Package: staRdom 1.1.29

staRdom: 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.'

Authors:Matthias Pucher [aut, cre], Daniel Graeber [aut, ctb], Stefan Preiner [ctb], Renata Pinto [ctb]

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staRdom.pdf |staRdom.html✨
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# Install 'staRdom' in R:
install.packages('staRdom', repos = c('https://matthiaspucher.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/matthiaspucher/stardom/issues

Datasets:
  • eem_list - 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.
  • pf1 - PARAFAC model, see vignette, unconstrained
  • pf1n - PARAFAC model, see vignette, non-negative constraints
  • pf2 - PARAFAC model, see vignette, non-negative constraints, normalised
  • pf3 - PARAFAC model, see vignette, non-negative constraints, normalised, outliers removed
  • pf4 - PARAFAC model, see vignette, non-negative constraints, normalised, outliers removed, high accuarcy
  • sh - Result from PARAFAC split-half analysis, periodic data split

On CRAN:

6.03 score 21 stars 85 scripts 488 downloads 3 mentions 93 exports 109 dependencies

Last updated 2 days agofrom:e7029d621a. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-winNOTENov 04 2024
R-4.5-linuxNOTENov 04 2024
R-4.4-winOKNov 04 2024
R-4.4-macOKNov 04 2024
R-4.3-winOKNov 01 2024
R-4.3-macOKNov 01 2024

Exports:A_missingabs_blcorabs_fit_slopeabs_parmsabsorbance_readeem_absdileem_applyeem_checkdataeem_checksizeeem_correctionseem_csveem_csv2eem_dilcorreem_dilutioneem_duplicateseem_easyeem_eemdileem_excludeeem_exporteem_extend2largesteem_getextremeeem_hitachieem_ife_correctioneem_import_direem_interpeem_is.naeem_load_dreemeem_matmulteem_metatemplateeem_name_replaceeem_overview_ploteem_parafaceem_raman_areaeem_raman_normalisation2eem_rangeeem_read_csveem_red2smallesteem_rem_scateem_scale_exteem_setNAeem_smootheem_spectral_coreem_write_csveem2arrayeempf_bindxceempf_comp_load_ploteempf_comp_mateempf_comp_nameseempf_comp_names<-eempf_compareeempf_comps3Deempf_convergenceeempf_corcondiaeempf_corploteempf_cortableeempf_eemqualeempf_excompeempf_exporteempf_fitseempf_leverageeempf_leverage_dataeempf_leverage_identeempf_leverage_ploteempf_load_ploteempf_mleverageeempf_OF_uploadeempf_openfluoreempf_plot_compseempf_plot_ssccheckeempf_reordereempf_reporteempf_rescaleBCeempf_residualseempf_residuals_metricseempf_residuals_ploteempf_ssceempf_ssccheckeempf_varimpeempf4analysisggeemlist_joinmaxlinesnorm_arraynorm2Aparafac_convsplithalfsplithalf_plotsplithalf_splitssplithalf_tccsscssc_maxtcctcc_find_pairs

Dependencies:abindassertthatbackportsBHbitbit64bootbroomcarcarDatacdomclicliprCMLScodetoolscolorspacecowplotcpp11crayondata.tableDerivdoBydoParalleldplyrdrceemRfansifarverforcatsforeachFormulagenericsGGallyggplot2ggstatsgluegridExtragtablegtoolshmsisobanditeratorsjsonlitelabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmatrixStatsMBAmgcvmicrobenchmarkminpack.lmminqamodelrmultcompmultiwaymunsellmvtnormnlmenloptrnnetnumDerivpatchworkpbkrtestpillarpkgconfigplotrixplyrpracmaprettyunitsprogresspurrrquadprogquantregR.matlabR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenreadrrlangrlistsandwichscalesSparseMstringistringrsurvivalTH.datatibbletidyrtidyselecttzdbutf8vctrsviridisviridisLitevroomwithrXMLyamlzoo

