# PARAFAC Analysis of EEMs from DOM

## Documentation for package ‘staRdom’ version 1.1.32

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

A E G L M N P S T misc

## -- A --

absorbance_read | Reading absorbance data from txt and csv files.
abs_blcor | Baseline correction for absorbance data
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 sample loadings for samples not involved in model building

## -- E --

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_bindxc | Combining extracted components of PARAFAC models
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_comp_names | Extract names from PARAFAC model components
eempf_comp_names<- | Set names of PARAFAC components
eempf_convergence | Extract modelling information from a PARAFAC model.
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_excomp | Extracting components of a PARAFAC model
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_OF_upload | Upload PARAFAC models to openfluor.org
eempf_openfluor | Write out PARAFAC components to submit to openfluor.org.
eempf_plot_comps | Plot all components of PARAFAC models
eempf_plot_ssccheck | Plot results from an SSC check
eempf_reorder | Reorder PARAFAC components
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_metrics | Calculate residual metrics from a PARAFAC model
eempf_residuals_plot | Plot samples by means of whole sample, each single component and residuum
eempf_ssc | Calculate the shift-and shape-sensitive congruence (SSC) between model components
eempf_ssccheck | Check SSCs between different models or initialisations of one model
eempf_varimp | Calculate the importance of each component.
eem_absdil | Multiply absorbance data according to the dilution and remove absorbance from samples where undiluted data is used.
eem_apply | Applying functions on EEMs
eem_checkdata | Check your EEM, absorption and metadata before processing
eem_checksize | Check size of EEMs
eem_corrections | Return names of samples where certain corrections are missing.
eem_csv | Importer function for generic csv files to be used with eem_read().
eem_csv2 | Importer function for generic csv files to be used with eem_read().
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_export | Export all samples of an eem_list
eem_extend2largest | EEM sample data is extended to include all wavelengths in all samples
eem_getextreme | Determines the the biggest range of EEM spectrum where data is available from each sample.
eem_hitachi | Importer function for Hitachi F-7000 txt files to be used with eem_read().
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 or RDa files in a folder.
eem_interp | Missing values are interpolated within EEM data
eem_is.na | Check for NAs in EEM data
eem_list | 15 fluorescence samples from drEEM used for examples.
eem_list_outliers | 2 fluorescence samples from drEEM that were excluded as outliers from the PARAFAC model.
eem_load_dreem | Load original data from the drEEM tutorial and return it as eemlist
eem_matmult | Multiply all EEMs with a matrix
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_read_csv | Import EEMs from generic csv tables (deprecated)
eem_red2smallest | Remove wavelengths, that are missing in at least one sample form the whole 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_setNA | set parts of specific samples to NA and optionally interpolate these parts
eem_smooth | Smooth fluorescence data by calculating rolling mean along excitation wavelengths.
eem_spectral_cor | Multiply EEMs with spectral correction vectors (Emission and Excitation)
eem_write_csv | Export samples in an EEM list to a single csv files

## -- G --

geom_eempeakloc | Mark common EEM peaks
geom_eemregions | Mark common reagions to EEMs to show molecular groups
geom_eemscatter | Mark EEM scatter bands
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
ggeem_overlay | Add layers of scatter bands, molecular regions and common peaks to EEM plots

## -- L --

list_join | Full join of a list of data frames.

## -- M --

maxlines | Extract data from emission and excitation wavelengths of the components of a PARAFAC model (scaled B- and C-modes)

## -- N --

norm2A | Compensate for normalisation in C-modes
norm_array | Normalise 3-dimensional array in first and second dimension

## -- P --

parafac_conv | Calculate a PARAFAC model similar to and using 'parafac'.
peaks | data.frame containing common EEM peaks with the wavelengths and possible deviations
pf1 | PARAFAC model, see vignette, unconstrained
pf1n | PARAFAC model, see vignette, non-negative constraints
pf2 | PARAFAC model, see vignette, non-negative constraints, normalised
pf3 | PARAFAC model, see vignette, non-negative constraints, normalised, outliers removed
pf4 | PARAFAC model, see vignette, non-negative constraints, normalised, outliers removed, high accuarcy

## -- S --

sh | result from PARAFAC split-half analysis, periodic data split
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
ssc | Calculate the shift-and shape-sensitive congruence (SSC) between two matrices
ssc_max | Calculate the combination of components giving the maximum of geometric mean of TCCs

## -- T --

tcc | Caluclate Tucker's Congruence Coefficient of PARAFAC components
tcc_find_pairs | Reorders components of different PARAFAC models according to best fit (TCC)

## -- misc --

.eem_csv | Import EEMs from generic csv files.
.trans_parafac | Add data of a PARAFAC model derived from multiway from EEMs