staRdom v1.0.8

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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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