Package: ChemoSpec2D 0.5.0

ChemoSpec2D: Exploratory Chemometrics for 2D Spectroscopy

A collection of functions for exploratory chemometrics of 2D spectroscopic data sets such as COSY (correlated spectroscopy) and HSQC (heteronuclear single quantum coherence) 2D NMR (nuclear magnetic resonance) spectra. 'ChemoSpec2D' deploys methods aimed primarily at classification of samples and the identification of spectral features which are important in distinguishing samples from each other. Each 2D spectrum (a matrix) is treated as the unit of observation, and thus the physical sample in the spectrometer corresponds to the sample from a statistical perspective. In addition to chemometric tools, a few tools are provided for plotting 2D spectra, but these are not intended to replace the functionality typically available on the spectrometer. 'ChemoSpec2D' takes many of its cues from 'ChemoSpec' and tries to create consistent graphical output and to be very user friendly.

Authors:Bryan A. Hanson [aut, cre]

ChemoSpec2D_0.5.0.tar.gz
ChemoSpec2D_0.5.0.zip(r-4.5)ChemoSpec2D_0.5.0.zip(r-4.4)ChemoSpec2D_0.5.0.zip(r-4.3)
ChemoSpec2D_0.5.0.tgz(r-4.4-any)ChemoSpec2D_0.5.0.tgz(r-4.3-any)
ChemoSpec2D_0.5.0.tar.gz(r-4.5-noble)ChemoSpec2D_0.5.0.tar.gz(r-4.4-noble)
ChemoSpec2D_0.5.0.tgz(r-4.4-emscripten)ChemoSpec2D_0.5.0.tgz(r-4.3-emscripten)
ChemoSpec2D.pdf |ChemoSpec2D.html✨
ChemoSpec2D/json (API)
NEWS

# Install 'ChemoSpec2D' in R:
install.packages('ChemoSpec2D', repos = c('https://bryanhanson.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bryanhanson/chemospec2d/issues

Datasets:
  • MUD1 - Made Up 2D NMR-Like Data Sets
  • MUD2 - Made Up 2D NMR-Like Data Sets

On CRAN:

2d-spectranmrspectroscopy

52 exports 2 stars 0.85 score 73 dependencies 11 scripts 323 downloads

Last updated 3 years agofrom:7c0df10c14. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 20 2024
R-4.5-winWARNINGAug 20 2024
R-4.5-linuxWARNINGAug 20 2024
R-4.4-winWARNINGAug 20 2024
R-4.4-macWARNINGAug 20 2024
R-4.3-winWARNINGAug 20 2024
R-4.3-macWARNINGAug 20 2024

Exports:.addLegend.AlignArraysMBO.chkArgs.chkReqGraphicsPkgs.cleanArgs2D.createScale.drawScale.evalArrayOverlapMBO.findExtreme.findNA.findZeros.getAlignOrder.getLimits.getPN.makeArray.makeArray2.mapColors.noiseSurface.plotEngine.rescale.sH.shiftArray.symAroundZero.unstackcalcLvlscentscaleSpectra2Dcheck4GapschkSpectracomputeVolumefiles2Spectra2DObjecthats_alignSpectra2Dimport2DspectrainspectLvlsLofCLofLmiaSpectra2DnormSpectra2DpfacSpectra2DplotLoadings2DplotScoresplotScreeplotSliceplotSpectra2DpopSpectra2DremoveFreqremoveGroupremovePeaks2DremoveSampleshiftSpectra2DshowScalesumGroupssumSpectra

Dependencies:askpassbase64encbslibcachemChemoSpecUtilsclicolorspacecpp11crosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcppreadJDXrlangrmarkdownsassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

An Introduction to ChemoSpec2D

Bryan A. Hanson^1^

Rendered fromChemoSpec2D.Rmdusingknitr::rmarkdownon Aug 20 2024.

Last update: 2021-10-11
Started: 2017-10-20

Readme and manuals

Help Manual

Help pageTopics
Exploratory Chemometrics for 2D SpectroscopyChemoSpec2D-package ChemoSpec2D
Calculate Levels for Contour and Image Type PlotscalcLvls
Center and Scale a Spectra2D Object Along the Samples DimensioncentscaleSpectra2D
Check for Discontinuities (Gaps) in a Vector & Optionally Make a Plotcheck4Gaps
Verify the Integrity of a Spectra or Spectra2D ObjectchkSpectra
Color and Symbols in ChemoSpec and ChemoSpec2DcolorSymbol
Compute the Volume of a Specified Shift Range in a 2D SpectrumcomputeVolume
Import Data into a Spectra2D Objectfiles2Spectra2DObject
Align the Spectra in a Spectra2D Object using the HATS algorithm.hats_alignSpectra2D
Import 2D Spectroscopic Dataimport2Dspectra
Inspect Levels for Contour Plots of Spectra2D ObjectsinspectLvls
Create a List of ColorsLofC
Create a List of Contour LevelsLofL
Multivariate Image Analysis (Tucker 1) of a Spectra2D ObjectmiaSpectra2D
Made Up 2D NMR-Like Data SetsMUD MUD1 MUD2
Normalize a Spectra2D ObjectnormSpectra2D
PARAFAC Analysis of a Spectra2D ObjectpfacSpectra2D
Plot Loadings from a PARAFAC, MIA or POP Analysis of a Spectra2D ObjectplotLoadings2D
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 a Slice of a Spectra2D ObjectplotSlice
Plot a Spectra2D ObjectplotSpectra2D
Plain Old PCA (POP) of Spectra2D ObjectspopSpectra2D
Remove Frequencies from a Spectra or Spectra2D ObjectremoveFreq
Remove Groups from a Spectra or Spectra2D ObjectremoveGroup
Remove Peaks in a Spectra2D ObjectremovePeaks2D
Remove Samples from a Spectra or Spectra2D ObjectremoveSample
Compute the Distances Between Samples in a Spectra or Spectra2D ObjectsampleDist
Shift the Spectra in a Spectra2D ObjectshiftSpectra2D
Display a pdf Version of the Contour ScaleshowScale
Spectra2D ObjectsSpectra2D
Summarize the Group Membership of a Spectra or Spectra2D ObjectsumGroups
Summarize a Spectra or Spectra2D ObjectsumSpectra
Update Group Names in a Spectra or Spectra2D ObjectupdateGroups