Calculate absorption coefficients and/or absorbance data at given wavelengths, spectral slopes, and their ratios.
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
)A data.frame with one row per sample, containing
the following columns:
Names or numbers of the samples.
Absorbance values, for every wavelength in out.A.
Absorption coefficients, for every wavelength in out.a.
Ratios of absorption coefficients, for every wl in
out.a.ratio.
Spectral slopes, for every wl in out.slope.
If out.slope.nrmse is TRUE, root-mean-square errors
normalised by the range of the absorption coefficients for the
models providing spectral slopes.
Ratios of spectral slopes, for every wl in
out.slope.ratio.
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.
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.
Specifies whether x contains absorbance (log10;
\(A = \log_{10}\frac{I_0}{I}\);
unitless) or absorption coefficients (m^-1;
\(
\alpha = \frac{\ln \frac{I_0}{I}}{l}
\);
\([\mathrm{m}^{-1}]\)).
Return absorbance values at the wavelengths given as a numeric vector.
Return absorption coefficients at the wavelengths given as a numeric vector.
Return ratios of absorption coefficients at the wavelengths given as a list of two-element numeric vectors. For every pair of wavelengths, \(\frac{\alpha(\lambda_1)}{\alpha(\lambda_2)} \) is returned.
Return spectral slopes at wavelength ranges given as a list of
two-element numeric vectors. See the slope.method for the
description of how spectral slopes are computed.
Return ratios of spectral slopes for pairs of wavelength ranges given as a list of four-element numeric vectors. For every list element, the value returned is \( \frac{S(\lambda_1, \lambda_2)}{S(\lambda_3, \lambda_4)} \).
When computing slopes, also return the root-mean-square error for the models providing them, divided by the range of the response: \( \frac{1}{y_\mathrm{max} - y_\mathrm{min}} \sqrt{\sum_{i=1}^n\frac{(\hat{y}_i - y_i)^2}{n}} \).
Currently, the spectral slopes are calculated by fitting a linear model \( \ln \alpha = b_0 - b_1 \lambda \) and returning \(b_1\) as the slope. See albatross:::.Rdcite('Twardowski2004') for a discussion of the calculation methods for spectral slopes.
Requested wavelengths missing from the original grid are interpolated
using spline. NA values are returned
outside the original wavelength range.
albatross:::.Rdbibliography()
feemife