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:
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staRdom.pdf |staRdom.html✨
staRdom/json (API)
# Install 'staRdom' in R: |
install.packages('staRdom', repos = c('https://matthiaspucher.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/matthiaspucher/stardom/issues
- 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
Last updated 17 days agofrom:e7029d621a. Checks:OK: 5 NOTE: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 04 2024 |
R-4.5-win | NOTE | Nov 04 2024 |
R-4.5-linux | NOTE | Nov 04 2024 |
R-4.4-win | OK | Nov 04 2024 |
R-4.4-mac | OK | Nov 04 2024 |
R-4.3-win | OK | Nov 01 2024 |
R-4.3-mac | OK | Nov 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
Rendered fromBasic_analysis_of_DOM_samples.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2023-06-13
Started: 2018-04-06
PARAFAC analysis of EEM data to separate DOM components in R
Rendered fromPARAFAC_analysis_of_EEM.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2024-11-04
Started: 2018-04-06