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

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.


version 3.11

  • include plot method for list of spectra version 3.8
  • include localBaseline correction ( needed for reactionTrends ) version 3.6
  • skip to 3.6 because of merge conflict version 3.4 and 3.5
  • include semi-NMF
  • include saving and reading spectraInTime to JSON-format
  • split off processing temperature xml files to chemDataProcessing version 3.5
  • adapted plot function (to work in Rmarkdown) version 3.4
  • allow missing values in alignment if cutting not possible, only a warning no error
  • change default time format in alignment version 3.3
  • Fix bug in preprocessing on a list ( wrong arguments passed of adding more then one step) + add test on it
  • include latest version of NMF

Reference manual

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3.12.0 by Adriaan Blommaert, 3 years ago

Browse source code at

Authors: Robin Van Oirbeek [aut] , Adriaan Blommaert [aut, cre] , Nicolas Sauwen [aut] , Tor Maes [ctb] , Jan Dijkmans [ctb] , Jef Cuypers [ctb] , Tatsiana Khamiakova [ctb] , Michel Tiel [ctb] , Claudia Beleites [ctb]

Documentation:   PDF Manual  

Task views: Chemometrics and Computational Physics

GPL-3 license

Imports baseline, BiocGenerics, data.table, ggplot2, jsonlite, magrittr, methods, nnls, NMF, plotly, plyr, RColorBrewer, signal, stats, viridis, hNMF

Suggests testthat

See at CRAN