eemR (version 1.0.1)

eem_coble_peaks: Extract fluorescence peaks

Description

Extract fluorescence peaks

Usage

eem_coble_peaks(eem, verbose = TRUE)

Arguments

eem

An object of class eemlist.

verbose

Logical determining if additional messages should be printed.

Value

An object of class eemlist.

A data frame containing peaks B, T, A, M and C for each eem. See details for more information.

Interpolation

Different excitation and emission wavelengths are often used to measure EEMs. Hence, it is possible to have mismatchs between measured wavelengths and wavelengths used to calculate specific metrics. In these circumstances, EEMs are interpolated using the interp2 function from the parcma library. A message warning the user will be prompted if data interpolation is performed.

Details

According to Coble (1996), peaks are defined as follow:

Peak B: ex = 275 nm, em = 310 nm

Peak T: ex = 275 nm, em = 340 nm

Peak A: ex = 260 nm, em = 380:460 nm

Peak M: ex = 312 nm, em = 380:420 nm

peak C: ex = 350 nm, em = 420:480 nm

Given that peaks A, M and C are not defined at fix emission wavelength, the maximum fluorescence value in the region is extracted.

References

Coble, P. G. (1996). Characterization of marine and terrestrial DOM in seawater using excitation-emission matrix spectroscopy. Marine Chemistry, 51(4), 325-346.

http://doi.org/10.1016/0304-4203(95)00062-3

See Also

interp2

Examples

# NOT RUN {
file <- system.file("extdata/cary/scans_day_1/", "sample1.csv", package = "eemR")
eem <- eem_read(file, import_function = "cary")

eem_coble_peaks(eem)
# }