ChemoSpec6.1.10 package

Exploratory Chemometrics for Spectroscopy

aov_pcaSpectra

ANOVA-PCA Analysis of Spectra Data

aovPCAloadings

Plot aovPCAscores Loadings of a Spectra Object

aovPCAscores

Plot ANOVA-PCA Scores from a Spectra Object

averageReplicates

Average Replicates in a Spectra Object

baselineSpectra

Baseline Correction of a Spectra Object

binSpectra

Bin or Bucket a Spectra Object

c_pcaSpectra

Classical PCA of Spectra Objects

check4Gaps

Check for Discontinuities (Gaps) in a Vector & Optionally Make a Plot

ChemoSpec-package

Exploratory Chemometrics for Spectroscopy

chkGraphicsOpt

Check the Graphics Output Option/Mode

chkSpectra

Verify the Integrity of a Spectra or Spectra2D Object

clupaSpectra

Hierarchical Cluster-Based Peak Alignment on a Spectra Object

colorSymbol

Color and Symbols in ChemoSpec and ChemoSpec2D

conColScheme

Change the Color Scheme of a Spectra or Spectra2D Object

cv_pcaSpectra

Cross-Validation of Classical PCA Results for a Spectra Object

evalClusters

Evaluate or Compare the Quality of Clusters Quantitatively

files2SpectraObject

Import Data into a Spectra Object

hcaScores

HCA on PCA/MIA/PARAFAC scores from a Spectra or Spectra2D Object

hcaSpectra

Plot HCA Results of a Spectra Object

hmapSpectra

Seriated Heat Map for a Spectra Object

hypTestScores

Conduct MANOVA using PCA Scores and Factors in a Spectra Object

irlba_pcaSpectra

IRLBA PCA of Spectra Objects

mclust3dSpectra

mclust Analysis of a Spectra Object in 3D

mclustSpectra

mclust Analysis of a Spectra Object PCA Results

normSpectra

Normalize a Spectra Object

pcaDiag

Outlier Diagnostic Plots for PCA of a Spectra Object

plot2Loadings

Plot PCA Loadings from a Spectra Object Against Each Other

plot3dScores

3D PCA Score Plot for a Spectra Object

plotLoadings

Plot PCA Loadings for a Spectra Object

plotScores

Plot Scores from PCA, MIA or PARAFAC Analysis of a Spectra or Spectra2...

plotScree

Scree Plots from PCA or MIA Analysis of a Spectra or Spectra2D Object

plotSpectra

Plot Spectra Object

plotSpectraDist

Plot the Distance Between Spectra and a Reference Spectrum in a Spectr...

plotSpectraJS

Plot a Spectra Object Interactively

r_pcaSpectra

Robust PCA of a Spectra Object

removeFreq

Remove Frequencies from a Spectra or Spectra2D Object

removeGroup

Remove Groups from a Spectra or Spectra2D Object

removeSample

Remove Samples from a Spectra or Spectra2D Object

reviewAllSpectra

Review All the Spectra in a Spectra Object

rowDist

Compute Distance Between Rows of a Matrix

s_pcaSpectra

Sparse PCA of Spectra Objects

sampleDist

Compute the Distances Between Samples in a Spectra or Spectra2D Object

sgfSpectra

Apply Savitzky-Golay filters to a Spectra object

Spectra

Spectra Objects

splitSpectraGroups

Create New Groups from an Existing Spectra Object

sPlotSpectra

s-Plot of Spectra Data (Post PCA)

sumGroups

Summarize the Group Membership of a Spectra or Spectra2D Object

sumSpectra

Summarize a Spectra or Spectra2D Object

surveySpectra

Plot Measures of Central Tendency and Spread for a Spectra Object

updateGroups

Update Group Names in a Spectra or Spectra2D Object

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.

  • Maintainer: Bryan A. Hanson
  • License: GPL-3
  • Last published: 2024-02-03