Man pages for MatthiasPucher/staRdom
PARAFAC Analysis of EEMs from DOM

abs_blcorBaseline correction for absorbance data
abs_fit_slopeFit absorbance data to exponential curve. 'drm' is used for...
absorbance_readReading absorbance data from txt and csv files.
abs_parmsCalculating slopes and slope ratios of a data frame of...
A_missingCalculate the amount of each component for samples not...
as.data.frame.eemConverting EEM data from class eem to data.frame.
dot-eem_csvImport EEMs from generic csv files.
eem2arrayData from an eemlist is transformed into an array
eem_absdilMultiply absorbance data according to the dilution and remove...
eem_checkdataCheck your EEM, absorption and metadata before processing
eem_checksizeCheck size of EEMs
eem_correctionsReturn names of samples where certain corrections are...
eem_csvImporter function for generic csv files to be used with...
eem_csv2Importer function for generic csv files to be used with...
eem_dilcorrCreate table how samples should be corrected because of...
eem_dilutionModifying fluorescence data according to dilution.
eem_duplicatesCheck for duplicate sample names
eem_easyOpens an R markdown template for an easy and userfriendly...
eem_eemdilCorrect names of EEM samples to match undiluted absorbance...
eem_excludeExclude complete wavelengths or samples form data set
eem_extend2largestEEM sample data is extended to include all wavelengths in all...
eem_getextremeDetermines the the biggest range of EEM spectrum where data...
eem_hitachiImporter function for Hitachi F-7000 txt files to be used...
eem_ife_correctionWrapper function to allow eem_inner_filter_effect (eemR)...
eem_import_dirLoad all eemlist obects saved in different Rdata or RDa files...
eem_interpMissing values are interpolated within EEM data
eem_is.naCheck for NAs in EEM data
eem_list15 fluorescence samples from drEEM used for examples.
eem_list_outliers2 fluorescence samples from drEEM that were excluded as...
eem_load_dreemLoad original data from the drEEM tutorial and return it as...
eem_matmultMultiply all EEMs with a matrix
eem_metatemplateCreate table that contains sample names and locations of...
eem_name_replaceReplace matched patterns in sample names
eem_overview_plotPlot fluorescence data from several samples split into...
eem_parafacRuns a PARAFAC analysis on EEM data
eempf4analysisCreate table of PARAFAC components and (optionally) EEM peaks...
eempf_bindxcCombining extracted components of PARAFAC models
eempf_comparePlot a set of PARAFAC models to compare the single components
eempf_comp_load_plotPlot components from a PARAFAC model
eempf_comp_matExtract EEM matrix for single components determined in the...
eempf_comp_namesExtract names from PARAFAC model components
eempf_comp_names-setSet names of PARAFAC components
eempf_comps3D3D plots of PARAFAC components
eempf_corcondiaCalculate the core consistancy of an EEM PARAFAC model
eempf_corplotPlot correlations of components in samples
eempf_cortableCalculating correlations between the component loadings in...
eempf_eemqualCalculating EEMqual which is an indicator of a PARAFAC...
eempf_excompExtracting components of a PARAFAC model
eempf_exportCreate one table containing the PARAFAC models factors and...
eempf_fitsFits vs. components of PARAFAC models are plotted
eempf_leverageCalculate the leverage of each emission and excitation...
eempf_leverage_dataCombine leverages into one data frame and add optional...
eempf_leverage_identPlot leverage of emission wavelengths, excitation wavelengths...
eempf_leverage_plotPlot leverage of emission wavelengths, excitation wavelengths...
eempf_load_plotPlot amount of each component in each sample as bar plot
eempf_mleverageCalculate the leverage of each emission and excitation...
eempf_openfluorWrite out PARAFAC components to submit to openfluor.org.
eempf_plot_compsPlot all components of PARAFAC models
eempf_reorderReorder PARAFAC components
eempf_reportCreate a html report of a PARAFAC analysis
eempf_rescaleBCRescale B and C modes of PARAFAC model
eempf_residualsCalculate residuals of EEM data according to a certain model
eempf_residuals_plotPlot samples by means of whole sample, each single component...
eempf_varimpCalculate the importance of each component.
eem_raman_areaCalculate raman area of EEM samples
eem_raman_normalisation2Wrapper function to eem_raman_normalisation (eemR).
eem_rangeCut EEM data matching a given wavelength range
eem_read_csvImport EEMs from generic csv tables (deprecated)
eem_red2smallestRemove wavelengths, that are missing in at least one sample...
eem_rem_scatRemove Raman and Rayleigh scattering in fluorescence data
eem_scale_extDetermine the range of fluorescence values in a set of...
eem_setNAset parts of specific samples to NA and optionally...
eem_smoothSmooth fluorescence data by calculating rolling mean along...
eem_spectral_corMultiply EEMs with spectral correction vectors (Emission and...
ggeemEEM spectra plotted with ggplot2
list_joinFull join of a list of data frames.
maxlinesExtract data from emission and excitation wavelengths of the...
norm2ACompensate for normalisation in C-modes
norm_arrayNormalise 3-dimensional array in first and second dimension
parafac_convCalculate a PARAFAC model similar to and using 'parafac'.
pf1PARAFAC model, see vignette, unconstrained
pf1nPARAFAC model, see vignette, non-negative constraints
pf2PARAFAC model, see vignette, non-negative constraints,...
pf3PARAFAC model, see vignette, non-negative constraints,...
pf4PARAFAC model, see vignette, non-negative constraints,...
shresult from PARAFAC split-half analysis, periodic data split
splithalfRunning a Split-Half analysis on a PARAFAC model
splithalf_plotPlot results from a splithalf analysis
splithalf_splitsExtracting a list of sample names in each subsample from a...
splithalf_tccExtracting TCC values from a splithalf analysis
tccCaluclate Tucker's Congruence Coefficient of PARAFAC...
tcc_find_pairsReorders components of different PARAFAC models according to...
MatthiasPucher/staRdom documentation built on June 29, 2019, 1:24 a.m.