Package: ChemoSpec 6.3.1

ChemoSpec: Exploratory Chemometrics for Spectroscopy

A collection of functions for top-down exploratory data analysis of spectral data including nuclear magnetic resonance (NMR), infrared (IR), Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed for structured experiments, such as metabolomics investigations, where the samples fall into treatment and control groups. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and to help you get usable results quickly. A vignette covering typical operations is available.

Authors:Bryan A. Hanson [aut, cre], Mike Bostock [cph, ctb], Matt Keinsley [ctb], Tejasvi Gupta [ctb]

ChemoSpec_6.3.1.tar.gz
ChemoSpec_6.3.1.zip(r-4.7)ChemoSpec_6.3.1.zip(r-4.6)ChemoSpec_6.3.1.zip(r-4.5)
ChemoSpec_6.3.1.tgz(r-4.6-any)ChemoSpec_6.3.1.tgz(r-4.5-any)
ChemoSpec_6.3.1.tar.gz(r-4.7-any)ChemoSpec_6.3.1.tar.gz(r-4.6-any)
ChemoSpec_6.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ChemoSpec/json (API)

# Install 'ChemoSpec' in R:

install.packages('ChemoSpec', repos = c('https://bryanhanson.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bryanhanson/chemospec/issues

Pkgdown/docs site:https://bryanhanson.github.io

Datasets:

alignMUD - Made Up NMR Data Sets
metMUD1 - Made Up NMR Data Sets
metMUD2 - Made Up NMR Data Sets
SrE.IR - IR and NMR Spectra of Serenoa repens (Saw Palmetto) Oil Extracts and Reference Oils
SrE.NMR - IR and NMR Spectra of Serenoa repens (Saw Palmetto) Oil Extracts and Reference Oils

On CRAN:

infrared nmr raman spectroscopy ultraviolet visible xrf

6.92 score 65 stars 51 scripts 1.0k downloads 48 exports 71 dependencies

Last updated from:0e963a9ebb. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	193
source / vignettes	OK	257
linux-release-x86_64	OK	194
macos-release-arm64	OK	139
macos-oldrel-arm64	OK	198
windows-devel	OK	131
windows-release	OK	149
windows-oldrel	OK	178
wasm-release	OK	149

Exports:.chkReqPkgs aov_pcaSpectra aovPCAloadings aovPCAscores averageReplicates baselineSpectra binSpectra c_pcaSpectra check4Gaps chkGraphicsOpt chkSpectra clupaSpectra cv_pcaSpectra evalClusters files2SpectraObject hcaScores hcaSpectra hmapSpectra hypTestScores irlba_pcaSpectra matrix2SpectraObject mclust3dSpectra mclustSpectra normSpectra pcaDiag plot2Loadings plot3dScores plotLoadings plotScores plotScree plotSpectra plotSpectraDist plotSpectraJS r_pcaSpectra removeFreq removeGroup removeSample reviewAllSpectra rowDist s_pcaSpectra sampleDist sgfSpectra splitSpectraGroups sPlotSpectra sumGroups sumSpectra surveySpectra surveySpectra2

Dependencies:askpass base64enc bslib cachem ChemoSpecUtils cli cpp11 crosstalk curl data.table digest dplyr evaluate farver fastmap fontawesome fs generics ggplot2 ggrepel glue gtable highr htmltools htmlwidgets httr isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr memoise mime openssl otel patchwork pillar pkgconfig plotly plyr promises purrr R6 rappdirs RColorBrewer Rcpp readJDX reshape2 rlang rmarkdown S7 sass scales stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

