Package: ChemoSpec 6.1.10

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_6.1.10.tar.gz
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ChemoSpec.pdf |ChemoSpec.html✨
ChemoSpec/json (API)
NEWS

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

Peer review:

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

Datasets:
  • 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
  • alignMUD - Made Up NMR Data Sets
  • metMUD1 - Made Up NMR Data Sets
  • metMUD2 - Made Up NMR Data Sets

On CRAN:

infrarednmrramanspectroscopyultravioletvisiblexrf

47 exports 57 stars 4.19 score 76 dependencies 1 dependents 14 mentions 44 scripts 1.3k downloads

Last updated 8 months agofrom:fdaf42bb7e. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 31 2024
R-4.5-winNOTEAug 31 2024
R-4.5-linuxNOTEAug 31 2024
R-4.4-winOKAug 31 2024
R-4.4-macOKAug 31 2024
R-4.3-winOKAug 31 2024
R-4.3-macOKAug 31 2024

Exports:aov_pcaSpectraaovPCAloadingsaovPCAscoresaverageReplicatesbaselineSpectrabinSpectrac_pcaSpectracheck4GapschkGraphicsOptchkSpectraclupaSpectracv_pcaSpectraevalClustersfiles2SpectraObjecthcaScoreshcaSpectrahmapSpectrahypTestScoresirlba_pcaSpectramatrix2SpectraObjectmclust3dSpectramclustSpectranormSpectrapcaDiagplot2Loadingsplot3dScoresplotLoadingsplotScoresplotScreeplotSpectraplotSpectraDistplotSpectraJSr_pcaSpectraremoveFreqremoveGroupremoveSamplereviewAllSpectrarowDists_pcaSpectrasampleDistsgfSpectrasplitSpectraGroupssPlotSpectrasumGroupssumSpectrasurveySpectrasurveySpectra2

Dependencies:askpassbase64encbslibcachemChemoSpecUtilsclicolorspacecpp11crosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplotlyplyrpromisespurrrR6rappdirsRColorBrewerRcppreadJDXreshape2rlangrmarkdownsassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

An Introduction to ChemoSpec

Bryan A. Hanson^[Professor Emeritus of Chemistry & Biochemistry, DePauw University, Greencastle IN USA., [email protected]]

Rendered fromChemoSpec.Rmdusingknitr::rmarkdownon Aug 31 2024.

Last update: 2024-02-03
Started: 2018-09-23

Readme and manuals

Help Manual

Help pageTopics
Exploratory Chemometrics for SpectroscopyChemoSpec-package ChemoSpec
ANOVA-PCA Analysis of Spectra Dataaov_pcaSpectra
Plot aovPCAscores Loadings of a Spectra ObjectaovPCAloadings
Plot ANOVA-PCA Scores from a Spectra ObjectaovPCAscores
Average Replicates in a Spectra ObjectaverageReplicates
Baseline Correction of a Spectra ObjectbaselineSpectra
Bin or Bucket a Spectra ObjectbinSpectra
Classical PCA of Spectra Objectsc_pcaSpectra
Check for Discontinuities (Gaps) in a Vector & Optionally Make a Plotcheck4Gaps
Check the Graphics Output Option/ModechkGraphicsOpt
Verify the Integrity of a Spectra or Spectra2D ObjectchkSpectra
Hierarchical Cluster-Based Peak Alignment on a Spectra ObjectclupaSpectra
Color and Symbols in ChemoSpec and ChemoSpec2DcolorSymbol
Change the Color Scheme of a Spectra or Spectra2D ObjectconColScheme
Cross-Validation of Classical PCA Results for a Spectra Objectcv_pcaSpectra
Evaluate or Compare the Quality of Clusters QuantitativelyevalClusters
Import Data into a Spectra Objectfiles2SpectraObject matrix2SpectraObject
HCA on PCA/MIA/PARAFAC scores from a Spectra or Spectra2D ObjecthcaScores
Plot HCA Results of a Spectra ObjecthcaSpectra
Seriated Heat Map for a Spectra ObjecthmapSpectra
Conduct MANOVA using PCA Scores and Factors in a Spectra ObjecthypTestScores
IRLBA PCA of Spectra Objectsirlba_pcaSpectra
mclust Analysis of a Spectra Object in 3Dmclust3dSpectra
mclust Analysis of a Spectra Object PCA ResultsmclustSpectra
Made Up NMR Data SetsalignMUD metMUD1 metMUD2
Normalize a Spectra ObjectnormSpectra
Outlier Diagnostic Plots for PCA of a Spectra ObjectpcaDiag
Plot PCA Loadings from a Spectra Object Against Each Otherplot2Loadings
3D PCA Score Plot for a Spectra Objectplot3dScores
Plot PCA Loadings for a Spectra ObjectplotLoadings
Plot Scores from PCA, MIA or PARAFAC Analysis of a Spectra or Spectra2D ObjectplotScores
Scree Plots from PCA or MIA Analysis of a Spectra or Spectra2D ObjectplotScree
Plot Spectra ObjectplotSpectra
Plot the Distance Between Spectra and a Reference Spectrum in a Spectra ObjectplotSpectraDist
Plot a Spectra Object InteractivelyplotSpectraJS
Robust PCA of a Spectra Objectr_pcaSpectra
Remove Frequencies from a Spectra or Spectra2D ObjectremoveFreq
Remove Groups from a Spectra or Spectra2D ObjectremoveGroup
Remove Samples from a Spectra or Spectra2D ObjectremoveSample
Review All the Spectra in a Spectra ObjectreviewAllSpectra
Compute Distance Between Rows of a MatrixrowDist
Sparse PCA of Spectra Objectss_pcaSpectra
Compute the Distances Between Samples in a Spectra or Spectra2D ObjectsampleDist
Apply Savitzky-Golay filters to a Spectra objectsgfSpectra
Spectra ObjectsSpectra
Create New Groups from an Existing Spectra ObjectsplitSpectraGroups
s-Plot of Spectra Data (Post PCA)sPlotSpectra
IR and NMR Spectra of Serenoa repens (Saw Palmetto) Oil Extracts and Reference OilsSrE.IR SrE.NMR
Summarize the Group Membership of a Spectra or Spectra2D ObjectsumGroups
Summarize a Spectra or Spectra2D ObjectsumSpectra
Plot Measures of Central Tendency and Spread for a Spectra ObjectsurveySpectra surveySpectra2
Update Group Names in a Spectra or Spectra2D ObjectupdateGroups