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ChemoSpec (version 5.0.88)

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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Install

install.packages('ChemoSpec')

Monthly Downloads

931

Version

5.0.88

License

GPL-3

Issues

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Repository

https://github.com/bryanhanson/ChemoSpec

Maintainer

Bryan Hanson

Last Published

October 15th, 2018

Functions in ChemoSpec (5.0.88)

HCA on PCA scores from a Spectra Object

Made Up NMR Data Sets

files2SpectraObject

Import Data into a Spectra Object

mclust Analysis of a Spectra Object PCA Results

3D PCA Score Plot for a Spectra Object

Interactive 3D Score Plot of a Spectra Object

Compute Distance Between Rows of a Matrix

Check for Missing Values (Gaps) in a Spectra Object

s-Plot of Spectra Data (Post PCA)

mclust Analysis in 3D

mclust3dSpectra

mclust Analysis of a Spectra Object in 3D

Cross-Validation of Classical PCA Results for a Spectra Object

plotSpectraDist

Plot the Distance Between Spectra in a Spectra Object

Plot a Spectra Object Interactively

Colors and Symbols in ChemoSpec and Spectra Objects

Evaluate or Compare the Quality of Clusters Quantitatively

Plot HCA Results of a Spectra Object

Remove Frequencies from a Spectra or Spectra2D Object

Normalize a Spectra Object

Robust PCA of a Spectra Object

Verify the Integrity of a Spectra or Spectra2D Object

Outlier Diagnostic Plots for PCA of a Spectra Object

Seriated Heat Map for a Spectra Object

Plot PCA Loadings from a Spectra Object Against Each Other

Change the Color Scheme of a Spectra Object

Hierarchical Cluster-Based Peak Alignment on a Spectra Object

sampleDistSpectra

Compute the Distance Between Samples in a Spectra Object

Plot Dendrogram for Spectra Object

Scree Plots of PCA Results for a Spectra Object

Apply Savitzky-Golay filters to a Spectra object

Summarize the Group Membership of a Spectra or Spectra2D Object

splitSpectraGroups

Create New Groups from an Existing Spectra Object

Conduct MANOVA using PCA Scores and Factors in a Spectra Object

Plot Spectra Object

loopThruSpectra

Display the Spectra in a Spectra Object One at a Time

Summarize a Spectra or Spectra2D Object

Plot PCA Loadings for a Spectra Object

Plot Measures of Central Tendency and Spread for a Spectra Object

Plot PCA Scores of a Spectra Object

Remove Groups or Samples from a Spectra or Spectra2D Object

Remove Groups or Samples from a Spectra or Spectra2D Object

baselineSpectra

Baseline Correction of a Spectra Object

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

Plot aovPCAscores Loadings of a Spectra Object

Spectra Objects

ChemoSpec-package

Exploratory Chemometrics for Spectroscopy

Classical PCA of Spectra Objects

Plot ANOVA-PCA Scores from a Spectra Object

ANOVA-PCA Analysis of Spectra Data

Bin or Bucket a Spectra Object