# PARAFAC Analysis of EEMs from DOM

## Documentation for package ‘staRdom’ version 1.0.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

absorbance_read | Reading absorbance data from txt and csv files.
abs_data | raw data from absorbance measurements, 5cm pathlength
abs_fit_slope | Fit absorbance data to exponential curve. 'drm' is used for the fitting process.
abs_parms | Calculating slopes and slope ratios of a data frame of absorbance data.
as.data.frame.eem | Converting EEM data from class eem to data.frame.
A_missing | Calculate the amount of each component for samples not involved in model building
blank | blank samples
eem2array | Data from an eemlist is transformed into an array
eempf4analysis | Create table of PARAFAC components and (optionally) EEM peaks and indices as well as absorbance slope parameters.
eempf_compare | Plot a set of PARAFAC models to compare the single components
eempf_comps3D | 3D plots of PARAFAC components
eempf_comp_load_plot | Plot components from a PARAFAC model
eempf_comp_mat | Extract EEM matrix for single components determined in the PARAFAC analysis
eempf_corcondia | Calculate the core consistancy of an EEM PARAFAC model
eempf_corplot | Plot correlations of components in samples
eempf_cortable | Calculating correlations between the component loadings in all samples (C-Modes).
eempf_eemqual | Calculating EEMqual which is an indicator of a PARAFAC model's quality
eempf_export | Create one table containing the PARAFAC models factors and optionally exporting it to csv or txt
eempf_fits | Fits vs. components of PARAFAC models are plotted
eempf_leverage | Calculate the leverage of each emission and excitation wavelength and each sample from a single PARAFAC model
eempf_leverage_data | Combine leverages into one data frame and add optional labels.
eempf_leverage_ident | Plot leverage of emission wavelengths, excitation wavelengths and samples.
eempf_leverage_plot | Plot leverage of emission wavelengths, excitation wavelengths and samples.
eempf_load_plot | Plot amount of each component in each sample as bar plot
eempf_mleverage | Calculate the leverage of each emission and excitation wavelength and each sample from a list of PARAFAC models
eempf_openfluor | Write out PARAFAC components to submit to openfluor.org.
eempf_plot_comps | Plot all components of PARAFAC models
eempf_report | Create a html report of a PARAFAC analysis
eempf_rescaleBC | Rescale B and C modes of PARAFAC model
eempf_residuals | Calculate residuals of EEM data according to a certain model
eempf_residuals_plot | Plot samples by means of whole sample, each single component and residuum
eem_absdil | Multiply absorbance data according to the dilution and remove absorbance from samples where undiluted data is used.
eem_checkdata | Check your EEM, absorption and metadata before processing
eem_corrections | Return names of samples where certain corrections are missing.
eem_dilcorr | Create table how samples should be corrected because of dilution
eem_dilution | Modifying fluorescence data according to dilution.
eem_duplicates | Check for duplicate sample names
eem_duplicates.data.frame | Check for duplicate sample names
eem_duplicates.default | Check for duplicate sample names
eem_duplicates.eemlist | Check for duplicate sample names
eem_easy | Opens an R markdown template for an easy and userfriendly analysis of EEM data.
eem_eemdil | Correct names of EEM samples to match undiluted absorbance data.
eem_exclude | Exclude complete wavelengths or samples form data set
eem_getextreme | Determines the the biggest range of EEM spectrum where data is available from each sample.
eem_ife_correction | Wrapper function to allow eem_inner_filter_effect (eemR) handling different cuvette lengths.
eem_import_dir | Load all eemlist obects saved in different Rdata files in folder
eem_interp | Missing values are interpolated within EEM data
eem_is.na | Check for NAs in EEM data
eem_list | Fluorescence data of 52 corrected samples.
eem_metatemplate | Create table that contains sample names and locations of files.
eem_name_replace | Replace matched patterns in sample names
eem_overview_plot | Plot fluorescence data from several samples split into several plots.
eem_parafac | Runs a PARAFAC analysis on EEM data
eem_raman_area | Calculate raman area of EEM samples
eem_raman_normalisation2 | Wrapper function to eem_raman_normalisation (eemR).
eem_range | Cut EEM data matching a given wavelength range
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
eem_scale_ext | Determine the range of fluorescence values in a set of samples
eem_smooth | Smooth fluorescence data by calculating rolling mean along excitation wavelengths.
ggeem | EEM spectra plotted with ggplot2
ggeem.data.frame | EEM spectra plotted with ggplot2
ggeem.default | EEM spectra plotted with ggplot2
ggeem.eem | EEM spectra plotted with ggplot2
ggeem.eemlist | EEM spectra plotted with ggplot2
ggeem.parafac | EEM spectra plotted with ggplot2
list_join | Full join of a list of data frames.
maxlines | Extract data from emission and excitation wavelengths of the components of a PARAFAC model
norm2A | Compensate for normalisation in C-modes
norm_array | Normalise 3-dimensional array in first and second dimension
pfres_comps | PARAFAC model
pfres_comps2 | Absorption data of 7 samples
sh | result from PARAFAC split-half analysis
splithalf | Running a Split-Half analysis on a PARAFAC model
splithalf_plot | Plot results from a splithalf analysis
splithalf_splits | Extracting a list of sample names in each subsample from a splithalf analysis
splithalf_tcc | Extracting TCC values from a splithalf analysis
tcc | Caluclate Tucker's Congruence Coefficient of PARAFAC components
tcc_find_pairs | Reorders components of different PARAFAC models according to best fit (TCC)