PARAFAC Analysis of EEMs from DOM

Documentation for package ‘staRdom’ version 1.1.25

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-- 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_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)

-- G --

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

-- 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'.
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