An R Package for Chemometric Analysis of Spectra (NMR, IR etc

Rendered fromChemoSpec.Rnwusingutils::Sweave

Last update: 2025-06-27
Started: 2011-10-31

Help page	Topics
Exploratory Chemometrics for Spectroscopy	ChemoSpec-package ChemoSpec
ANOVA-PCA Analysis of Spectra Data	aov_pcaSpectra
Plot aovPCAscores Loadings of a Spectra Object	aovPCAloadings
Plot ANOVA-PCA Scores from a Spectra Object	aovPCAscores
Average Replicates in a Spectra Object	averageReplicates
Baseline Correction of a Spectra Object	baselineSpectra
Bin or Bucket a Spectra Object	binSpectra
Classical PCA of Spectra Objects	c_pcaSpectra
Check for Discontinuities (Gaps) in a Vector & Optionally Make a Plot	check4Gaps
Check the Graphics Output Option/Mode	chkGraphicsOpt
Verify the Integrity of a Spectra or Spectra2D Object	chkSpectra
Hierarchical Cluster-Based Peak Alignment on a Spectra Object	clupaSpectra
Color and Symbols in ChemoSpec and ChemoSpec2D	colorSymbol
Change the Color Scheme of a Spectra or Spectra2D Object	conColScheme
Cross-Validation of Classical PCA Results for a Spectra Object	cv_pcaSpectra
Evaluate or Compare the Quality of Clusters Quantitatively	evalClusters
Import Data into a Spectra Object	files2SpectraObject matrix2SpectraObject
HCA on PCA/MIA/PARAFAC scores from a Spectra or Spectra2D Object	hcaScores
Plot HCA Results of a Spectra Object	hcaSpectra
Seriated Heat Map for a Spectra Object	hmapSpectra
Conduct MANOVA using PCA Scores and Factors in a Spectra Object	hypTestScores
IRLBA PCA of Spectra Objects	irlba_pcaSpectra
mclust Analysis of a Spectra Object in 3D	mclust3dSpectra
mclust Analysis of a Spectra Object PCA Results	mclustSpectra
Made Up NMR Data Sets	alignMUD metMUD1 metMUD2
Normalize a Spectra Object	normSpectra
Outlier Diagnostic Plots for PCA of a Spectra Object	pcaDiag
Plot PCA Loadings from a Spectra Object Against Each Other	plot2Loadings
3D PCA Score Plot for a Spectra Object	plot3dScores
Plot PCA Loadings for a Spectra Object	plotLoadings
Plot Scores from PCA, MIA or PARAFAC Analysis of a Spectra or Spectra2D Object	plotScores
Scree Plots from PCA or MIA Analysis of a Spectra or Spectra2D Object	plotScree
Plot Spectra Object	plotSpectra
Plot the Distance Between Spectra and a Reference Spectrum in a Spectra Object	plotSpectraDist
Plot a Spectra Object Interactively	plotSpectraJS
Robust PCA of a Spectra Object	r_pcaSpectra
Remove Frequencies from a Spectra or Spectra2D Object	removeFreq
Remove Groups from a Spectra or Spectra2D Object	removeGroup
Remove Samples from a Spectra or Spectra2D Object	removeSample
Review All the Spectra in a Spectra Object	reviewAllSpectra
Compute Distance Between Rows of a Matrix	rowDist
Sparse PCA of Spectra Objects	s_pcaSpectra
Compute the Distances Between Samples in a Spectra or Spectra2D Object	sampleDist
Apply Savitzky-Golay filters to a Spectra object	sgfSpectra
Spectra Objects	Spectra
Create New Groups from an Existing Spectra Object	splitSpectraGroups
s-Plot of Spectra Data (Post PCA)	sPlotSpectra
IR and NMR Spectra of Serenoa repens (Saw Palmetto) Oil Extracts and Reference Oils	SrE.IR SrE.NMR
Summarize the Group Membership of a Spectra or Spectra2D Object	sumGroups
Summarize a Spectra or Spectra2D Object	sumSpectra
Plot Measures of Central Tendency and Spread for a Spectra Object	surveySpectra surveySpectra2
Update Group Names in a Spectra or Spectra2D Object	updateGroups

Package: ChemoSpec 6.3.1

ChemoSpec: Exploratory Chemometrics for Spectroscopy

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Help Manual

Usage by other packages (reverse dependencies)