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staRdom (version 1.1.25)

PARAFAC Analysis of EEMs from DOM

Description

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

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Install

install.packages('staRdom')

Monthly Downloads

680

Version

1.1.25

License

AGPL

Maintainer

Matthias Pucher

Last Published

March 21st, 2022

Functions in staRdom (1.1.25)

absorbance_read

Reading absorbance data from txt and csv files.

Calculate the sample loadings for samples not involved in model building

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.

Import EEMs from generic csv files.

Add data of a PARAFAC model derived from multiway from EEMs

Fit absorbance data to exponential curve. drm is used for the fitting process.

Baseline correction for absorbance data

Data from an eemlist is transformed into an array

Create table how samples should be corrected because of dilution

Multiply absorbance data according to the dilution and remove absorbance from samples where undiluted data is used.

eem_ife_correction

Wrapper function to allow eem_inner_filter_effect (eemR) handling different cuvette lengths.

Cut EEM data matching a given wavelength range

eem_red2smallest

Remove wavelengths, that are missing in at least one sample form the whole set.

Extract EEM matrix for single components determined in the PARAFAC analysis

eem_raman_normalisation2

Wrapper function to eem_raman_normalisation (eemR).

eempf_comp_load_plot

Plot components from a PARAFAC model

Import EEMs from generic csv tables (deprecated)

Importer function for Hitachi F-7000 txt files to be used with eem_read().

Importer function for generic csv files to be used with eem_read().

Check size of EEMs

eem_corrections

Return names of samples where certain corrections are missing.

Check for NAs in EEM data

Multiply all EEMs with a matrix

Modifying fluorescence data according to dilution.

15 fluorescence samples from drEEM used for examples.

Plot correlations of components in samples

eem_metatemplate

Create table that contains sample names and locations of files.

Calculating correlations between the component loadings in all samples (C-Modes).

Extracting components of a PARAFAC model

Calculating EEMqual which is an indicator of a PARAFAC model's quality

Applying functions on EEMs

eempf_openfluor

Write out PARAFAC components to submit to openfluor.org.

Remove Raman and Rayleigh scattering in fluorescence data

Determine the range of fluorescence values in a set of samples

Check your EEM, absorption and metadata before processing

eempf_convergence

Extract modelling information from a PARAFAC model.

Calculate the shift-and shape-sensitive congruence (SSC) between model components

eempf_residuals_plot

Plot samples by means of whole sample, each single component and residuum

PARAFAC model, see vignette, unconstrained

Check for duplicate sample names

Opens an R markdown template for an easy and userfriendly analysis of EEM data.

Importer function for generic csv files to be used with eem_read().

EEM spectra plotted with ggplot2

eempf_plot_comps

Plot all components of PARAFAC models

PARAFAC model, see vignette, non-negative constraints

Full join of a list of data frames.

Load all eemlist obects saved in different Rdata or RDa files in a folder.

Correct names of EEM samples to match undiluted absorbance data.

Runs a PARAFAC analysis on EEM data

Exclude complete wavelengths or samples form data set

eem_extend2largest

EEM sample data is extended to include all wavelengths in all samples

Determines the the biggest range of EEM spectrum where data is available from each sample.

result from PARAFAC split-half analysis, periodic data split

Caluclate Tucker's Congruence Coefficient of PARAFAC components

Calculate raman area of EEM samples

set parts of specific samples to NA and optionally interpolate these parts

PARAFAC model, see vignette, non-negative constraints, normalised, outliers removed, high accuarcy

eempf_OF_upload

Upload PARAFAC models to openfluor.org

eem_list_outliers

2 fluorescence samples from drEEM that were excluded as outliers from the PARAFAC model.

Load original data from the drEEM tutorial and return it as eemlist

Reorders components of different PARAFAC models according to best fit (TCC)

eem_name_replace

Replace matched patterns in sample names

eem_spectral_cor

Multiply EEMs with spectral correction vectors (Emission and Excitation)

Missing values are interpolated within EEM data

eem_overview_plot

Plot fluorescence data from several samples split into several plots.

eempf_comp_names<-

Set names of PARAFAC components

Smooth fluorescence data by calculating rolling mean along excitation wavelengths.

Create table of PARAFAC components and (optionally) EEM peaks and indices as well as absorbance slope parameters.

Plot a set of PARAFAC models to compare the single components

Combining extracted components of PARAFAC models

3D plots of PARAFAC components

eempf_leverage_ident

Plot leverage of emission wavelengths, excitation wavelengths and samples.

Fits vs. components of PARAFAC models are plotted

eempf_residuals_metrics

Calculate residual metrics from a PARAFAC model

Create one table containing the PARAFAC models factors and optionally exporting it to csv or txt

eempf_residuals

Calculate residuals of EEM data according to a certain model

PARAFAC model, see vignette, non-negative constraints, normalised

Create a html report of a PARAFAC analysis

eempf_leverage_plot

Plot leverage of emission wavelengths, excitation wavelengths and samples.

PARAFAC model, see vignette, non-negative constraints, normalised, outliers removed

eempf_load_plot

Plot amount of each component in each sample as bar plot

eempf_corcondia

Calculate the core consistancy of an EEM PARAFAC model

eempf_comp_names

Extract names from PARAFAC model components

eempf_mleverage

Calculate the leverage of each emission and excitation wavelength and each sample from a list of PARAFAC models

Check SSCs between different models or initialisations of one model

eempf_plot_ssccheck

Plot results from an SSC check

Calculate the leverage of each emission and excitation wavelength and each sample from a single PARAFAC model

Reorder PARAFAC components

eempf_leverage_data

Combine leverages into one data frame and add optional labels.

Calculate the importance of each component.

Normalise 3-dimensional array in first and second dimension

eempf_rescaleBC

Rescale B and C modes of PARAFAC model

Calculate a PARAFAC model similar to and using parafac.

Running a Split-Half analysis on a PARAFAC model

Plot results from a splithalf analysis

Compensate for normalisation in C-modes

Calculate the combination of components giving the maximum of geometric mean of TCCs

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

Calculate the shift-and shape-sensitive congruence (SSC) between two matrices

splithalf_splits

Extracting a list of sample names in each subsample from a splithalf analysis

Extracting TCC values from a splithalf analysis