| baselineCorrect | generic function to perfom baseline correction |
| baselineCorrect-method | generic function to perfom baseline correction |
| checkCompatible | Check object compatibility |
| checkCompatible-method | Check object compatibility |
| checkForRedundantSources | Check for redunt NMF source vectors |
| checkIdenticalClass | check wether all elements of of the same class |
| combineSpectralObjects | Function to combine 'SpectraInTime-class' objects containing 1 spectrum each |
| computeNMFResidu | NMF relative residual per observation |
| e | Create an 'ElementsToSelect-class' from a numeric vector or multiple numeric values or vectors |
| ElementsToSelect-class | Elements S4 class useful for closest elements subsetting |
| firstSpectrum | Get the first spectrum |
| firstSpectrum-method | Get the first spectrum |
| getDefaultSumFunc | function to get default summary functions |
| getDefaultTimeFormat | function to get default time format in the package |
| getDimensionReduction | generic function to extract 'dimensionReduction'-slot |
| getDimensionReduction-method | SpectraInTimeComp-class (time resolved spectra ) |
| getElements | generic function to extract 'elements'-slot |
| getElements-method | generic function to extract 'elements'-slot |
| getExperimentName | generic function to extract 'experimentName'-slot |
| getExperimentName-method | generic function to extract 'experimentName'-slot |
| getExtraInfo | generic function to extract 'extraInfo'-slot |
| getExtraInfo-method | generic function to extract 'extraInfo'-slot |
| getListOfSpectraExample | get example list of spectra |
| getNMFInputMatrix | Get spectralData as input NMF model |
| getPathProcessTimesExample | example path process times |
| getPreprocessing | generic function to extract 'preprocessing'-slot |
| getPreprocessing-method | 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 |
| getRange-method | generic function to extract 'range'-slot |
| getSpectra | generic function to extract 'spectra'-slot |
| getSpectra-method | generic function to extract 'spectra'-slot |
| getSpectraInTimeCompExample | Artificial example of 'SpectraInTimeComp-class' |
| getSpectraInTimeExample | Artificial example 'SpectraInTime-class' |
| getSpectralAxis | generic function to extract 'spectralAxis'-slot |
| getSpectralAxis-method | generic function to extract 'spectralAxis'-slot |
| getStartTime | generic function to extract 'startTime'-slot |
| getStartTime-method | generic function to extract 'startTime'-slot |
| getTimePoints | generic function to extract 'timePoints'-slot |
| getTimePoints-method | generic function to extract 'timePoints'-slot |
| getUnits | generic function to extract 'units'-slot |
| getUnits-method | generic function to extract 'units'-slot |
| includeRedundantSources | Re-introduce redundant sources in NMF-model |
| initializeNMFModel | Initialize NMF model with initial spectral data |
| lastSpectrum | Get the last spectrum |
| lastSpectrum-method | Get the last spectrum |
| loadAllSPCFiles | Load all or a selection of SPC files from a given directory. |
| localBaselineCorrect | Local baseline correction |
| nonNegativePreprocessing | condition datamatrix to input in and condition properly for NMF |
| normalize | generic normalization function |
| normalize-method | 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 |
| preprocess-method | generic function to preprocess an S4 object |
| ProcessTimes | S4 Class key process times |
| ProcessTimes-class | S4 Class key process times |
| ProcessTimesFrame-class | ProcessTimes-class |
| r | create a 'RangeToSubset-class' object from 2 elements or from a vector |
| r-method | create a 'RangeToSubset-class' object from 2 elements or from a vector |
| RangeToSubset | RangeToSubset-class |
| Rangetosubset | RangeToSubset-class |
| rangetosubset | RangeToSubset-class |
| RangeToSubset-class | RangeToSubset-class |
| read | read or save a 'SpectraInTime-class' from or to a '.txt' file |
| readProcessTimes | read .csv file as process times |
| readSPC | Read-in of a SPC file. |
| readSpectra | read or save a 'SpectraInTime-class' from or to a '.txt' file |
| removeRedundantSources | Remove redundant sources from the initial NMF model |
| runNMF | Actual NMF analysis |
| save | read or save a 'SpectraInTime-class' from or to a '.txt' file |
| saveSpectra | read or save a 'SpectraInTime-class' from or to a '.txt' file |
| scaleNMFResult | Apply fixed scaling to NMF model |
| setExperimentName<- | set the experiment name |
| setExperimentName<--method | set the experiment name |
| setTimePointsAlt<- | set time alternative time axis |
| setTimePointsAlt<--method | set the experiment name |
| smooth | generic smoothing function |
| smooth-method | generic smoothing function |
| SpectraInTimeComp | SpectraInTimeComp-class (time resolved spectra ) |
| spectraInTimeComp | SpectraInTimeComp-class (time resolved spectra ) |
| spectraintimecomp | SpectraInTimeComp-class (time resolved spectra ) |
| SpectraInTimeComp-class | SpectraInTimeComp-class (time resolved spectra ) |
| spectralIntegration | Integrate spectraInTime object |
| spectralNMF | Perform Non-Negative Matrix factorization on spectral data |
| spectralNMFList | Perform Non-Negative Matrix factorization on list of SPC files |
| spectralPLSCalibration | Compute PLS model |
| spectralPlsPrediction | Perform PLS prediction |
| subset-methods | Subsetting 'SpectraInTime-class' |
| TemperatureInfo | S4 Class key process times |
| temperatureInfo | S4 Class key process times |
| temperatureinfo | S4 Class key process times |
| timeAlign | Time align first object, using info in the second object |
| timeAlign-method | Time align first object, using info in the second object |
| upsampleNMFResult | Upsample NMF result to original temporal resolution |
| wavelengthAlign | Wavelength align spectral data |
| wavelengthAlign-method | Wavelength align spectral data |
| [-method | Subsetting 'SpectraInTime-class' |
| [ProcessTimes-method | Check object compatibility |
| [SpectraInTime-method | Check object compatibility |