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staRdom (version 1.0.8)

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.packages('staRdom')

Monthly Downloads

352

Version

1.0.8

License

AGPL

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Repository

https://github.com/MatthiasPucher/staRdom

Maintainer

Matthias Pucher

Last Published

June 21st, 2018

Functions in staRdom (1.0.8)

Calculate the amount of each component for samples not involved in model building

3D plots of PARAFAC components

Data from an eemlist is transformed into an array

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

Exclude complete wavelengths or samples form data set

eem_ife_correction

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

absorbance_read

Reading absorbance data from txt and csv files.

Load all eemlist obects saved in different Rdata files in folder

Cut EEM data matching a given wavelength range

Missing values are interpolated within EEM data

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

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

eempf_rescaleBC

Rescale B and C modes of PARAFAC model

Runs a PARAFAC analysis on EEM data

Check for NAs in EEM data

Create table how samples should be corrected because of dilution

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

eem_red2smallest

Reduce wavelength range of EEM spectra to widest available in the whole sample set.

Calculate raman area of EEM samples

Fluorescence data of 52 corrected samples.

Fits vs. components of PARAFAC models are plotted

eempf_leverage_ident

Plot leverage of emission wavelengths, excitation wavelengths and samples.

Remove Raman and Rayleigh scattering in fluorescence data

eem_metatemplate

Create table that contains sample names and locations of files.

eempf_corcondia

Calculate the core consistancy of an EEM PARAFAC model

eem_raman_normalisation2

Wrapper function to eem_raman_normalisation (eemR).

Extracting TCC values from a splithalf analysis

eempf_leverage_data

Combine leverages into one data frame and add optional labels.

eempf_plot_comps

Plot all components of PARAFAC models

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

Determine the range of fluorescence values in a set of samples

Smooth fluorescence data by calculating rolling mean along excitation wavelengths.

Plot correlations of components in samples

eempf_comp_load_plot

Plot components from a PARAFAC model

result from PARAFAC split-half analysis

Caluclate Tucker's Congruence Coefficient of PARAFAC components

EEM spectra plotted with ggplot2

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

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

Plot a set of PARAFAC models to compare the single components

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

Plot results from a splithalf analysis

eempf_residuals

Calculate residuals of EEM data according to a certain model

eempf_mleverage

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

eempf_residuals_plot

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

splithalf_splits

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

eem_name_replace

Replace matched patterns in sample names

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

eempf_openfluor

Write out PARAFAC components to submit to openfluor.org.

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

Create a html report of a PARAFAC analysis

Check for duplicate sample names

Modifying fluorescence data according to dilution.

Compensate for normalisation in C-modes

eem_overview_plot

Plot fluorescence data from several samples split into several plots.

Running a Split-Half analysis on a PARAFAC model

Extract EEM matrix for single components determined in the PARAFAC analysis

Normalise 3-dimensional array in first and second dimension

Full join of a list of data frames.

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

Extract data from emission and excitation wavelengths of the components of a PARAFAC model

Absorption data of 7 samples

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

Check your EEM, absorption and metadata before processing

Correct names of EEM samples to match undiluted absorbance data.

as.data.frame.eem

Converting EEM data from class eem to data.frame.

eem_corrections

Return names of samples where certain corrections are missing.

raw data from absorbance measurements, 5cm pathlength