ElementsToSelect-class
                        Elements S4 class useful for closest elements
                        subsetting
ProcessTimes-class      S4 Class key process times
ProcessTimesFrame-class
                        S4 Class key process times in a data frame,
                        every line is convertable to a
                        'ProcessTimes-class '
RangeToSubset-class     Range S4 class (range) useful for subsetting
                        with actual values instead of indicators
baselineCorrect         generic function to perfom baseline correction
checkCompatible         Check whether 2 objects are compatible before
                        using them together For instance, same
                        experiment name and matching time frames
checkForRedundantSources
                        Check if any of the source vectors in the
                        initialized NMF model are redundant, and should
                        be omitted from the actual NMF analysis
checkIdenticalClass     check wether all elements of of the same class
computeNMFResidu        Compute relative residual per observation of an
                        NMF fit to a spectral data set
e                       Create an 'ElementsToSelect-class' from a
                        numeric vector or multiple numeric values or
                        vectors
firstSpectrum           Get the first spectrum
getDefaultSumFunc       function to get default summary functions
getDefaultTimeFormat    function to get default time format in the
                        package
getElements             generic function to extract 'elements'-slot
getExperimentName       generic function to extract
                        'experimentName'-slot
getExtraInfo            generic function to extract 'extraInfo'-slot
getListOfSpectraExample
                        get example list of spectra
getNMFInputMatrix       Extract spectral input matrix from SPC file and
                        condition properly for NMF
getPathProcessTimesExample
                        example path process times ecport
getPreprocessing        generic function to extract
                        'preprocessing'-slot
getProcessTimesExample
                        get a minimal 'ProcessTimes-class' example
                        based on 'getSpectraInTimeExample'
getProcessTimesFrameExample
                        get mimimal example 'ProcessTimesFrame-class'
getRange                generic function to extract 'range'-slot
getSpectra              generic function to extract 'spectra'-slot
getSpectraInTimeExample
                        Artificial example 'SpectraInTime-class'
getStartTime            generic function to extract 'startTime'-slot
getTimePoints           generic function to extract 'timePoints'-slot
getUnits                generic function to extract 'units'-slot
getWavelengths          generic function to extract 'wavelengths'-slot
includeRedundantSources
                        Re-introduce redundant source vectors and
                        corresponding zero abundances into final NMF
                        result
initializeNMFModel      Initialize NMF model with initial spectral data
lastSpectrum            Get the last spectrum
loadAllSPCFiles         Load all or a selection of SPC files from a
                        given directory.
localBaselineCorrect    local baseline correct, substract a baseline
                        either trough 1 or 2 points
nonNegativePreprocessing
                        condition datamatrix to input in and condition
                        properly for NMF
normalize               generic normalization function
predictNNLS             Based on previously obtained NMF result
                        'NMFResult', estimate coefficients for a new
                        spectralData object 'object' using non-negative
                        least squares fitting. The result is returned
                        as as an NMF model.
preprocess              generic function to preprocess an S4 object
r                       create a 'RangeToSubset-class' object from 2
                        elements or from a vector
readProcessTimes        read .csv file as process times
readSPC                 Read-in of a SPC file.
removeRedundantSources
                        Remove redundant sources from the initial NMF
                        model
runNMF                  Actual NMF analysis
saveSpectra             save a 'SpectraInTime-class' as a '.txt' file
scaleNMFResult          Apply fixed scaling to NMF model matrices by
                        normalizing the basis vectors
setExperimentName<-     set the experiment name
setTimePointsAlt<-      set time alternative time axis
smooth                  generic smoothing function
spectralAnalysis        spectralAnalysis: a package to read-in,
                        pre-process, visualise and analyse spectral
                        data
spectralIntegration     Integrate spectraInTime object
spectralNMF             Perform Non-Negative Matrix factorization on
                        spectral data
spectralNMFList         Perform Non-Negative Matrix factorization on
                        list of SPC files
subset-methods          Subsetting 'SpectraInTime-class'
timeAlign               Time align first object, using info in the
                        second object
upsampleNMFResult       Upsample NMF result to original temporal
                        resolution
wavelengthAlign         Align SpectraInTime objects with differing
                        wavelength axes to a common wavelength axis
                        using cubic spline interpolation.
