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staRdom (version 1.1.28)

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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Version

Install

install.packages('staRdom')

Monthly Downloads

483

Version

1.1.28

License

AGPL

Maintainer

Matthias Pucher

Last Published

June 16th, 2023

Functions in staRdom (1.1.28)

eem_corrections

Return names of samples where certain corrections are missing.

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

Check size of EEMs

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

eem_extend2largest

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

Exclude complete wavelengths or samples form data set

Export all samples of an eem_list

Correct names of EEM samples to match undiluted absorbance data.

Check your EEM, absorption and metadata before processing

eem_ife_correction

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

Multiply all EEMs with a matrix

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

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

eem_metatemplate

Create table that contains sample names and locations of files.

Check for NAs in EEM data

Missing values are interpolated within EEM data

eem_name_replace

Replace matched patterns in sample names

Modifying fluorescence data according to dilution.

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_red2smallest

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

Cut EEM data matching a given wavelength range

Import EEMs from generic csv tables (deprecated)

eempf_comp_names<-

Set names of PARAFAC components

eempf_comp_names

Extract names from PARAFAC model components

eempf_corcondia

Calculate the core consistancy of an EEM PARAFAC model

eempf_convergence

Extract modelling information from a PARAFAC model.

Calculate raman area of EEM samples

eem_spectral_cor

Multiply EEMs with spectral correction vectors (Emission and Excitation)

eem_raman_normalisation2

Wrapper function to eem_raman_normalisation (eemR).

Smooth fluorescence data by calculating rolling mean along excitation wavelengths.

eem_overview_plot

Plot fluorescence data from several samples split into several plots.

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

Determine the range of fluorescence values in a set of samples

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

Runs a PARAFAC analysis on EEM data

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

Plot a set of PARAFAC models to compare the single components

Remove Raman and Rayleigh scattering in fluorescence data

eempf_OF_upload

Upload PARAFAC models to openfluor.org

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

Combining extracted components of PARAFAC models

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.

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

eempf_comp_load_plot

Plot components from a PARAFAC model

eempf_plot_ssccheck

Plot results from an SSC check

3D plots of PARAFAC components

eempf_leverage_ident

Plot leverage of emission wavelengths, excitation wavelengths and samples.

eempf_leverage_plot

Plot leverage of emission wavelengths, excitation wavelengths and samples.

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

Reorder PARAFAC components

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

Compensate for normalisation in C-modes

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

Calculate the importance of each component.

Check SSCs between different models or initialisations of one model

Extracting components of a PARAFAC model

splithalf_splits

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

Create a html report of a PARAFAC analysis

eempf_rescaleBC

Rescale B and C modes of PARAFAC model

eempf_openfluor

Write out PARAFAC components to submit to openfluor.org.

Plot correlations of components in samples

Extract EEM matrix for single components determined in the PARAFAC analysis

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

Calculate a PARAFAC model similar to and using parafac.

eempf_plot_comps

Plot all components of PARAFAC models

Normalise 3-dimensional array in first and second dimension

Extracting TCC values from a splithalf analysis

PARAFAC model, see vignette, unconstrained

Caluclate Tucker's Congruence Coefficient of PARAFAC components

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

Fits vs. components of PARAFAC models are plotted

eempf_load_plot

Plot amount of each component in each sample as bar plot

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

Export samples in an EEM list to a single csv files

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

PARAFAC model, see vignette, non-negative constraints

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

Running a Split-Half analysis on a PARAFAC model

eempf_residuals_plot

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

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

Plot results from a splithalf analysis

eempf_mleverage

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

eempf_residuals_metrics

Calculate residual metrics from a PARAFAC model

EEM spectra plotted with ggplot2

result from PARAFAC split-half analysis, periodic data split

eempf_residuals

Calculate residuals of EEM data according to a certain model

Full join of a list of data frames.

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

Calculating slopes and slope ratios of a data frame of absorbance data.

Baseline correction for absorbance data

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

Import EEMs from generic csv files.

Calculate the sample loadings for samples not involved in model building

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

Add data of a PARAFAC model derived from multiway from EEMs

Data from an eemlist is transformed into an array

as.data.frame.eem

Converting EEM data from class eem to data.frame.

absorbance_read

Reading absorbance data from txt and csv files.

Applying functions on EEMs

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

Create table how samples should be corrected because of dilution

Check for duplicate sample names