Calculate fluorescence indices or peak values for individual FEEMs or groups of them.
feemindex(x, ...)
# S3 method for feem
feemindex(
x,
indices = c(
"HIX", "BIX", "MFI", "CFI", "YFI", "FrI",
"A", "B", "C", "M", "P", "T"
),
tolerance = 1, interpolate = FALSE, ...
)
# S3 method for feemcube
feemindex(x, ..., progress = FALSE)
# S3 method for list
feemindex(x, ..., progress = FALSE)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).
A FEEM, a FEEM cube, or a list of feem objects.
Fluorescence indices or peaks to return. By default, all indices and peaks known to the function are returned. See Details for their meaning.
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.
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.
Set to TRUE to enable a progress bar (implemented via
txtProgressBar).
With edits and suggestions by Anastasia Drozdova.
Available indices and peaks are:
$$ \mathrm{HIX} = \frac{ \int_{435 \, \mathrm{nm}}^{480 \, \mathrm{nm}} I \, d\lambda_\mathrm{em} }{ \int_{300 \, \mathrm{nm}}^{345 \, \mathrm{nm}} I \, d\lambda_\mathrm{em} } \; \mathrm{at} \; \lambda_\mathrm{ex} = 254 \, \mathrm{nm} $$
Higher values of the humification index correspond to more condensed fluorescing molecules (higher C/H), more humified matter. albatross:::.Rdcite('Zsolnay1999')
$$ \mathrm{BIX} = \frac{ I(\lambda_\mathrm{em} = 380 \, \mathrm{nm}) }{ I(\lambda_\mathrm{em} = 430 \, \mathrm{nm}) } \; \mathrm{at} \; \lambda_\mathrm{ex} = 310 \, \mathrm{nm} $$
Index of recent autochthonous contribution determines the presence of the \(\beta\) fluorophore, characteristic of autochthonous biological activity in water samples. albatross:::.Rdcite('Huguet2009')
$$ \mathrm{MFI} = \frac{ I(\lambda_\mathrm{em} = 450 \, \mathrm{nm}) }{ I(\lambda_\mathrm{em} = 500 \, \mathrm{nm}) } \; \mathrm{at} \; \lambda_\mathrm{ex} = 370 \, \mathrm{nm} $$
The fluorescence index by albatross:::.Rdcite('McKnight2001') helps distinguish sources of isolated aquatic fulvic acids and may indicate their aromaticity.
$$ \mathrm{CFI} = \frac{ I(\lambda_\mathrm{em} = 470 \, \mathrm{nm}) }{ I(\lambda_\mathrm{em} = 520 \, \mathrm{nm}) } \; \mathrm{at} \; \lambda_\mathrm{ex} = 370 \, \mathrm{nm} $$
The fluorescence index by albatross:::.Rdcite('Cory2005') is correlated to relative contribution of microbial versus higher plant-derived organic matter to the DOM pool.
$$ \mathrm{YFI} = \frac{ \bar{I}(\lambda_\mathrm{em} \in [350, 400] \, \mathrm{nm}) }{ \bar{I}(\lambda_\mathrm{em} \in [400, 450] \, \mathrm{nm}) } \; \mathrm{at} \; \lambda_\mathrm{ex} = 280 \, \mathrm{nm} $$
Yeomin fluorescence index albatross:::.Rdcite('Heo2016') is lowest for humic-like and fulvic-like samples, higher for aminosugar-like samples and highest for protein-like samples.
$$ \mathrm{FrI} = \frac{ I(\lambda_\mathrm{em} = 380 \, \mathrm{nm}) }{ \max I(\lambda_\mathrm{em} \in [420, 435] \, \mathrm{nm}) } \; \mathrm{at} \; \lambda_\mathrm{ex} = 310 \, \mathrm{nm} $$
The freshness index, also known as \(\frac{\beta}{\alpha}\), is an indicator of autochthonous inputs albatross:::.Rdcite('Wilson2009') and may provide indication of relative contribution of microbially produced DOM.
Fluorophore peaks taken from albatross:::.Rdcite('Coble2007'):
| Peak | \(\lambda_\mathrm{ex}\) | \(\lambda_\mathrm{em}\) | Fluorescence |
| A | 260 | 400-460 | humic-like |
| B | 275 | 305 | tyrosine-like |
| C | 320-360 | 420-460 | humic-like |
| M | 290-310 | 370-410 | marine humic-like |
| P | 398 | 660 | pigment-like |
| T | 275 | 340 | tryptophan-like |
When a range of wavelengths specified in one or both axes, the maximal signal value over that range is taken.
albatross:::.Rdbibliography()
feem
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))
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