Man pages for spectralAnalysis
Pre-Process, Visualize and Analyse Process Analytical Data, by Spectral Data Measurements Made During a Chemical Process

addMessageadd an message to list of messages for printing #
addPreprocessingStepfunction to use by preprocessing step
baselineCorrectgeneric function to perfom baseline correction
changeDevSettingsFunction to overwrite default settings, print to console when...
checkCompatibleCheck whether 2 objects are compatible before using them...
checkForRedundantSourcesCheck if any of the source vectors in the initialized NMF...
checkIdenticalClasscheck wether all elements of of the same class
checkMethodcheck method in list of allowd method
checkTimeUnitcheck timeeUnit and produce error if not correct unit
completeSourceMatrixcomplete source matrix
computeNMFResiduCompute relative residual per observation of an NMF fit to a...
convertListToS4convert an a named list to S4 object
convertS4ToListconvert an S4 object into a list
eCreate an 'ElementsToSelect-class' from a numeric vector or...
ElementsToSelect-classElements S4 class useful for closest elements subsetting
firstreturn first element (of a vector)
firstSpectrumGet the first spectrum
flagVectorInIntervalflag vector elements within interval (closed interval )
getClosestElementsget closest element for elements looked up in a vector
getDefaultSumFuncfunction to get default summary functions
getDefaultTimeFormatfunction to get default time format in the package
getElementsgeneric function to extract 'elements'-slot
getExperimentNamegeneric function to extract 'experimentName'-slot
getExtraInfogeneric function to extract 'extraInfo'-slot
getListOfSpectraExampleget example list of spectra
getNMFInputMatrixExtract spectral input matrix from SPC file and condition...
getPathProcessTimesExampleexample path process times ecport
getPreprocessinggeneric function to extract 'preprocessing'-slot
getProcessTimesExampleget a minimal 'ProcessTimes-class' example based on...
getProcessTimesFrameExampleget mimimal example 'ProcessTimesFrame-class'
getRangegeneric function to extract 'range'-slot
getSpectrageneric function to extract 'spectra'-slot
getSpectraInTimeExampleArtificial example 'SpectraInTime-class'
getStartTimegeneric function to extract 'startTime'-slot
getTimeConversionFactortransform timeUnit to convert from seconds to specified unit
getTimePointsgeneric function to extract 'timePoints'-slot
getUnitsgeneric function to extract 'units'-slot
getWavelengthsgeneric function to extract 'wavelengths'-slot
includeRedundantSourcesRe-introduce redundant source vectors and corresponding zero...
initializeNMFModelInitialize NMF model with initial spectral data
lastreturn laste element( of a vector )
lastSpectrumGet the last spectrum
loadAllSPCFilesLoad all or a selection of SPC files from a given directory.
localBaselineCorrectlocal baseline correct, substract a baseline either trough 1...
nonNegativePreprocessingcondition datamatrix to input in and condition properly for...
normalizegeneric normalization function
plotlyAxishelp function to make plotly axis title
predictNNLSBased on previously obtained NMF result 'NMFResult', estimate...
preprocessgeneric function to preprocess an S4 object
preprocessSpectraInTimeWithListinternal function to wrap multiple preprocessing steps
ProcessTimes-classS4 Class key process times
ProcessTimesFrame-classS4 Class key process times in a data frame, every line is...
rcreate a 'RangeToSubset-class' object from 2 elements or from...
RangeToSubset-classRange S4 class (range) useful for subsetting with actual...
readProcessTimesread .csv file as process times
readSPCRead-in of a SPC file.
removeRedundantSourcesRemove redundant sources from the initial NMF model
runNMFActual NMF analysis
saveSpectrasave a 'SpectraInTime-class' as a '.txt' file
scaleNMFResultApply fixed scaling to NMF model matrices by normalizing the...
setExperimentNameset the experiment name
setTimePointsAltset time alternative time axis
smoothgeneric smoothing function
SpectraInTime-classSpectraInTime-class (time resolved spectra ) wavelength-time...
spectralAnalysisspectralAnalysis: a package to read-in, pre-process,...
spectralIntegrationIntegrate spectraInTime object
spectralNMFPerform Non-Negative Matrix factorization on spectral data
spectralNMFListPerform Non-Negative Matrix factorization on list of SPC...
spectralNormalizationnormalization function
spectralSmoothAndDifferentiateinternal smoothing and differentiation function
subset-methodsSubsetting 'SpectraInTime-class'
subset.SpectraTimeinternal function for subsetting
SummaryByWavelengths-classS4-class for summary object SpectraInTime
testListOfSpectrainternal function to check all elements are spectraInTime
timeAlignTime align first object, using info in the second object
timeAlign.listOfSpectraAlign all spectra in a list
timeAlign.SpectraInTimealign 1 SpectraInTime with 1 cooling information
trapzintegration via trapezium ruls originally from caTools...
upsampleNMFResultUpsample NMF result to original temporal resolution
wavelengthAlignAlign SpectraInTime objects with differing wavelength axes to...
spectralAnalysis documentation built on May 1, 2019, 10:25 p.m.