Man pages for spectralAnalysis
Pre-Process, Visualize and Analyse Spectral Data
| addMessage | add an message to list of messages for printing # |
| addPreprocessingStep | function to use by preprocessing step |
| baselineCorrect | generic function to perfom baseline correction |
| changeDevSettings | Function to overwrite default settings |
| checkCompatible | Check object compatibility |
| checkForRedundantSources | Check for redunt NMF source vectors |
| checkIdenticalClass | check wether all elements of of the same class |
| checkMethod | check method in list of allowd method |
| checkTimeUnit | check timeeUnit and produce error if not correct unit |
| combineSpectralObjects | Function to combine 'SpectraInTime-class' objects containing... |
| completeSourceMatrix | complete source matrix |
| computeNMFResidu | NMF relative residual per observation |
| convertListToS4 | convert an a named list to S4 object |
| convertS4ToList | convert an S4 object into a list |
| e | Create an 'ElementsToSelect-class' from a numeric vector or... |
| ElementsToSelect-class | Elements S4 class useful for closest elements subsetting |
| first | return first element (of a vector) |
| firstSpectrum | Get the first spectrum |
| flagVectorInInterval | flag vector elements within interval (closed interval ) |
| getClosestElements | get closest element for elements looked up in a vector |
| getDefaultSumFunc | function to get default summary functions |
| getDefaultTimeFormat | function to get default time format in the package |
| getDimensionReduction | generic function to extract 'dimensionReduction'-slot |
| 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 | Get spectralData as input NMF model |
| getPathProcessTimesExample | example path process times |
| getPreprocessing | generic function to extract 'preprocessing'-slot |
| getProcessTimesExample | get a minimal 'ProcessTimes-class' example based on... |
| getProcessTimesFrameExample | get mimimal example 'ProcessTimesFrame-class' |
| getRange | generic function to extract 'range'-slot |
| getSpectra | generic function to extract 'spectra'-slot |
| getSpectraInTimeCompExample | Artificial example of 'SpectraInTimeComp-class' |
| getSpectraInTimeExample | Artificial example 'SpectraInTime-class' |
| getSpectralAxis | generic function to extract 'spectralAxis'-slot |
| getStartTime | generic function to extract 'startTime'-slot |
| getTimeConversionFactor | transform timeUnit to convert from seconds to specified unit |
| getTimePoints | generic function to extract 'timePoints'-slot |
| getUnits | generic function to extract 'units'-slot |
| includeRedundantSources | Re-introduce redundant sources in NMF-model |
| initializeNMFModel | Initialize NMF model with initial spectral data |
| last | return laste element( of a vector ) |
| lastSpectrum | Get the last spectrum |
| loadAllSPCFiles | Load all or a selection of SPC files from a given directory. |
| localBaselineCorrect | Local baseline correction |
| multiplicativeScatterCorrect | multiplicative scatter correction on 1 function |
| nonNegativePreprocessing | condition datamatrix to input in and condition properly for... |
| normalize | generic normalization function |
| plotlyAxis | help function to make plotly axis title |
| predictNNLS | Based on previously obtained NMF result 'NMFResult', estimate... |
| preprocess | generic function to preprocess an S4 object |
| preprocessSpectraInTimeWithList | internal function to wrap multiple preprocessing steps |
| ProcessTimes-class | S4 Class key process times |
| ProcessTimesFrame-class | ProcessTimes-class |
| r | create a 'RangeToSubset-class' object from 2 elements or from... |
| RangeToSubset-class | RangeToSubset-class |
| 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 | read or save a 'SpectraInTime-class' from or to a '.txt' file |
| scaleNMFResult | Apply fixed scaling to NMF model |
| scatterCorrect | perform multiplicative scatter correction |
| scatterCorrectSpectra | perform multiplicative scatter correction on spectralData |
| setExperimentName | set the experiment name |
| setTimePointsAlt | set time alternative time axis |
| smooth | generic smoothing function |
| SpectraInTime-class | SpectraInTime-class |
| 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... |
| spectralNormalization | normalization function |
| spectralPLSCalibration | Compute PLS model |
| spectralPlsPrediction | Perform PLS prediction |
| spectralSmoothAndDifferentiate | internal smoothing and differentiation function |
| subset-methods | Subsetting 'SpectraInTime-class' |
| subset.SpectraTime | internal function for subsetting |
| SummaryByWavelengths-class | S4-class for summary object SpectraInTime |
| testListOfSpectra | internal function to check all elements are spectraInTime |
| timeAlign | Time align first object, using info in the second object |
| timeAlign.listOfSpectra | Align all spectra in a list |
| timeAlign.SpectraInTime | align 1 SpectraInTime with 1 cooling information |
| trapz | Integration via trapezium rule |
| upsampleNMFResult | Upsample NMF result to original temporal resolution |
| wavelengthAlign | Wavelength align spectral data |
