eemR (version 1.0.1)

eem_inner_filter_effect: Inner-filter effect correction

Description

Inner-filter effect correction

Usage

eem_inner_filter_effect(eem, absorbance, pathlength = 1)

Arguments

eem

An object of class eemlist.

absorbance

A data frame with:

wavelength

A numeric vector containing wavelengths.

...

One or more numeric vectors containing absorbance spectra.

pathlength

A numeric value indicating the pathlength (in cm) of the cuvette used for absorbance measurement. Default is 1 (1cm).

Value

An object of class eemlist.

An object of class eem containing:

• sample The file name of the eem.

• x A matrix with fluorescence values.

• em Emission vector of wavelengths.

• ex Excitation vector of wavelengths.

Names matching

The names of absorbance variables are expected to match those of the eems. If the appropriate absorbance spectrum is not found, an uncorrected eem will be returned and a warning message will be printed.

Sample dilution

Kothawala et al. 2013 have shown that a 2-fold dilution was required for sample presenting total absorbance > 1.5 in a 1 cm cuvette. Accordingly, a message will warn the user if total absorbance is greater than this threshold.

Details

The inner-filter effect correction procedure is assuming that fluorescence has been measured in 1 cm cuvette. Hence, absorbance will be converted per cm. Note that absorbance spectra should be provided (i.e. not absorption).

References

Parker, C. a., & Barnes, W. J. (1957). Some experiments with spectrofluorometers and filter fluorimeters. The Analyst, 82(978), 606. http://doi.org/10.1039/an9578200606

Kothawala, D. N., Murphy, K. R., Stedmon, C. A., Weyhenmeyer, G. A., & Tranvik, L. J. (2013). Inner filter correction of dissolved organic matter fluorescence. Limnology and Oceanography: Methods, 11(12), 616-630. http://doi.org/10.4319/lom.2013.11.616

Examples

# NOT RUN {
library(eemR)
data("absorbance")

folder <- system.file("extdata/cary/scans_day_1", package = "eemR")
eems <- eem_read(folder, import_function = "cary")
eems <- eem_extract(eems, "nano") # Remove the blank sample

# Remove scattering (1st order)
eems <- eem_remove_scattering(eems, "rayleigh")

eems_corrected <- eem_inner_filter_effect(eems, absorbance = absorbance, pathlength = 1)

op <- par(mfrow = c(2, 1))
plot(eems, which = 1)
plot(eems_corrected, which = 1)
par(op)
# }