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ChemoSpec (version 1.51-0)

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

1.51-0

License

GPL-3

Maintainer

Bryan Hanson

Last Published

May 23rd, 2012

Functions in ChemoSpec (1.51-0)

removeFreq

Remove Frequencies from a Spectra Object
mclustSpectra

mclust Analysis of a Spectra Object PCA Results
shrinkLeaf

Shrink the Leaves of a Dendrogram
mclust3dSpectra

mclust Analysis of a Spectra Object in 3D
labelExtremes3d

Identify Extreme Values in 3D
pcaBoot

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

Plot PCA Scores of a Spectra Object
seXy

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

Interactive 3D Score Plot of a Spectra Object
sPlotSpectra

s-Plot of Spectra Data
mclust3D

mclust Analysis in 3D
hmapSpectra

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

Create New Groups from an Existing Spectra Object
plotScoresG

Plot PCA Scores of a Spectra Object using GGobi
plot2Loadings

Plot PCA Loadings from a Spectra object Against Each Other
sumSpectra

Summarize a Spectra Object
robPCA

Robust PCA of a Spectra Object
baselineSpec

Carry out baseline correction on a Spectra object
labelExtremes

Label Extreme Values in a 2D Data Set
plotLoadings

Plot PCA Loadings for a Spectra Object
colorSymbol

Colors and Symbols in ChemoSpec and Spectra Objects
Spectra

Spectra Objects
SrE.IR

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

Assign Group Membership and Colors for a Spectra Object
isWholeNo

Determine if a Number is a Whole Number
colLeaf

Color the Leaves of a Dendrogram
binBuck

Bin or Bucket a Spectra Object
LoopThruSpectra

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

Scree Plots of PCA Results for a Spectra Object
normVec

Normalize a Vector to range -1 to +1
sumGroups

Summarize the Group Parameters of a Spectra Object
plotScoresDecoration

Decorate PCA Score Plot of a Spectra Object
check4Gaps

Check for Missing Values (Gaps)
rowDist

Compute Distance Between Rows of a Matrix
avgFacLvls

Average levels of a factor in a data matrix
plotScores3D

3D PCA Score Plot for a Spectra Object
binData

Bin or Bucket Data
hcaScores

HCA on PCA scores from a Spectra Object
specSurvey

Plot Measures of Central Tendency and Spread for a Spectra Object
q2rPCA

Conversion Between PCA Classes
getManyCsv

Merge CSV Files in a Directory into a Spectra Object
aovPCAscores

Conduct PCA and plot aovPCA Scores of a Spectra Object
pcaDiag

Outlier Diagnostic Plots for PCA of a Spectra Object
coordProjCS

Modified Version of coordProj from mclust
chkSpectra

Verify the Integrity of a Spectra Object
plotSpectra

Plot Spectra Object
makeEllipsoid

Create Ellipsoid
aovPCAloadings

Plot aovPCA Loadings of a Spectra Object
normSpectra

Normalize a Spectra Object
conColScheme

Change the Color Scheme of a Spectra Object
hypTestScores

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

Plot HCA Results of a Spectra Object
CuticleIR

IR Spectra of Plant Cuticles by Genotype and Treatment
classPCA

Classical PCA of Spectra Objects
plotScoresCor

Compute Confidence Ellipses
ChemoSpec-package

Exploratory Chemometrics for Spectroscopy
aovPCA

ANOVA-PCA Analysis of Spectra Data
removeSample

Remove Samples or Groups from a Spectra Object
plotHCA

Plot Dendrogram for Spectra Object