eemR package implements various functions used calculate metrics from excitation-emission matrix (EEM) as well as to preform pre-processing corrections before PARAFAC analysis. All functions from this package start with the
eem_ prefix. Please note this is a very alpha version of the package for testing purpose only.
The package can be installed using the following command.
At the moment, to following EEM types are supported:
- Cary Eclipse
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.
The current implemented metrics are:
The fluorescence index (FI).
The fluorescence peaks.
The fluorescence humification index (HIX).
The biological fluorescence index (BIX).
Three types of correction are currently supported:
eem_remove_blank()which subtract a water blank from the eem.
eem_remove_scattering()which remove both Raman and Rayleigh scattering.
eem_raman_normalisation()which normalize EEM fluoresence intensities.
eem_inner_filter()which correct for both primary and secondary inner-filter effect.
Removing Raman and Rayleigh scattering (1st and 2nd order)
eem_remove_scattering() function removes both Raman and Rayleigh scattering from EEMs.
eem_remove_blank() function subtract blank (miliq) water from eem. Scatter bands can often be reduced by subtracting water blank.
eem_raman_normalisation() function implement a simple calibration method for fluorescence intensity using only the integrated area of a water Raman peak.
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.
Export to Matlab
PARAFAC analysis was made easy with the fantastic Matlab
drEEM toolbox. The function
eem_export_matlab() can be used to export the EEMs into a
m-file directly usable in Matlab by the
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