absindex: Functions of absorbance data
In albatross: PARAFAC Analysis of Fluorescence Excitation-Emission Matrices

absindex

R Documentation

Functions of absorbance data

Description

Calculate absorption coefficients and/or absorbance data at given wavelengths, spectral slopes, and their ratios.

Usage

  absindex(
    x, abs.path, unit = c("log10", "m^-1"), out.A = 254,
    out.a = c(350, 355, 374, 443),
    out.a.ratio = list(c(250, 365), c(465, 665)),
    out.slope = list(c(275, 295), c(350, 400)),
    out.slope.ratio = list(c(275, 295, 350, 400)),
    out.slope.nrmse = FALSE
  )

Arguments

`x`	Absorption data, either a `list` of two-column matrix-like objects with wavelengths in first column and values in second column, or a multi-column matrix-like object with wavelengths in first column and values in all other columns. Can be named in order to match with the `abs.path` values, see `feemife` for details.
`abs.path`	A numeric vector of optical path lengths for every spectrum, in centimetres. Defaults to `1` for all samples. If specified, should be either named, with names matching `x`, or unnamed and containing exactly the same number of path lengths.
`unit`	Specifies whether `x` contains absorbance (`⁠log10⁠`; 3{A = \log_{10}\frac{I_0}{I}

A = log10(I0 / I) A = log10(I0/I); unitless) or absorption coefficients (⁠m^-1⁠; 3{ \alpha = \frac{\ln \frac{I_0}{I}}{l}

Details

Currently, the spectral slopes are calculated by fitting a linear model 3{ \ln \alpha = b_0 - b_1 \lambda

Value

A data.frame with one row per sample, containing the following columns:

`sample`	Names or numbers of the samples.
`A.<wavelength>`	Absorbance values, for every \vwavelength in `out.A`.
`a.<wavelength>`	Absorption coefficients, for every \vwavelength in `out.a`.
`aR.<wl[1]>.<wl[2]>`	Ratios of absorption coefficients, for every \vwl in `out.a.ratio`.
`S.<wl[1]>.<wl[2]>`	Spectral slopes, for every \vwl in `out.slope`.
`NRMSE.S.<wl[1]>.<wl[2]>`	If `out.slope.nrmse` is `TRUE`, root-mean-square errors normalised by the range of the absorption coefficients for the models providing spectral slopes.
`SR.<wl[1]>.<wl[2]>.<wl[3]>.<wl[4]>`	Ratios of spectral slopes, for every \vwl in `out.slope.ratio`.