CRAN Task View: Chemometrics and Computational Physics

Chemometrics and computational physics are concerned with the analysis of data arising in chemistry and physics experiments, as well as the simulation of physico-chemico systems. Many of the functions in base R are useful for these ends.

The second edition of Chemometrics with R: Multivariate Data Analysis in the Natural and Life Sciences by Ron Wehrens, ISBN 978-3-662-62027-4, Springer, 2020, provides an introduction to multivariate statistics in the life sciences, as well as coverage of several specific topics from the area of chemometrics. The associated package ChemometricsWithR facilitates reproduction of the examples in the book.

The book Modern Statistical Methods for Astronomy With R Applications by Eric D. Feigelson and G. Jogesh Babu, ISBN-13: 9780521767279, Cambridge, 2012, provides an introduction to statistics for astronomers and an overview of the foremost methods being used in astrostatistical analysis, illustrated by examples in R.

The book by Kurt Varmuza and Peter Filzmoser, Introduction to Multivariate Statistical Analysis in Chemometrics, ISBN 978-1-420-05947-2, CRC Press, 2009, is associated with the package chemometrics.

A special issue of R News with a focus on R in Chemistry was published in August 2006. A special volume of Journal of Statistical Software (JSS) dedicated to Spectroscopy and Chemometrics in R was published in January 2007.

Please e-mail the maintainer, submit an issue or pull request in the GitHub repository linked above, if we have omitted something of importance, or if a new package or function should be mentioned here.

Linear Regression Models

• Linear models can be fitted (via OLS) with lm() (from stats). A least squares solution for x in Ax = b can also be computed as qr.coef(qr(A), b).
• The package nnls provides a means of constraining x to non-negative or non-positive values; the package bvls allows other bounds on x to be applied.
• Functions for isotonic regression are available in the package Iso, and are useful to determine the unimodal vector that is closest to a given vector x under least squares criteria.
• Heteroskedastic linear models can be fit using the gls() function of the nlme package.

Nonlinear Regression Models

• The nls() function (from stats) as well as the package minpack.lm allow the solution of nonlinear least squares problems.
• Correlated and/or unequal variances can be modeled using the gnls() function of the nlme package and by nlreg.

Curve Resolution

• The PTAk package provides functions for Principal Tensor Analysis on k modes. The package includes also some other multiway methods: PCAn (Tucker-n) and PARAFAC/CANDECOMP.
• Multivariate curve resolution alternating least squares (MCR-ALS) is implemented in the package ALS.
• The alsace package provides MCR-ALS support for Liquid chromatography with PhotoDiode Array Detection (LC-DAD) data with many injections, with features for peak alignment and identification.
• The package drc provides functions for the analysis of one or multiple non-linear curves with focus on models for concentration-response, dose-response and time-response data.
• The package mdatools provides functions for MCR-ALS with constraints and a purity based methods similar to SIMPLISMA.
  
• The albatross package specialises in non-negative Parallel Factor Analysis of fluorescence excitation-emission matrices and provides auxillary functions relevant to analysis of natural waters.

Partial Least Squares

• The package pls implements Partial Least Squares Regression (PLSR) and Principal Component Regression (PCR).
• The package lspls implements the least squares-partial least squares (LS-PLS) method.
• Sparse PLS is implemented in the package spls package.
• The gpls package implements generalized partial least squares, based on the Iteratively ReWeighted Least Squares (IRWLS) method of Brian Marx.
• The package enpls implements ensemble partial least squares, a framework for measuring feature importance, outlier detection, and ensemble modeling based on (sparse) partial least squares regressions.
• The package mdatools provides functions for both PLS regression and discriminant analysis (PLSDA), including numerous plots, Jack-Knifing inference for regression coefficients and many other supplementary tools.

Principal Component Analysis

• Principal component analysis (PCA) is in the package stats as functions princomp(). Some graphical PCA representations can be found in the psy package.
• The homals package provides nonlinear PCA and, by defining sets, nonlinear canonical correlation analysis (models of the Gifi-family).
• A desired number of robust principal components can be computed with the pcaPP package. The package elasticnet is applicable to sparse PCA.
• The package mdatools provides functions for PCA analysis. The functions work both with conventional datasets as well as with images, including spectral images. A randomized version of PCA can be used to speed up calculations for large datasets. The package also implements PCA based classification method, Soft Independent Modelling of Class Analogy (SIMCA).
• The package pcv implements the Procrustes cross-validation method for PCA, Principal Component Regression and Partial Least Squares regression models.
• The LearnPCA package provides a series of vignettes explaining PCA.

