eemR

The eemR package implements various functions used calculate metrics from excitation-emission matrix (EEM) as well as to preform pre-processing corrections before PARAFAC analysis (Bro 1997; C. A. Stedmon and Markager 2005; Murphy et al. 2013). All functions from this package start with the eem_ prefix.

library(eemR)
ls("package:eemR")
#>  [1] "absorbance"              "eem_biological_index"   
#>  [3] "eem_coble_peaks"         "eem_cut"                
#>  [5] "eem_export_matlab"       "eem_fluorescence_index" 
#>  [7] "eem_humification_index"  "eem_inner_filter_effect"
#>  [9] "eem_raman_normalisation" "eem_read"               
#> [11] "eem_remove_blank"        "eem_remove_scattering"  
#> [13] "eem_set_wavelengths"

The package can be installed using the following command.

devtools::install_github("PMassicotte/eemR")

Please note this is a very alpha version of the package for testing purpose only.

Reading EEMs

At the moment, the following EEM types are supported:

• Cary Eclipse .csv files

• Aqualog .dat files

• Shimadzu .TXT files

EEM can be read using the eem_read() function. Please fill an issue if you have other file formats you would like to add to the package.

At the moment I need files from:

• FluoromaxIII

• Perkin elmer

• Hitachi

library(eemR)

## Reading a single eem
file <- system.file("extdata/cary/eem", "sample1.csv", package = "eemR")
eem <- eem_read(file)

plot(eem)

## Reading a folder

folder <- system.file("extdata/cary/eem", package = "eemR")
eem <- eem_read(folder)

plot(eem) ## Plot the first eem

plot(eem, which = 2) ## Plot the second eem

## Aqualog EEM

folder <- system.file("extdata/aqualog", package = "eemR")
eem <- eem_read(folder)

plot(eem) ## Plot the first eem

Shimadzu files

Some spectrophotometers (such as Shimadzu) do not include excitation wavelengths in the fluorescence files. In these cases, we can use the eem_set_wavelengths() function to manually provide vectors of emission and/or excitation wavelengths.

folder <- system.file("extdata/shimadzu", package = "eemR")
eems <- eem_read(folder)
#> Shimadzu files do not contain excitation wavelengths.
#> Please provide them using the eem_set_wavelengths() function.

eems <- eem_set_wavelengths(eems, ex = seq(230, 450, by = 5))

Implemented metrics

The current implemented metrics are:

1. The fluorescence index (FI) developed by McKnight et al. (2001).

2. The fluorescence peaks proposed by Coble (1996).

3. The fluorescence humification index (HIX) by Ohno (2002).

4. The biological fluorescence index (BIX) by Huguet et al. (2009).

library(eemR)

folder <- system.file("extdata/cary/eem", package = "eemR")
eem <- eem_read(folder)

eem_fluorescence_index(eem, verbose = FALSE)
#> Source: local data frame [3 x 2]
#> 
#>    sample       fi
#>     (chr)    (dbl)
#> 1 sample1 1.264782
#> 2 sample2 1.455333
#> 3 sample3 1.329413

eem_coble_peaks(eem, verbose = FALSE)
#> Source: local data frame [3 x 6]
#> 
#>    sample        b         t        a        m         c
#>     (chr)    (dbl)     (dbl)    (dbl)    (dbl)     (dbl)
#> 1 sample1 1.545298 1.0603312 3.731836 2.424096 1.8149415
#> 2 sample2 1.262997 0.6647042 1.583489 1.023593 0.7709074
#> 3 sample3 1.474086 1.3162812 8.416034 6.063355 6.3179129

eem_humification_index(eem, verbose = FALSE)
#> Source: local data frame [3 x 2]
#> 
#>    sample       hix
#>     (chr)     (dbl)
#> 1 sample1  6.379562
#> 2 sample2  4.254848
#> 3 sample3 13.024623

eem_humification_index(eem, verbose = FALSE, scale = TRUE)
#> Source: local data frame [3 x 2]
#> 
#>    sample       hix
#>     (chr)     (dbl)
#> 1 sample1 0.8644906
#> 2 sample2 0.8096995
#> 3 sample3 0.9286968

eem_biological_index(eem, verbose = FALSE)
#> Source: local data frame [3 x 2]
#> 
#>    sample       bix
#>     (chr)     (dbl)
#> 1 sample1 0.7062640
#> 2 sample2 0.8535423
#> 3 sample3 0.4867927

PARAFAC pre-processing

Three types of correction are currently supported:

1. eem_remove_blank() which subtract a water blank from the eem.

2. eem_remove_scattering() which remove both Raman and Rayleigh scattering.

3. eem_raman_normalisation() which normalize EEM fluoresence intensities (Lawaetz and Stedmon 2009).

4. eem_inner_filter() which correct for both primary and secondary inner-filter effect.

