feemindex {albatross}

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

\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

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))