Factor Analysis

• Factor analysis (FA) is in the package stats as functions factanal(); see Psychometrics task view for details on extensions.

Compositional Data Analysis

• The package compositions provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations). See also the book, Analyzing Compositional Data with R by K. Gerald von den Boogaart und Raimon Tolosana-Delgado, ISBN: 978-3-642-36808-0, Springer, 2013.

Independent Component Analysis

• Independent component analysis (ICA) can be computed using fastICA.

Clustering

• The Cluster task view provides a list of packages that can be used for clustering problems.

Variable Selection

• Stepwise variable selection for linear models, using AIC, is available in function step(); package leaps implements leaps-and-bounds variable selection, by default using Mallow’s Cp. stepPlr provides stepwise variable selection for penalized logistic regression.
• Package varSelRF provides variable selection methods for random forests. Package clustvarsel implements variable selection for model-based clustering.
• The BioMark package implements two meta-methods for variable selection: stability selection (applying a primary selection method like a t-test, VIP value or PLSDA regression coefficient) to different subsets of the data, and higher criticism, which provides a data-driven choice of significance cutoffs in statistical testing.
• The package mdatools implements methods based on VIP scores, Selectivity Ratio (SR) as well as interval PLS.

Self-Organizing Maps

• The kohonen package implements self-organizing maps as well as some extensions for supervised pattern recognition and data fusion. The som package provides functions for self-organizing maps.

Differential Equations

• See the DifferentialEquations task view packages dealing with differential equations.

Metrology

• The units package attaches unit metadata to vectors, matrices and arrays, providing automatic propagation, conversion, derivation and simplification of units.
• The errors package attaches uncertainty metadata to vectors, matrices and arrays, providing automatic propagation and reporting.
• The quantities package integrates the packages units and errors to provide a quantity calculus system for vectors, matrices and arrays.
• The constants package provides values of the fundamental physical constants based on values reported by the Committee on Data for Science and Technology (CODATA), an interdisciplinary committee of the International Council for Science.
• NISTunits also provides values of the fundamental physical constants. The values it contains are based on the values reported by the National Institute of Standards and Technology, (NIST).
• measurements contains tools to make working with physical measurements easier, such as functions to convert between metric and imperial units, or to calculate a dimension’s unknown value from other dimensions’ measurements.
• The metRology package provides support for metrology applications, including measurement uncertainty estimation and inter-laboratory metrology comparison studies.

Calibration

• The investr package facilitates calibration/inverse estimation with linear and nonlinear regression models.
• The chemCal package provides functions for plotting linear calibration functions and estimating standard errors for measurements.
• The nlreg package is useful for nonlinear calibration models.

Cellular Automata

• The simecol package includes functions for cellular automata modeling.

Thermodynamics

• The CHNOSZ package provides functions for calculating the standard Gibbs energies and other thermodynamic properties, and chemical affinities of reactions between species contained in a thermodynamic database.
• The IAPWS95 package provides functions to calculate the thermodynamic properties of water according to the International Association for the Properties of Water and Steam (IAPWS) 1995 formulations.

Interfaces to External Libraries

• The package rcdk allows the user to access functionality in the Chemistry Development Kit (CDK), a Java framework for cheminformatics. This allows the user to load molecules, evaluate fingerprints (via the package fingerprint), calculate molecular descriptors and so on. In addition, the CDK API allows the user to view structures in 2D. The rcdklibs package provides the CDK libraries for use in R.
• ChemmineR is a cheminformatics toolkit for analyzing small molecules in R. Its add-on packages include fmcsR for mismatch tolerant maximum common substructure matching, eiR for accelerated structure similarity searching; bioassayR for analyzing bioactivity data, and ChemmineOB for accessing OpenBabel functionalities from R.
• The webchem package allows users to retrieve chemical information from various sources on the web and to interact with various APIs. Sources include: Chemical Identifier Resolver, ChemSpider, PubChem, Chemical Translation Service, PAN Pesticide Database, Alan Wood’s Compendium of Pesticide Common Names, PHYSPROP Database, ETOX, PPDB, and ChemIDplus.
• The package standartox allows the user to access the Standartox database of ecotoxicological test data.

