feemindex {albatross} | R Documentation |
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 |
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 |
interpolate |
A string specifying an interpolation method (“whittaker”,
“loess”, “kriging”, “pchip”), or If interpolation is disabled, an index will get an When interpolation is enabled, required points that are missing from
the grid or present but set to |
... |
Additional parameters eventually passed to interpolation methods.
See |
progress |
Set to |
Details
Available indices and peaks are:
- HIX
-
\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. (Zsolnay, Baigar, Jimenez, Steinweg, and Saccomandi 1999)
- BIX
-
\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. (Huguet, Vacher, Relexans, Saubusse, Froidefond, and Parlanti 2009) - MFI
-
\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 (McKnight, Boyer, Westerhoff, Doran, Kulbe, and Andersen 2001) helps distinguish sources of isolated aquatic fulvic acids and may indicate their aromaticity.
- CFI
-
\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 (Cory and McKnight 2005) is correlated to relative contribution of microbial versus higher plant-derived organic matter to the DOM pool.
- YFI
-
\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 (Heo, Yoon, Kim, Lee, Lee, and Her 2016) is lowest for humic-like and fulvic-like samples, higher for aminosugar-like samples and highest for protein-like samples.
- FrI
-
\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 (Wilson and Xenopoulos 2009) and may provide indication of relative contribution of microbially produced DOM. - A, B, C, M, P, T
-
Fluorophore peaks taken from (Coble 2007):
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.
Positions of the peaks and the areas used to determine the
fluorescence indices of an EEM. The Rayleigh and Raman scattering
areas for both 1st and 2nd diffraction orders are shown in grey,
assuming a width of \pm 20
nm and a Raman
shift of 3400 \: \mathrm{cm}^{-1}
. The
tolerance interval of \pm 1
nm is invisible
at the scale of the figure.
Integration for HIX and YFI is done using the trapezoidal method:
\int_a^b f(x) dx \approx (b - a) \frac{f(a) + f(b)}{2}
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
Coble PG (2007). “Marine Optical Biogeochemistry: The Chemistry of Ocean Color.” Chemical Reviews, 107(2), 402-418. doi:10.1021/cr050350+.
Cory RM, McKnight DM (2005). “Fluorescence spectroscopy reveals ubiquitous presence of oxidized and reduced quinones in dissolved organic matter.” Environmental science & technology, 39(21), 8142-8149. doi:10.1021/es0506962.
Heo J, Yoon Y, Kim D, Lee H, Lee D, Her N (2016). “A new fluorescence index with a fluorescence excitation-emission matrix for dissolved organic matter (DOM) characterization.” Desalination and Water Treatment, 57(43), 20270-20282. doi:10.1080/19443994.2015.1110719.
Huguet A, Vacher L, Relexans S, Saubusse S, Froidefond JM, Parlanti E (2009). “Properties of fluorescent dissolved organic matter in the Gironde Estuary.” Organic Geochemistry, 40(6), 706-719. doi:10.1016/j.orggeochem.2009.03.002.
McKnight DM, Boyer EW, Westerhoff PK, Doran PT, Kulbe T, Andersen DT (2001). “Spectrofluorometric characterization of dissolved organic matter for indication of precursor organic material and aromaticity.” Limnology and Oceanography, 46(1), 38-48. doi:10.4319/lo.2001.46.1.0038.
Wilson HF, Xenopoulos MA (2009). “Effects of agricultural land use on the composition of fluvial dissolved organic matter.” Nature Geoscience, 2(1), 37-41. doi:10.1038/ngeo391.
Zsolnay A, Baigar E, Jimenez M, Steinweg B, Saccomandi F (1999). “Differentiating with fluorescence spectroscopy the sources of dissolved organic matter in soils subjected to drying.” Chemosphere, 38(1), 45-50. doi:10.1016/S0045-6535(98)00166-0.
See Also
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))