”), or FALSE to disable interpolation (default). If interpolation is disabled, an index will get an NA value when required points are too far from the measured grid or are present in the grid but set to NA. When interpolation is enabled, required points that are missing from the grid or present but set to NA will be interpolated using feemgrid as long as they are within the wavelength bounds of the FEEM. NAs may still be returned only when the desired value is impossible to interpolate due to it being outside the wavelength range.
...	Additional parameters eventually passed to interpolation methods. See feemscatter for details.
progress	Set to TRUE to enable a progress bar (implemented via txtProgressBar).

Details

Available indices and peaks are:

HIX

3{ \mathrm{HIX} = \frac{ \int_{435 \, \mathrm{nm}}^{480 \, \mathrm{nm}} I \, d\lambda_\mathrm{em} }{ \int_{300 \, \mathrm{nm}}^{345 \, \mathrm{nm}} I \, d\lambda_\mathrm{em} } \; \mathrm{at} \; \lambda_\mathrm{ex} = 254 \, \mathrm{nm}

HIX = area(em in [435, 480])/area(em in [300, 345]) at ex = 254 HIX = ^{∫ I(λ_em ∈ [435, 480] nm)}/_{∫ I(λ_em ∈ [300, 345] nm)} at λ_ex = 254 nm

Higher values of the humification index correspond to more condensed fluorescing molecules (higher C/H), more humified matter. Zsolnay1999 \itemBIX 3{ \mathrm{BIX} = \frac{ I(\lambda_\mathrm{em} = 380 \, \mathrm{nm}) }{ I(\lambda_\mathrm{em} = 430 \, \mathrm{nm}) } \; \mathrm{at} \; \lambda_\mathrm{ex} = 310 \, \mathrm{nm} BIX = I(em = 380 nm)/I(em = 430 nm) at ex = 310 nm BIX = ^{I(λ_em = 380 nm)}/_{I(λ_em = 430 nm)} at λ_ex = 310 nm Index of recent autochthonous contribution determines the presence of the \eqn{\beta

Value

For individual feem objects, a named numeric vector containing the values requested via the indices argument.

Otherwise, a data.frame containing the values from the vectors above and a column named sample containing the names of the samples (or numbers, if names were absent).

Author(s)

With edits and suggestions by Anastasia Drozdova.

References

\bibliography

See Also

feem

Examples

  data(feems)

  x <- feemscatter(feems$a, rep(25, 4), 'omit')
  feemindex(x)
  feemindex(x, interpolate = 'whittaker')

  feemindex(feems[2:3])
  feemindex(feemcube(feems[4:5], TRUE))

albatross documentation built on May 29, 2024, 9:10 a.m.