Spectroscopy

• Bryan Hanson has compiled a broad range of Free and Open Source Software (FOSS) for Spectroscopy, much of which is in the form of R packages.
• The spectralAnalysis package allows users to pre-process, visualize and analyze spectroscopy data. Non-negative matrix factorization analysis is included.
• The ChemoSpec package collects user-friendly functions for plotting spectra (NMR, IR, etc) and carrying top-down exploratory data analysis, such as HCA, PCA and model-based clustering.
• The HyperChemoBridge interconverts ChemoSpec (and hyperSpec) objects
• The speaq package implements the hierarchical Cluster-based Peak Alignment (CluPA) and may be used for aligning NMR spectra.
• The package TIMP provides a problem solving environment for fitting separable nonlinear models in physics and chemistry applications, and has been extensively applied to time-resolved spectroscopy data.
• The package ChemoSpec2D allows exploratory chemometrics of 2D spectroscopic data sets such as COSY (correlated spectroscopy) and HSQC (heteronuclear single quantum coherence) 2D NMR (nuclear magnetic resonance) spectra.
• The spectrino package provides tools for spectra viewing and organization.
• The NIRStat package provides transfusion-related differential tests on near-infrared spectroscopy (NIRS) time series.
• The serrsBayes package allows Bayesian modeling of raman spectroscopy data.
• The ir package performs IR data analysis functions (such as baseline correction, binning, clipping, interpolating, smoothing, averaging, adding, subtracting, dividing, multiplying, plotting).
• The PlotFTIR package easily produces journal-quality IR spectral graphics using ggplot2 and interfaces with ir and ChemoSpec.

Chromatography

• chromConverter provides parsers to read chromatographic data into R. It can work with a wide range of formats.
• GCalignR aligns peaks based on peak retention times and matches homologous peaks across samples.
• The LCMSQA package provides tools to check the quality of liquid chromatograph/mass spectrometry (LC/MS) experiments.
• RGCxGC is a toolbox for the analysis of bidimensional gas chromatography data.
• The RpeakChrom package contains tools for chromatographic column characterization and modeling chromatographic peaks.

Mass Spectrometry

• MSnbase defines infrastructure for mass spectrometry-based proteomics data handling, plotting, processing and quantification.
• MALDIquant provides tools for quantitative analysis of MALDI-TOF mass spectrometry data, with support for baseline correction, peak detection and plotting of mass spectra. MALDIquantForeign imports data into/from ‘MALDIquant’ objects.
• The OrgMassSpecR package is for organic/biological mass spectrometry, with a focus on graphical display, quantification using stable isotope dilution, and protein hydrogen/deuterium exchange experiments.
• The Bioconductor packages MassSpecWavelet, PROcess, and xcms are designed for the analysis of mass spectrometry data.
• The apLCMS package is designed for the processing of LC/MS based metabolomics data.
• The xMSanalyzer package allows merging apLCMS sample processing results from multiple sets of parameter settings, among other features.
• The MSPrep package is for post-processing of metabolomic data, including summarization of replicates, filtering, imputation, and normalization.
• The metaMS package is an MS-based metabolomics data processing and compound annotation pipeline.
• The RaMS package reads in mzML and mzXML files as data.table objects for visualization and data manipulation with the tidyverse.
• readMzXmlData imports data in the mzXML format.
• readBrukerFlexData imports data in the Bruker *flex format.
• MSbox provides a suite of tools for mass spectrometry data analysis.
• enviPat allows isotope pattern, profile and centroid calculation for mass spectrometry.
• HaDeX provides functions for processing, analysis and visualization of Hydrogen Deuterium eXchange monitored by Mass Spectrometry experiments (HDX-MS).
• accucor implements an isotope natural abundance correction algorithm that is needed especially for high resolution mass spectrometers.

Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy

• The MedicalImaging task view provides a list of packages that can be used on fMRI, MRI, and related data.

Fluorescence Lifetime Imaging Microscopy

• Functions for visualization and analysis of Fluorescence Lifetime Imaging Microscopy (FLIM) datasets are available in the package TIMP.

Carbon Dating

• The package Bchron creates chronologies based on radiocarbon and non-radiocarbon dated depths.
• The package rcarbon enables the calibration and analysis of radiocarbon dates.
• The package ISRaD provides data and tools for the development, maintenance, analysis, and deployment of the International Soil Radiocarbon Database (ISRaD).
• The package nimbleCarbon provides functions for Bayesian analyses of radiocarbon dates.
• The package rcarbon enables the calibration and analysis of radiocarbon dates.
• The package spDates allows analysis of spatial gradients in radiocarbon dates.

