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

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Documentation for package ‘spectralAnalysis’ version 3.12.0

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spectralAnalysis-package spectralAnalysis: a package to read-in, pre-process, visualise and analyse spectral data
baselineCorrect generic function to perfom baseline correction
baselineCorrect-method 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
checkCompatible-method 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
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
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 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
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
getSpectraInTimeExample Artificial example 'SpectraInTime-class'
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
getWavelengths generic function to extract 'wavelengths'-slot
getWavelengths-method 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
lastSpectrum-method 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
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 S4 Class key process times in a data frame, every line is convertable to a '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 Range S4 class (range) useful for subsetting with actual values instead of indicators
Rangetosubset Range S4 class (range) useful for subsetting with actual values instead of indicators
rangetosubset Range S4 class (range) useful for subsetting with actual values instead of indicators
RangeToSubset-class Range S4 class (range) useful for subsetting with actual values instead of indicators
read save a 'SpectraInTime-class' as a '.txt' file
readProcessTimes read .csv file as process times
readSPC Read-in of a SPC file.
readSpectra save a 'SpectraInTime-class' as a '.txt' file
removeRedundantSources Remove redundant sources from the initial NMF model
runNMF Actual NMF analysis
save save a 'SpectraInTime-class' as a '.txt' file
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
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
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'
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 Align SpectraInTime objects with differing wavelength axes to a common wavelength axis using cubic spline interpolation.
wavelengthAlign-method Align SpectraInTime objects with differing wavelength axes to a common wavelength axis using cubic spline interpolation.
[-method Subsetting 'SpectraInTime-class'
[ProcessTimes-method Check whether 2 objects are compatible before using them together For instance, same experiment name and matching time frames
[SpectraInTime-method Check whether 2 objects are compatible before using them together For instance, same experiment name and matching time frames