PARAFAC Analysis of EEMs from DOM

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Documentation for package ‘staRdom’ version 1.1.28

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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 --

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