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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 ofChemometrics 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 packageChemometricsWithR facilitates reproduction of the examples in the book.

The bookModern 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 packagechemometrics.

A special issue of R News with a focus onR in Chemistry was published in August 2006. A special volume of Journal of Statistical Software (JSS) dedicated toSpectroscopy 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) withlm() (from stats). A least squares solution forx inAx = b can also be computed asqr.coef(qr(A), b).
• The packagennls provides a means of constrainingx to non-negative or non-positive values; the packagebvls allows other bounds onx to be applied.
• Functions for isotonic regression are available in the packageIso, and are useful to determine the unimodal vector that is closest to a given vectorx under least squares criteria.
• Heteroskedastic linear models can be fit using thegls() function of thenlme package.

Nonlinear Regression Models

• Thenls() function (from stats) as well as the packageminpack.lm allow the solution of nonlinear least squares problems.
• Correlated and/or unequal variances can be modeled using thegnls() function of thenlme package and bynlreg.

Curve Resolution

• ThePTAk 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 packageALS.
• Thealsace 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 packagedrc 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 packagemdatools provides functions for MCR-ALS with constraints and a purity based methods similar to SIMPLISMA.
  
• Thealbatross 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 packagepls implements Partial Least Squares Regression (PLSR) and Principal Component Regression (PCR).
• The packagelspls implements the least squares-partial least squares (LS-PLS) method.
• Sparse PLS is implemented in the packagespls package.
• Thegpls package implements generalized partial least squares, based on the Iteratively ReWeighted Least Squares (IRWLS) method of Brian Marx.
• The packageenpls implements ensemble partial least squares, a framework for measuring feature importance, outlier detection, and ensemble modeling based on (sparse) partial least squares regressions.
• The packagemdatools 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 functionsprincomp(). Some graphical PCA representations can be found in thepsy package.
• Thehomals 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 thepcaPP package. The packageelasticnet is applicable to sparse PCA.
• The packagemdatools 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 packagepcv implements the Procrustes cross-validation method for PCA, Principal Component Regression and Partial Least Squares regression models.
• TheLearnPCA package provides a series of vignettes explaining PCA.

Factor Analysis

• Factor analysis (FA) is in the package stats as functionsfactanal(); seePsychometrics task view for details on extensions.

Compositional Data Analysis

• The packagecompositions 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 usingfastICA.

Clustering

• TheCluster 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 functionstep(); packageleaps implements leaps-and-bounds variable selection, by default using Mallow’s Cp.stepPlr provides stepwise variable selection for penalized logistic regression.
• PackagevarSelRF provides variable selection methods for random forests. Packageclustvarsel implements variable selection for model-based clustering.
• The packagemdatools implements methods based on VIP scores, Selectivity Ratio (SR) as well as interval PLS.

Self-Organizing Maps

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

Differential Equations

• See theDifferentialEquations task view packages dealing with differential equations.

Metrology

• Theunits package attaches unit metadata to vectors, matrices and arrays, providing automatic propagation, conversion, derivation and simplification of units.
• Theerrors package attaches uncertainty metadata to vectors, matrices and arrays, providing automatic propagation and reporting.
• Thequantities package integrates the packagesunits anderrors to provide a quantity calculus system for vectors, matrices and arrays.
• Theconstants 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.
• ThemetRology package provides support for metrology applications, including measurement uncertainty estimation and inter-laboratory metrology comparison studies.

Calibration

• Theinvestr package facilitates calibration/inverse estimation with linear and nonlinear regression models.
• ThechemCal package provides functions for plotting linear calibration functions and estimating standard errors for measurements.
• Thenlreg package is useful for nonlinear calibration models.

Cellular Automata

• Thesimecol package includes functions for cellular automata modeling.

Thermodynamics

• TheCHNOSZ 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.
• TheIAPWS95 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 packagercdk allows the user to access functionality in theChemistry Development Kit (CDK), a Java framework for cheminformatics. This allows the user to load molecules, evaluate fingerprints (via the packagefingerprint), calculate molecular descriptors and so on. In addition, the CDK API allows the user to view structures in 2D. Thercdklibs package provides the CDK libraries for use in R.
• ChemmineR is a cheminformatics toolkit for analyzing small molecules in R. Its add-on packages includefmcsR for mismatch tolerant maximum common substructure matching,eiR for accelerated structure similarity searching;bioassayR for analyzing bioactivity data, andChemmineOB for accessingOpenBabel functionalities from R.
• Thewebchem 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, andChemIDplus.
• The packagestandartox allows the user to access theStandartox database of ecotoxicological test data.
• The packageECOTOXr allows the user to create a copy of and query theUS EPA ECOTOX database.

