Pre-Process, Visualize and Analyse Spectral Data
add an message to list of messages for printing #
function to use by preprocessing step
generic function to perfom baseline correction
Function to overwrite default settings
Check object compatibility
Check for redunt NMF source vectors
check wether all elements of of the same class
check method in list of allowd method
check timeeUnit and produce error if not correct unit
Function to combine SpectraInTime-class objects containing 1 spectru...
complete source matrix
NMF relative residual per observation
convert an a named list to S4 object
convert an S4 object into a list
Create an ElementsToSelect-class from a numeric vector or multiple n...
Elements S4 class useful for closest elements subsetting
return first element (of a vector)
Get the first spectrum
flag vector elements within interval (closed interval )
get closest element for elements looked up in a vector
function to get default summary functions
function to get default time format in the package
generic function to extract dimensionReduction-slot
generic function to extract elements-slot
generic function to extract experimentName-slot
generic function to extract extraInfo-slot
get example list of spectra
Get spectralData as input NMF model
example path process times
generic function to extract preprocessing-slot
get a minimal ProcessTimes-class example based on `getSpectraInTimeE...
get mimimal example ProcessTimesFrame-class
generic function to extract range-slot
generic function to extract spectra-slot
Artificial example of SpectraInTimeComp-class
Artificial example SpectraInTime-class
generic function to extract spectralAxis-slot
generic function to extract startTime-slot
transform timeUnit to convert from seconds to specified unit
generic function to extract timePoints-slot
generic function to extract units-slot
Re-introduce redundant sources in NMF-model
Initialize NMF model with initial spectral data
return laste element( of a vector )
Get the last spectrum
Load all or a selection of SPC files from a given directory.
Local baseline correction
multiplicative scatter correction on 1 function
condition datamatrix to input in and condition properly for NMF
generic normalization function
help function to make plotly axis title
Based on previously obtained NMF result NMFResult, estimate coeffici...
generic function to preprocess an S4 object
internal function to wrap multiple preprocessing steps
S4 Class key process times
ProcessTimes-class
create a RangeToSubset-class object from 2 elements or from a vector
RangeToSubset-class
read .csv file as process times
Read-in of a SPC file.
Remove redundant sources from the initial NMF model
Actual NMF analysis
read or save a SpectraInTime-class from or to a .txt file
Apply fixed scaling to NMF model
perform multiplicative scatter correction
perform multiplicative scatter correction on spectralData
set the experiment name
set time alternative time axis
generic smoothing function
SpectraInTime-class
SpectraInTimeComp-class (time resolved spectra )
Integrate spectraInTime object
Perform Non-Negative Matrix factorization on spectral data
Perform Non-Negative Matrix factorization on list of SPC files
normalization function
Compute PLS model
Perform PLS prediction
internal smoothing and differentiation function
Subsetting SpectraInTime-class
internal function for subsetting
S4-class for summary object SpectraInTime
internal function to check all elements are spectraInTime
Align all spectra in a list
Time align first object, using info in the second object
align 1 SpectraInTime with 1 cooling information
Integration via trapezium rule
Upsample NMF result to original temporal resolution
Wavelength align spectral data
Infrared, near-infrared and Raman spectroscopic data measured during chemical reactions, provide structural fingerprints by which molecules can be identified and quantified. The application of these spectroscopic techniques as inline process analytical tools (PAT), provides the pharmaceutical and chemical industry with novel tools, allowing to monitor their chemical processes, resulting in a better process understanding through insight in reaction rates, mechanistics, stability, etc. Data can be read into R via the generic spc-format, which is generally supported by spectrometer vendor software. Versatile pre-processing functions are available to perform baseline correction by linking to the 'baseline' package; noise reduction via the 'signal' package; as well as time alignment, normalization, differentiation, integration and interpolation. Implementation based on the S4 object system allows storing a pre-processing pipeline as part of a spectral data object, and easily transferring it to other datasets. Interactive plotting tools are provided based on the 'plotly' package. Non-negative matrix factorization (NMF) has been implemented to perform multivariate analyses on individual spectral datasets or on multiple datasets at once. NMF provides a parts-based representation of the spectral data in terms of spectral signatures of the chemical compounds and their relative proportions. See 'hNMF'-package for references on available methods. The functionality to read in spc-files was adapted from the 'hyperSpec' package.