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ChemoSpec (version 1.60-9)

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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Version

Install

install.packages('ChemoSpec')

Monthly Downloads

957

Version

1.60-9

License

GPL-3

Maintainer

Bryan Hanson

Last Published

August 16th, 2013

Functions in ChemoSpec (1.60-9)

Assign Group Membership and Colors for a Spectra Object

Classical PCA of Spectra Objects

Carry out baseline correction on a Spectra object

IR Spectra of Plant Cuticles by Genotype and Treatment

Verify the Integrity of a Spectra Object

Color the Leaves of a Dendrogram

Read and process a Bruker NMR spectrum (.txt) as written by their software.

ChemoSpec-package

Exploratory Chemometrics for Spectroscopy

Cross-Validation of Classical PCA Results for a Spectra Object

LoopThruSpectra

Display the spectra in a Spectra object one at a time

Bin or Bucket Data

3D PCA Score Plot for a Spectra Object

mclust3dSpectra

mclust Analysis of a Spectra Object in 3D

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

Normalize a Vector to range -1 to +1

Change the Color Scheme of a Spectra Object

mclust Analysis of a Spectra Object PCA Results

Scree Plots of PCA Results for a Spectra Object

Determine if a Number is a Whole Number

Summarize the Group Parameters of a Spectra Object

Conduct MANOVA using PCA Scores and Factors in a Spectra Object

HCA on PCA scores from a Spectra Object

Shrink the Leaves of a Dendrogram

Find the TMS/TSP Peak in an NMR Spectrum.

Remove Frequencies from a Spectra Object

plotScoresDecoration

Decorate PCA Score Plot of a Spectra Object

Interactive 3D Score Plot of a Spectra Object

Plot PCA Loadings for a Spectra Object

Robust PCA of a Spectra Object

Colors and Symbols in ChemoSpec and Spectra Objects

Merge CSV Files in a Directory into a Spectra Object

Check for Missing Values (Gaps)

Plot HCA Results of a Spectra Object

Label Extreme Values in a 2D Data Set

Bin or Bucket a Spectra Object

Create Ellipsoid

Plot PCA Loadings from a Spectra object Against Each Other

labelExtremes3d

Identify Extreme Values in 3D

Plot Dendrogram for Spectra Object

s-Plot of Spectra Data Post PCA

Compute Distance Between Rows of a Matrix

Plot Measures of Central Tendency and Spread for a Spectra Object

Plot Spectra Object

Modified Version of coordProj from mclust

splitSpectraGroups

Create New Groups from an Existing Spectra Object

Normalize a Spectra Object

Average levels of a factor in a data matrix

Outlier Diagnostic Plots for PCA of a Spectra Object

Remove Samples or Groups from a Spectra Object

mclust Analysis in 3D

Summarize a Spectra Object

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

Spectra Objects

Conversion Between PCA Classes

Plot aovPCA Loadings of a Spectra Object

ANOVA-PCA Analysis of Spectra Data

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

Compute Confidence Ellipses

files2SpectraObject

Merge Files in a Directory into a Spectra Object

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

Conduct PCA and plot aovPCA Scores of a Spectra Object

Plot PCA Scores of a Spectra Object

Read and process a JCAMP-DX file.