Blank removal

The eem_remove_blank() function subtract blank (miliq) water from eem. Scatter bands can often be reduced by subtracting water blank (Murphy et al. 2013).

file <- system.file("extdata/cary/eem", "sample1.csv", package = "eemR")
eem <- eem_read(file)

file <- system.file("extdata/cary", "nano.csv", package = "eemR")
blank <- eem_read(file)

res <- eem_remove_blank(eem, blank)

plot(eem)
plot(res)

Removing Raman and Rayleigh scattering (1st and 2nd order)

The eem_remove_scattering() function removes both Raman and Rayleigh scattering from EEMs.

res <- eem_remove_scattering(eem = eem, type = "raman", order = 1, width = 10)
res <- eem_remove_scattering(eem = res, type = "rayleigh", order = 1, width = 10)

plot(res)

Raman normalization

The eem_raman_normalisation() function implement a simple calibration method for fluorescence intensity using only the integrated area of a water Raman peak. More details can be found in Lawaetz and Stedmon (2009).

res <- eem_raman_normalisation(res, blank)
#> Raman area: 9.501974

plot(res)

Inner-filter effect correction

To account for reabsorption of the light emitted by fluorophores in the water, absorbance spectra are used for correction of both primary and secondary inner filtering effects in the EEMs (Ohno 2002; Parker and Barnes 1957).

data("absorbance")

res <- eem_inner_filter_effect(eem = res, 
                               absorbance = absorbance, 
                               pathlength = 1) ## 1 cm fluo pathlenght
#> Range of IFE correction factors: 0.6432503 0.9889723

plot(res)

Export to Matlab

PARAFAC analysis was made easy with the fantastic Matlab drEEM toolbox (Murphy et al. 2013). The function eem_export_matlab() can be used to export the EEMs into a m-file directly usable in Matlab by the drEEM toolbox.

folder <- system.file("extdata/cary/eem", package = "eemR")
eem <- eem_read(folder)

filename <- paste(tempfile(), ".mat", sep = "")

eem_export_matlab(filename, eem)
#> Successfully exported 3 EEMs to /tmp/RtmpkCgKqO/file3ad32b250736.mat.

## It is also possible to export more than one object at time
eem_export_matlab(filename, eem, eem)
#> Successfully exported 6 EEMs to /tmp/RtmpkCgKqO/file3ad32b250736.mat.

Note that the name of the structure generated by the function will be OriginalData to complement with PARAFAC standard. Then, the importation into Matlab is made easy using the load() function. Please note that there is a bug preventing to keep matrix dimension. Simply use the reshape() function after you exported data.

load('FileName.mat');

OriginalData.X = reshape(OriginalData.X, ...
    OriginalData.nSample, ...
    OriginalData.nEm, ...
    OriginalData.nEx);

% Start PARAFAC analysis here...

References

Bro, Rasmus. 1997. “PARAFAC. Tutorial and applications.” Chemometrics and Intelligent Laboratory Systems 38 (2): 149–71. doi:10.1016/S0169-7439(97)00032-4.

Coble, Paula G. 1996. “Characterization of marine and terrestrial DOM in seawater using excitation-emission matrix spectroscopy.” Marine Chemistry 51 (4): 325–46. doi:10.1016/0304-4203(95)00062-3.

Huguet, A., L. Vacher, S. Relexans, S. Saubusse, J.M. Froidefond, and E. Parlanti. 2009. “Properties of fluorescent dissolved organic matter in the Gironde Estuary.” Organic Geochemistry 40 (6). Elsevier Ltd: 706–19. doi:10.1016/j.orggeochem.2009.03.002.

Lawaetz, A J, and C A Stedmon. 2009. “Fluorescence Intensity Calibration Using the Raman Scatter Peak of Water.” Applied Spectroscopy 63 (8): 936–40. doi:10.1366/000370209788964548.

McKnight, Diane M., Elizabeth W. Boyer, Paul K. Westerhoff, Peter T. Doran, Thomas Kulbe, and Dale T. Andersen. 2001. “Spectrofluorometric characterization of dissolved organic matter for indication of precursor organic material and aromaticity.” Limnology and Oceanography 46 (1). American Society of Limnology; Oceanography: 38–48. doi:10.4319/lo.2001.46.1.0038.

Murphy, Kathleen R., Colin a. Stedmon, Daniel Graeber, and Rasmus Bro. 2013. “Fluorescence spectroscopy and multi-way techniques. PARAFAC.” Analytical Methods 5 (23): 6557. doi:10.1039/c3ay41160e.

Ohno, Tsutomu. 2002. “Fluorescence Inner-Filtering Correction for Determining the Humification Index of Dissolved Organic Matter.” Environmental Science & Technology 36 (4): 742–46. doi:10.1021/es0155276.

Parker, C. a., and W. J. Barnes. 1957. “Some experiments with spectrofluorimeters and filter fluorimeters.” The Analyst 82 (978): 606. doi:10.1039/an9578200606.

Stedmon, Colin A, and Stiig Markager. 2005. “Resolving the variability in dissolved organic matter fluorescence in a temperate estuary and its catchment using PARAFAC analysis.” Limnology and Oceanography 50 (2): 686–97. doi:10.4319/lo.2005.50.2.0686.