Spectroscopy

• Bryan Hanson has compiled a broad range ofFree and Open Source Software (FOSS) for Spectroscopy, much of which is in the form of R packages.
• TheChemoSpec 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.
• TheHyperChemoBridge interconvertsChemoSpec (and hyperSpec) objects
• Thespeaq package implements the hierarchical Cluster-based Peak Alignment (CluPA) and may be used for aligning NMR spectra.
• The packageTIMP 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 packageChemoSpec2D 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.
• Thespectrino package provides tools for spectra viewing and organization.
• TheNIRStat package provides transfusion-related differential tests on near-infrared spectroscopy (NIRS) time series.
• TheserrsBayes package allows Bayesian modeling of raman spectroscopy data.
• Their package performs IR data analysis functions (such as baseline correction, binning, clipping, interpolating, smoothing, averaging, adding, subtracting, dividing, multiplying, plotting).
• ThePlotFTIR package easily produces journal-quality IR spectral graphics usingggplot2 and interfaces withir andChemoSpec.

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.
• TheLCMSQA 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.
• TheRpeakChrom 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.
• TheOrgMassSpecR 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 packagesMassSpecWavelet,PROcess, andxcms are designed for the analysis of mass spectrometry data.
• TheapLCMS package is designed for the processing of LC/MS based metabolomics data.
• ThexMSanalyzer package allows mergingapLCMS sample processing results from multiple sets of parameter settings, among other features.
• TheMSPrep package is for post-processing of metabolomic data, including summarization of replicates, filtering, imputation, and normalization.
• ThemetaMS package is an MS-based metabolomics data processing and compound annotation pipeline.
• TheRaMS package reads in mzML and mzXML files asdata.table objects for visualization and data manipulation with thetidyverse.
• 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

• TheMedicalImaging task view provides a list of packages that can be used on fMRI, MRI, and related data.
• See for instance the packageAnalyzeFMRI for working with data stored in the ANALYZE or ‘NIFTI’ format.

Fluorescence Lifetime Imaging Microscopy

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

Carbon Dating

• The packageBchron creates chronologies based on radiocarbon and non-radiocarbon dated depths.
• The packagercarbon enables the calibration and analysis of radiocarbon dates.
• The packageISRaD provides data and tools for the development, maintenance, analysis, and deployment of theInternational Soil Radiocarbon Database (ISRaD).
• The packagenimbleCarbon provides functions for Bayesian analyses of radiocarbon dates.
• The packagercarbon enables the calibration and analysis of radiocarbon dates.
• The packagespDates allows analysis of spatial gradients in radiocarbon dates.

Astronomy and Astrophysics

• TheRobPer package calculates periodograms based on (robustly) fitting periodic functions to light curves.
• The packagesnapshot contains functions for reading and writing N-body snapshots from the GADGET code for cosmological N-body/SPH simulations.
• ThesolaR package provides functions to determine the movement of the sun from the earth and to determine incident solar radiation.
• TheFITSio package provides utilities to read and write files in the FITS (Flexible Image Transport System) format, a standard format in astronomy.
• ThestellaR package manages and displays stellar tracks and isochrones from the Pisa low-mass database.
• TheastroFns package provides miscellaneous astronomy functions, utilities, and data.
• ThecosmoFns package contains standard expressions for distances, times, luminosities, and other quantities useful in observational cosmology, including molecular line observations.
• Thecelestial package includes a number of common astronomy conversion routines, particularly the HMS and degrees schemes.
• TheSCEPtER package is used to estimate stellar mass and radius given observational data of effective temperature, [Fe/H], and astroseismic parameters.
• Thelira package performs Bayesian linear regression and forecasting in Astronomy, accounting for all kinds of errors and correlations in the data.
• TheSPADAR 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.
• TheSCEPtERbinary 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.
• Thepanstarrs 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.
• Thelorentz package performs the Lorentz transformations of special relativity. Active and passive transforms are implemented. It includes functionality for the gyrogroup structure of three-velocities.
• TheAstrostatistics and Astroinformatics Portal is an R-centric collection of information regarding statistical analysis in astronomy.
• Hans Werner Borchers has a page onAstronomy modules and links for R, Python, and Julia.

Energy Modeling

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

Water and Soil Chemistry

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

Titration Curves

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

Electrochemistry

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

Health Physics

• The packageradsafer provides functions for radiation safety; the packageRadData provides nuclear decay data for dosimetric calculations from the International Commission on Radiological Protection.
• The packageAeroSampleR 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
• US EPA ECOTOX database

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:Bchron
• GitHub Project:ChemometricsWithR
• GitHub Project:HyperChemoBridge