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ChemoSpec (version 5.3.21)

Exploratory Chemometrics for Spectroscopy

Description

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.

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Version

Install

install.packages('ChemoSpec')

Monthly Downloads

931

Version

5.3.21

License

GPL-3

Maintainer

Bryan Hanson

Last Published

July 6th, 2021

Functions in ChemoSpec (5.3.21)

ChemoSpec-package

Exploratory Chemometrics for Spectroscopy

ANOVA-PCA Analysis of Spectra Data

Plot ANOVA-PCA Scores from a Spectra Object

Spectra Objects

Color and Symbols in ChemoSpec and ChemoSpec2D

Cross-Validation of Classical PCA Results for a Spectra Object

Bin or Bucket a Spectra Object

baselineSpectra

Baseline Correction of a Spectra Object

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

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

Classical PCA of Spectra Objects

Plot HCA Results of a Spectra Object

Conduct MANOVA using PCA Scores and Factors in a Spectra Object

Seriated Heat Map for a Spectra Object

mclust3dSpectra

mclust Analysis of a Spectra Object in 3D

mclust Analysis of a Spectra Object PCA Results

irlba_pcaSpectra

IRLBA PCA of Spectra Objects

IR and NMR Spectra of Serenoa repens (Saw Palmetto) Oil Extracts and Reference Oils

Made Up NMR Data Sets

Normalize a Spectra Object

loopThruSpectra

Display the Spectra in a Spectra Object One at a Time

Evaluate or Compare the Quality of Clusters Quantitatively

files2SpectraObject

Import Data into a Spectra Object

Plot aovPCAscores Loadings of a Spectra Object

Plot Scores from PCA, MIA or PARAFAC Analysis of a Spectra or Spectra2D Object

Plot Spectra Object

Plot PCA Loadings for a Spectra Object

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

plotSpectraDist

Plot the Distance Between Spectra and a Reference Spectrum in a Spectra Object

Verify the Integrity of a Spectra or Spectra2D Object

Remove Samples from a Spectra or Spectra2D Object

Alternate Style Scree Plot DEPRECATED

Update Group Names in a Spectra or Spectra2D Object

Compute Distance Between Rows of a Matrix

s-Plot of Spectra Data (Post PCA)

Hierarchical Cluster-Based Peak Alignment on a Spectra Object

Sparse PCA of Spectra Objects

Outlier Diagnostic Plots for PCA of a Spectra Object

Plot PCA Loadings from a Spectra Object Against Each Other

Robust PCA of a Spectra Object

Plot a Spectra Object Interactively

Interactive 3D Score Plot of a Spectra Object

3D PCA Score Plot for a Spectra Object

splitSpectraGroups

Create New Groups from an Existing Spectra Object

Summarize the Group Membership of a Spectra or Spectra2D Object

Summarize a Spectra or Spectra2D Object

Plot Measures of Central Tendency and Spread for a Spectra Object

Remove Frequencies from a Spectra or Spectra2D Object

Compute the Distances Between Samples in a Spectra or Spectra2D Object

Remove Groups from a Spectra or Spectra2D Object

Apply Savitzky-Golay filters to a Spectra object