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ChemoSpec (version 3.0-1)

Exploratory Chemometrics for Spectroscopy

Description

A collection of functions for plotting spectra (NMR, IR etc) and carrying out various forms of top-down exploratory data analysis, such as HCA, PCA and model-based clustering. The design allows comparison of data from samples which fall into groups such as treatment vs. control. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed to be very user friendly and suitable for people with limited background in R.

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Install

install.packages('ChemoSpec')

Monthly Downloads

931

Version

3.0-1

License

GPL-3

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Repository

https://github.com/bryanhanson/ChemoSpec

Maintainer

Bryan Hanson

Last Published

January 21st, 2015

Functions in ChemoSpec (3.0-1)

Spectra Objects

Evaluate or Compare the Quality of Clusters Quantitatively

plotScoresDecoration

Decorate PCA Score Plot of a Spectra Object

Calculate the signal-to-noise ratio of a peak in a spectrum.

ANOVA-PCA Analysis of Spectra Data

Remove Frequencies from a Spectra Object

Robust PCA of a Spectra Object

Carry out baseline correction on a Spectra object

Assign Group Membership and Colors for a Spectra Object

Conduct MANOVA using PCA Scores and Factors in a Spectra Object

Bin or Bucket Data

IR Spectra of Plant Cuticles by Genotype and Treatment

Outlier Diagnostic Plots for PCA of a Spectra Object

Summarize a Spectra Object

Average levels of a factor in a data matrix

Determine if a Number is a Whole Number

Classical PCA of Spectra Objects

Change the Color Scheme of a Spectra Object

Colors and Symbols in ChemoSpec and Spectra Objects

Plot PCA Scores of a Spectra Object

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

s-Plot of Spectra Data Post PCA

labelExtremes3d

Identify Extreme Values in 3D

Functions to Compute Measures of Central Tendency and Spread. seX!

Create Ellipsoid

Interactive 3D Score Plot of a Spectra Object

Normalize a Vector to range -1 to +1

Scree Plots of PCA Results for a Spectra Object

LoopThruSpectra

Display the spectra in a Spectra object one at a time

Verify the Integrity of a Spectra Object

Normalize a Spectra Object

Conversion Between PCA Classes

Find the TMS/TSP Peak in an NMR Spectrum.

Plot aovPCA Loadings of a Spectra Object

Plot Measures of Central Tendency and Spread for a Spectra Object

mclust Analysis in 3D

HCA on PCA scores from a Spectra Object

Conduct PCA and plot aovPCA Scores of a Spectra Object

Modified Version of coordProj from mclust

Label Extreme Values in a 2D Data Set

Cross-Validation of Classical PCA Results for a Spectra Object

mclust3dSpectra

mclust Analysis of a Spectra Object in 3D

Check for Missing Values (Gaps)

Plot PCA Loadings from a Spectra object Against Each Other

Plot Dendrogram for Spectra Object

Read and process a Bruker NMR spectrum saved using Topspin

Create a Seriated Heat Map Comparing Samples and Spectral Data for a Spectra Object

Bin or Bucket a Spectra Object

files2SpectraObject

Merge Files in a Directory into a Spectra Object

Conduct Hierarchical Cluster-Based Peak Alignment on a Spectra Object

Compute Confidence Ellipses

Summarize the Group Parameters of a Spectra Object

Plot HCA Results of a Spectra Object

Plot Spectra Object

ChemoSpec-package

Exploratory Chemometrics for Spectroscopy

Color the Leaves of a Dendrogram

Compute Distance Between Rows of a Matrix

Plot PCA Loadings for a Spectra Object

mclust Analysis of a Spectra Object PCA Results

Shrink the Leaves of a Dendrogram

Read and process a JCAMP-DX file.

3D PCA Score Plot for a Spectra Object

Remove Samples or Groups from a Spectra Object

splitSpectraGroups

Create New Groups from an Existing Spectra Object