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 |