staRdom v1.0.8

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by Matthias Pucher View Source

PARAFAC Analysis of EEMs from DOM

This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) <doi:10.1039/c3ay41160e>. The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.

Functions in staRdom

Name	Description
A_missing	Calculate the amount of each component for samples not involved in model building
eempf_comps3D	3D plots of PARAFAC components
eem2array	Data from an eemlist is transformed into an array
eempf_cortable	Calculating correlations between the component loadings in all samples (C-Modes).
blank	blank samples
eem_exclude	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.
eem_import_dir	Load all eemlist obects saved in different Rdata files in folder
eem_range	Cut EEM data matching a given wavelength range
eem_interp	Missing values are interpolated within EEM data
eempf4analysis	Create table of PARAFAC components and (optionally) EEM peaks and indices as well as absorbance slope parameters.
eem_easy	Opens an R markdown template for an easy and userfriendly analysis of EEM data.
eempf_rescaleBC	Rescale B and C modes of PARAFAC model
eem_parafac	Runs a PARAFAC analysis on EEM data
eem_is.na	Check for NAs in EEM data
eem_dilcorr	Create table how samples should be corrected because of dilution
eem_getextreme	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.
eem_raman_area	Calculate raman area of EEM samples
eem_list	Fluorescence data of 52 corrected samples.
eempf_fits	Fits vs. components of PARAFAC models are plotted
eempf_leverage_ident	Plot leverage of emission wavelengths, excitation wavelengths and samples.
eem_rem_scat	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).
splithalf_tcc	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
eempf_eemqual	Calculating EEMqual which is an indicator of a PARAFAC model's quality
eem_scale_ext	Determine the range of fluorescence values in a set of samples
eem_smooth	Smooth fluorescence data by calculating rolling mean along excitation wavelengths.
eempf_corplot	Plot correlations of components in samples
eempf_comp_load_plot	Plot components from a PARAFAC model
sh	result from PARAFAC split-half analysis
tcc	Caluclate Tucker's Congruence Coefficient of PARAFAC components
ggeem	EEM spectra plotted with ggplot2
eempf_export	Create one table containing the PARAFAC models factors and optionally exporting it to csv or txt
abs_parms	Calculating slopes and slope ratios of a data frame of absorbance data.
eempf_compare	Plot a set of PARAFAC models to compare the single components
eempf_leverage	Calculate the leverage of each emission and excitation wavelength and each sample from a single PARAFAC model
splithalf_plot	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
abs_fit_slope	Fit absorbance data to exponential curve. drm is used for the fitting process.
eempf_openfluor	Write out PARAFAC components to submit to openfluor.org.
tcc_find_pairs	Reorders components of different PARAFAC models according to best fit (TCC)
pfres_comps	PARAFAC model
eempf_report	Create a html report of a PARAFAC analysis
eem_duplicates	Check for duplicate sample names
eem_dilution	Modifying fluorescence data according to dilution.
norm2A	Compensate for normalisation in C-modes
eem_overview_plot	Plot fluorescence data from several samples split into several plots.
splithalf	Running a Split-Half analysis on a PARAFAC model
eempf_comp_mat	Extract EEM matrix for single components determined in the PARAFAC analysis
norm_array	Normalise 3-dimensional array in first and second dimension
list_join	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
maxlines	Extract data from emission and excitation wavelengths of the components of a PARAFAC model
pfres_comps2	Absorption data of 7 samples
eem_absdil	Multiply absorbance data according to the dilution and remove absorbance from samples where undiluted data is used.
eem_checkdata	Check your EEM, absorption and metadata before processing
eem_eemdil	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.
abs_data	raw data from absorbance measurements, 5cm pathlength
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Vignettes of staRdom

Name
Basic_analysis_of_DOM_samples.Rmd
PARAFAC_analysis_of_EEM.Rmd
staRdom384.png
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Details

Type	Package
Date	2018-06-07
License	AGPL
Encoding	UTF-8
LazyData	true
RoxygenNote	6.0.1
VignetteBuilder	knitr
URL	https://github.com/MatthiasPucher/staRdom
BugReports	https://github.com/MatthiasPucher/staRdom/issues
NeedsCompilation	no
Packaged	2018-06-20 12:24:46 UTC; maetz
Repository	CRAN
Date/Publication	2018-06-21 13:59:05 UTC

imports	data.table (>= 1.11.2) , doParallel (>= 1.0.11) , drc (>= 3.0-1) , foreach (>= 1.4.4) , GGally (>= 1.3) , graphics (>= 3.3) , matrixStats (>= 0.53.1) , multiway (>= 1.0-5) , parallel (>= 3.4) , plotly (>= 4.7) , pracma (>= 2.1.1) , readr (>= 1.1.1) , stringr (>= 1.2.0) , tibble (>= 1.3) , tools (>= 3.3) , zoo (>= 1.8)
depends	dplyr (>= 0.7.4) , eemR (>= 0.1.5) , ggplot2 (>= 2.2.1) , R (>= 3.3) , tidyr (>= 0.7.1)
suggests	kableExtra , knitcitations , knitr , rmarkdown , xlsx
Contributors	Daniel Graeber, Stefan Preiner, Renata Pinto, Nora Maria Zechmeister, Christoph Zechmeister