Correcting raw data, calculating peaks and indices in EEMS and absorbance (slope) parameters

r packageDescription('staRdom')$Maintainer

Rendered fromBasic_analysis_of_DOM_samples.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2023-06-13
Started: 2018-04-06

PARAFAC analysis of EEM data to separate DOM components in R

r packageDescription('staRdom')$Maintainer

Rendered fromPARAFAC_analysis_of_EEM.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-11-04
Started: 2018-04-06

Readme and manuals

Help Manual

Help pageTopics
Import EEMs from generic csv files..eem_csv
Add data of a PARAFAC model derived from multiway from EEMs.trans_parafac
Calculate the sample loadings for samples not involved in model buildingA_missing
Baseline correction for absorbance dataabs_blcor
Fit absorbance data to exponential curve. 'drm' is used for the fitting process.abs_fit_slope
Calculating slopes and slope ratios of a data frame of absorbance data.abs_parms
Reading absorbance data from txt and csv files.absorbance_read
Converting EEM data from class eem to data.frame.as.data.frame.eem
Multiply absorbance data according to the dilution and remove absorbance from samples where undiluted data is used.eem_absdil
Applying functions on EEMseem_apply
Check your EEM, absorption and metadata before processingeem_checkdata
Check size of EEMseem_checksize
Return names of samples where certain corrections are missing.eem_corrections
Importer function for generic csv files to be used with eem_read().eem_csv
Importer function for generic csv files to be used with eem_read().eem_csv2
Create table how samples should be corrected because of dilutioneem_dilcorr
Modifying fluorescence data according to dilution.eem_dilution
Check for duplicate sample nameseem_duplicates eem_duplicates.data.frame eem_duplicates.default eem_duplicates.eemlist
Opens an R markdown template for an easy and userfriendly analysis of EEM data.eem_easy
Correct names of EEM samples to match undiluted absorbance data.eem_eemdil
Exclude complete wavelengths or samples form data seteem_exclude
Export all samples of an eem_listeem_export
EEM sample data is extended to include all wavelengths in all sampleseem_extend2largest
Determines the the biggest range of EEM spectrum where data is available from each sample.eem_getextreme
Importer function for Hitachi F-7000 txt files to be used with eem_read().eem_hitachi
Wrapper function to allow eem_inner_filter_effect (eemR) handling different cuvette lengths.eem_ife_correction
Load all eemlist obects saved in different Rdata or RDa files in a folder.eem_import_dir
Missing values are interpolated within EEM dataeem_interp
Check for NAs in EEM dataeem_is.na
15 fluorescence samples from drEEM used for examples.eem_list
2 fluorescence samples from drEEM that were excluded as outliers from the PARAFAC model.eem_list_outliers
Load original data from the drEEM tutorial and return it as eemlisteem_load_dreem
Multiply all EEMs with a matrixeem_matmult
Create table that contains sample names and locations of files.eem_metatemplate
Replace matched patterns in sample nameseem_name_replace
Plot fluorescence data from several samples split into several plots.eem_overview_plot
Runs a PARAFAC analysis on EEM dataeem_parafac
Calculate raman area of EEM sampleseem_raman_area
Wrapper function to eem_raman_normalisation (eemR).eem_raman_normalisation2
Cut EEM data matching a given wavelength rangeeem_range
Import EEMs from generic csv tables (deprecated)eem_read_csv
Remove wavelengths, that are missing in at least one sample form the whole set.eem_red2smallest
Remove Raman and Rayleigh scattering in fluorescence dataeem_rem_scat
Determine the range of fluorescence values in a set of sampleseem_scale_ext
set parts of specific samples to NA and optionally interpolate these partseem_setNA
Smooth fluorescence data by calculating rolling mean along excitation wavelengths.eem_smooth
Multiply EEMs with spectral correction vectors (Emission and Excitation)eem_spectral_cor
Export samples in an EEM list to a single csv fileseem_write_csv
Data from an eemlist is transformed into an arrayeem2array
