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ChemoSpec (version 1.50-2)

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

1,217

Version

1.50-2

License

GPL-3

Maintainer

Bryan Hanson

Last Published

January 4th, 2012

Functions in ChemoSpec (1.50-2)

aovPCAscores

Conduct PCA and plot aovPCA Scores of a Spectra Object
LoopThruSpectra

Display the spectra in a Spectra object one at a time
aovPCA

ANOVA-PCA Analysis of Spectra Data
avgFacLvls

Average levels of a factor in a data matrix
baselineSpec

Carry out baseline correction on a Spectra object
Spectra

Spectra Objects
pcaBoot

Cross-Validation of Classical PCA Results for a Spectra Object
groupNcolor

Assign Group Membership and Colors for a Spectra Object
plotSpectra

Plot Spectra Object
plotScree

Scree Plot of PCA Results for a Spectra Object
splitSpectraGroups

Create New Groups from an Existing Spectra Object
plotScoresG

Plot PCA Scores of a Spectra Object using GGobi
classPCA

Classical PCA of Spectra Objects
binData

Bin or Bucket Data
plotHCA

Plot Dendrogram for Spectra Object
chkSpectra

Verify the Integrity of a Spectra Object
normSpectra

Normalize a Spectra Object
CuticleIR

IR Spectra of Plant Cuticles by Genotype and Treatment
hypTestScores

Conduct MANOVA using PCA Scores and Factors in a Spectra Object
getManyCsv

Merge CSV Files in a Directory into a Spectra Object
hcaSpectra

Plot HCA Results of a Spectra Object
makeEllipsoid

Create Ellipsoid
normVec

Normalize a Vector to range -1 to +1
hcaScores

HCA on PCA scores from a Spectra Object
labelExtremes3d

Identify Extreme Values in 3D
plot2Loadings

Plot PCA Loadings from a Spectra object Against Each Other
mclust3dSpectra

mclust Analysis of a Spectra Object in 3D
q2rPCA

Conversion Between PCA Classes
plotScoresRGL

Interactive 3D Score Plot of a Spectra Object
SrE.IR

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

Plot PCA Scores of a Spectra Object
sPlotSpectra

s-Plot of Spectra Data
robPCA

Robust PCA of a Spectra Object
aovPCAloadings

Plot aovPCA Loadings of a Spectra Object
plotLoadings

Plot PCA Loadings for a Spectra Object
mclust3D

mclust Analysis in 3D
ChemoSpec-package

Exploratory Chemometrics for Spectroscopy
specSurvey

Plot Measures of Central Tendency and Spread for a Spectra Object
mclustSpectra

mclust Analysis of a Spectra Object PCA Results
colLeaf

Color the Leaves of a Dendrogram
shrinkLeaf

Shrink the Leaves of a Dendrogram
hmapSpectra

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

Change the Color Scheme of a Spectra Object
plotScores3D

3D PCA Score Plot for a Spectra Object
plotScoresDecoration

Decorate PCA Score Plot of a Spectra Object
removeSample

Remove Samples from a Spectra Object
labelExtremes

Label Extreme Values in a 2D Data Set
seXy

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

Modified Version of coordProj from mclust
check4Gaps

Check for Missing Values (Gaps)
binBuck

Bin or Bucket a Spectra Object
removeFreq

Remove Frequencies from a Spectra Object
sumGroups

Summarize the Group Parameters of a Spectra Object
pcaDiag

Outlier Diagnostic Plots for PCA of a Spectra Object
isWholeNo

Determine if a Number is a Whole Number
sumSpectra

Summarize a Spectra Object
rowDist

Compute Distance Between Rows of a Matrix
plotScoresCor

Compute Confidence Ellipses
colorSymbol

Colors and Symbols in ChemoSpec and Spectra Objects