Astronomy and Astrophysics

• The astrodatR package collects 19 datasets from contemporary astronomy research, many of which are described in the aforementioned textbook ‘Modern Statistical Methods for Astronomy with R Applications’.
• The RobPer package calculates periodograms based on (robustly) fitting periodic functions to light curves.
• The package snapshot contains functions for reading and writing N-body snapshots from the GADGET code for cosmological N-body/SPH simulations.
• The solaR package provides functions to determine the movement of the sun from the earth and to determine incident solar radiation.
• The FITSio package provides utilities to read and write files in the FITS (Flexible Image Transport System) format, a standard format in astronomy.
• The stellaR package manages and displays stellar tracks and isochrones from the Pisa low-mass database.
• The astroFns package provides miscellaneous astronomy functions, utilities, and data.
• The cosmoFns package contains standard expressions for distances, times, luminosities, and other quantities useful in observational cosmology, including molecular line observations.
• The celestial package includes a number of common astronomy conversion routines, particularly the HMS and degrees schemes.
• The SCEPtER package is used to estimate stellar mass and radius given observational data of effective temperature, [Fe/H], and astroseismic parameters.
• The lira package performs Bayesian linear regression and forecasting in Astronomy, accounting for all kinds of errors and correlations in the data.
• The SPADAR package provides functions to create all-sky grid plots of widely used astronomical coordinate systems (equatorial, ecliptic, galactic) and scatter plots of data on any of these systems, including on-the-fly system conversion.
• The SCEPtERbinary package allows for estimating the stellar age for double-lined detached binary systems, adopted from the effective temperature, the metallicity [Fe/H], the mass, and the radius of the two stars.
• The panstarrs package contains a data archive of the PS1 wide-field astronomical survey, and can be used to plan astronomical observations, make guidance pictures, and find magnitudes in five broadband filters.
• The lorentz package performs the Lorentz transformations of special relativity. Active and passive transforms are implemented. It includes functionality for the gyrogroup structure of three-velocities.
• The Astrostatistics and Astroinformatics Portal is an R-centric collection of information regarding statistical analysis in astronomy.
• Hans Werner Borchers has a page on Astronomy modules and links for R, Python, and Julia.

Energy Modeling

• The solaR package provides functions to simulate and model systems involved in the capture and use of solar energy, including photovoltaics.

Water and Soil Chemistry

• The AquaEnv package is a toolbox for aquatic chemical modelling focused on (ocean) acidification and CO2 air-water exchange.
• See the Environmetrics task view for further related packages related to water and soil chemistry.

Titration Curves

• The titrationCurves package provides functions to plot acid/base, complexation, redox, and precipitation titration curves.

Electrochemistry

• The eChem package provides functions to simulate voltammetry, chronoamperometry and chronocoulometry experiments, which may be useful in courses in analytical chemistry.

Health Physics

• The package radsafer provides functions for radiation safety; the package RadData provides nuclear decay data for dosimetric calculations from the International Commission on Radiological Protection.
• The package AeroSampleR allows estimation of ideal efficiencies of aerosol sampling.

CRAN packages

Related links

• R News: R in Chemistry
• Journal of Statistical Software: Spectroscopy and Chemometrics in R
• apLCMS
• Astrostatistics and Astroinformatics Portal Software Forum
• Chemistry Development Kit (CDK)
• MSPrep
• OpenBabel
• PubChem
• xMSanalyzer
• Chemical Identifier Resolver
• ChemSpider
• Free and Open Source Software (FOSS) for Spectroscopy
• Chemical Translation Service
• PAN Pesticide Database
• Alan Wood’s Compendium of Pesticide Common Names
• PHYSPROP Database
• ETOX
• PPDB
• ChemIDplus
• Astronomy modules and links for R, Python, and Julia
• mdatools: make Chemometrics easy
• Standartox

Other resources

• CRAN Task View: Cluster
• CRAN Task View: DifferentialEquations
• CRAN Task View: Environmetrics
• CRAN Task View: MedicalImaging
• CRAN Task View: Psychometrics
• Bioconductor Package: alsace
• Bioconductor Package: bioassayR
• Bioconductor Package: ChemmineOB
• Bioconductor Package: ChemmineR
• Bioconductor Package: eiR
• Bioconductor Package: fmcsR
• Bioconductor Package: gpls
• Bioconductor Package: MassSpecWavelet
• Bioconductor Package: metaMS
• Bioconductor Package: MSnbase
• Bioconductor Package: PROcess
• Bioconductor Package: xcms
• GitHub Project: ChemometricsWithR
• GitHub Project: HyperChemoBridge