Combining extracted components of PARAFAC modelseempf_bindxc
Plot components from a PARAFAC modeleempf_comp_load_plot
Extract EEM matrix for single components determined in the PARAFAC analysiseempf_comp_mat
Extract names from PARAFAC model componentseempf_comp_names
Set names of PARAFAC componentseempf_comp_names<-
Plot a set of PARAFAC models to compare the single componentseempf_compare
3D plots of PARAFAC componentseempf_comps3D
Extract modelling information from a PARAFAC model.eempf_convergence
Calculate the core consistancy of an EEM PARAFAC modeleempf_corcondia
Plot correlations of components in sampleseempf_corplot
Calculating correlations between the component loadings in all samples (C-Modes).eempf_cortable
Calculating EEMqual which is an indicator of a PARAFAC model's qualityeempf_eemqual
Extracting components of a PARAFAC modeleempf_excomp
Create one table containing the PARAFAC models factors and optionally exporting it to csv or txteempf_export
Fits vs. components of PARAFAC models are plottedeempf_fits
Calculate the leverage of each emission and excitation wavelength and each sample from a single PARAFAC modeleempf_leverage
Combine leverages into one data frame and add optional labels.eempf_leverage_data
Plot leverage of emission wavelengths, excitation wavelengths and samples.eempf_leverage_ident
Plot leverage of emission wavelengths, excitation wavelengths and samples.eempf_leverage_plot
Plot amount of each component in each sample as bar ploteempf_load_plot
Calculate the leverage of each emission and excitation wavelength and each sample from a list of PARAFAC modelseempf_mleverage
Upload PARAFAC models to openfluor.orgeempf_OF_upload
Write out PARAFAC components to submit to openfluor.org.eempf_openfluor
Plot all components of PARAFAC modelseempf_plot_comps
Plot results from an SSC checkeempf_plot_ssccheck
Reorder PARAFAC componentseempf_reorder
Create a html report of a PARAFAC analysiseempf_report
Rescale B and C modes of PARAFAC modeleempf_rescaleBC
Calculate residuals of EEM data according to a certain modeleempf_residuals
Calculate residual metrics from a PARAFAC modeleempf_residuals_metrics
Plot samples by means of whole sample, each single component and residuumeempf_residuals_plot
Calculate the shift-and shape-sensitive congruence (SSC) between model componentseempf_ssc
Check SSCs between different models or initialisations of one modeleempf_ssccheck
Calculate the importance of each component.eempf_varimp
Create table of PARAFAC components and (optionally) EEM peaks and indices as well as absorbance slope parameters.eempf4analysis
EEM spectra plotted with ggplot2ggeem ggeem.data.frame ggeem.default ggeem.eem ggeem.eemlist ggeem.parafac
Full join of a list of data frames.list_join
Extract data from emission and excitation wavelengths of the components of a PARAFAC model (scaled B- and C-modes)maxlines
Normalise 3-dimensional array in first and second dimensionnorm_array
Compensate for normalisation in C-modesnorm2A
Calculate a PARAFAC model similar to and using 'parafac'.parafac_conv
PARAFAC model, see vignette, unconstrainedpf1
PARAFAC model, see vignette, non-negative constraintspf1n
PARAFAC model, see vignette, non-negative constraints, normalisedpf2
PARAFAC model, see vignette, non-negative constraints, normalised, outliers removedpf3
PARAFAC model, see vignette, non-negative constraints, normalised, outliers removed, high accuarcypf4
result from PARAFAC split-half analysis, periodic data splitsh
Running a Split-Half analysis on a PARAFAC modelsplithalf
Plot results from a splithalf analysissplithalf_plot
Extracting a list of sample names in each subsample from a splithalf analysissplithalf_splits
Extracting TCC values from a splithalf analysissplithalf_tcc
Calculate the shift-and shape-sensitive congruence (SSC) between two matricesssc
Calculate the combination of components giving the maximum of geometric mean of TCCsssc_max
Caluclate Tucker's Congruence Coefficient of PARAFAC componentstcc
Reorders components of different PARAFAC models according to best fit (TCC)tcc_find_pairs