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spectralAnalysis (version 3.12.0)

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

Description

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 (pharma-)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. The functionality to read in spc-files was adapted from the 'hyperSpec' package.

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Version

Install

install.packages('spectralAnalysis')

Monthly Downloads

49

Version

3.12.0

License

GPL-3

Maintainer

Adriaan Blommaert

Last Published

June 12th, 2018

Functions in spectralAnalysis (3.12.0)

getStartTime

generic function to extract startTime-slot
localBaselineCorrect

local baseline correct, substract a baseline either trough 1 or 2 points
nonNegativePreprocessing

condition datamatrix to input in and condition properly for NMF
getProcessTimesFrameExample

getRange

generic function to extract range-slot
getTimeConversionFactor

transform timeUnit to convert from seconds to specified unit
initializeNMFModel

Initialize NMF model with initial spectral data
preprocessSpectraInTimeWithList

internal function to wrap multiple preprocessing steps
r

create a RangeToSubset-class object from 2 elements or from a vector
last

return laste element( of a vector )
e

Create an ElementsToSelect-class from a numeric vector or multiple numeric values or vectors
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.
spectralNMFList

Perform Non-Negative Matrix factorization on list of SPC files
spectralNormalization

normalization function
normalize

generic normalization function
setExperimentName<-

set the experiment name
SpectraInTime-class

SpectraInTime-class (time resolved spectra ) wavelength-time data for 1 experiment
plotlyAxis

help function to make plotly axis title
getExtraInfo

generic function to extract extraInfo-slot
setTimePointsAlt<-

set time alternative time axis
subset-methods

spectralSmoothAndDifferentiate

internal smoothing and differentiation function
SummaryByWavelengths-class

S4-class for summary object SpectraInTime
getListOfSpectraExample

get example list of spectra
getPreprocessing

generic function to extract preprocessing-slot
getDefaultSumFunc

function to get default summary functions
getWavelengths

generic function to extract wavelengths-slot
getProcessTimesExample

computeNMFResidu

Compute relative residual per observation of an NMF fit to a spectral data set
includeRedundantSources

Re-introduce redundant source vectors and corresponding zero abundances into final NMF result
getDefaultTimeFormat

function to get default time format in the package
getPathProcessTimesExample

example path process times ecport
readProcessTimes

read .csv file as process times
getNMFInputMatrix

Extract spectral input matrix from SPC file and condition properly for NMF
lastSpectrum

Get the last spectrum
convertListToS4

convert an a named list to S4 object
readSPC

Read-in of a SPC file.
first

return first element (of a vector)
firstSpectrum

Get the first spectrum
removeRedundantSources

Remove redundant sources from the initial NMF model
loadAllSPCFiles

Load all or a selection of SPC files from a given directory.
spectralAnalysis

spectralAnalysis: a package to read-in, pre-process, visualise and analyse spectral data
runNMF

Actual NMF analysis
spectralIntegration

Integrate spectraInTime object
getSpectra

generic function to extract spectra-slot
trapz

integration via trapezium ruls originally from caTools package, included to avoid dependency on old package with correction inverse scale, should give still possitive values (taken absolute values )
smooth

generic smoothing function
timeAlign.listOfSpectra

Align all spectra in a list
getUnits

generic function to extract units-slot
getSpectraInTimeExample

getTimePoints

generic function to extract timePoints-slot
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.
spectralNMF

Perform Non-Negative Matrix factorization on spectral data
preprocess

generic function to preprocess an S4 object
timeAlign

Time align first object, using info in the second object
timeAlign.SpectraInTime

align 1 SpectraInTime with 1 cooling information
saveSpectra

scaleNMFResult

Apply fixed scaling to NMF model matrices by normalizing the basis vectors
testListOfSpectra

internal function to check all elements are spectraInTime
subset.SpectraTime

internal function for subsetting
ElementsToSelect-class

Elements S4 class useful for closest elements subsetting
ProcessTimesFrame-class

ProcessTimes-class

S4 Class key process times
RangeToSubset-class

Range S4 class (range) useful for subsetting with actual values instead of indicators
baselineCorrect

generic function to perfom baseline correction
changeDevSettings

Function to overwrite default settings, print to console when changing default settings and add to default settings
checkIdenticalClass

check wether all elements of of the same class
addMessage

add an message to list of messages for printing #
checkCompatible

Check whether 2 objects are compatible before using them together For instance, same experiment name and matching time frames
checkMethod

check method in list of allowd method
completeSourceMatrix

complete source matrix
addPreprocessingStep

function to use by preprocessing step
checkTimeUnit

check timeeUnit and produce error if not correct unit
checkForRedundantSources

Check if any of the source vectors in the initialized NMF model are redundant, and should be omitted from the actual NMF analysis
convertS4ToList

convert an S4 object into a list
getElements

generic function to extract elements-slot
flagVectorInInterval

flag vector elements within interval (closed interval )
getExperimentName

generic function to extract experimentName-slot
getClosestElements

get closest element for elements looked up in a vector