staRdom v1.0.3

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PARAFAC Analysis of EEMs from DOM

This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) <doi:10.1039/c3ay41160e>. The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.

Functions in staRdom

Name Description
eempf_comps3D 3D plots of PARAFAC components
eempf_corplot Plot correlations of components in samples
eempf_load_plot Plot amount of each component in each sample as bar plot
eem_raman_normalisation2 Wrapper function to eem_raman_normalisation (eemR).
eem_range Cut EEM data matching a given wavelength range
list_join Full join of a list of data frames.
eempf_comp_mat Extract EEM matrix for single components determined in the PARAFAC analysis
eempf_comp_load_plot Plot components from a PARAFAC model
eempf_leverage_plot Plot leverage of emission wavelengths, excitation wavelengths and samples.
eempf_leverage_ident Plot leverage of emission wavelengths, excitation wavelengths and samples.
eempf_openfluor Write out PARAFAC components to submit to openfluor.org.
norm2A Compensate for normalisation in C-modes
splithalf_plot Plot results from a splithalf analysis
eem_list Fluorescence data of 52 corrected samples.
eempf_cortable Calculating correlations between the component loadings in all samples (C-Modes).
norm_array Normalise 3-dimensional array in first and second dimension
eempf_plot_comps Plot all components of PARAFAC models
tcc_find_pairs Reorders components of different PARAFAC models according to best fit (TCC)
eempf_residuals Calculate residuals of EEM data according to a certain model
eem_overview_plot Plot fluorescence data from several samples split into several plots.
eem_red2smallest Reduce wavelength range of EEM spectra to widest available in the whole sample set.
eem_rem_scat Remove Raman and Rayleigh scattering in fluorescence data
eempf_leverage Calculate the leverage of each emission and excitation wavelength and each sample
eem_scale_ext Determine the range of fluorescence values in a set of samples
splithalf_splits Extracting a list of sample names in each subsample from a splithalf analysis
maxlines Extract data from emission and excitation wavelengths of the components of a PARAFAC model
splithalf_tcc Extracting TCC values from a splithalf analysis
eempf_fits Fits vs. components of PARAFAC models are plotted
eempf_fit_sample Fitting amounts of components of any samples to a certain model
tcc Caluclate Tucker's Congruence Coefficient of PARAFAC components
eem_smooth Smooth fluorescence data by calculating rolling mean along excitation wavelengths.
ggeem EEM spectra plotted with ggplot2
eempf_leverage_data Combine leverages into one data frame and add optional labels.
pfres_comps PARAFAC model
pfres_comps2 Absorption data of 7 samples
sh result from PARAFAC split-half analysis
eempf_residuals_plot Plot samples by means of whole sample, each single component and residuum
splithalf Running a Split-Half analysis on a PARAFAC model
as.data.frame.eem Converting EEM data from class eem to data.frame.
abs_parms Calculating slopes and slope ratios of a data frame of absorbance data.
absorbance_read Reading absorbance data from txt and csv files.
eem_name_replace Replace matched patterns in sample names
eem_parafac Runs a PARAFAC analysis on EEM data
blank blank samples
A_missing Calculate the amount of each component for samples not involved in model building
eem_easy Opens an R markdown template for an easy and userfriendly analysis of EEM data.
eem2array Data from an eemlist is transformed into an array
eem_exclude Exclude complete wavelengths or samples form data set
abs_fit_slope Fit absorbance data to exponential curve. drm is used for the fitting process.
eem_dilution Modifying fluorescence data according to dilution.
eem_import_dir Load all eemlist obects saved in different Rdata files in folder
eem_raman_area Calculate raman area of EEM samples
eem_ife_correction Wrapper function to allow eem_inner_filter_effect (eemR) handling different cuvette lengths.
abs_data raw data from absorbance measurements, 5cm pathlength
eempf_compare Plot a set of PARAFAC models to compare the single components
eem_getextreme Determines the the biggest range of EEM spectrum where data is available from each sample.
eem_interp Missing values are interpolated within EEM data
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Vignettes of staRdom

Name
Basic_analysis_of_DOM_samples.Rmd
PARAFAC_analysis_of_EEM.Rmd
staRdom384.png
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