# Exploratory Chemometrics for Spectroscopy

## Documentation for package ‘ChemoSpec’ version 3.0-1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ChemoSpec-package | Exploratory Chemometrics for Spectroscopy
aovPCA | ANOVA-PCA Analysis of Spectra Data
aovPCAloadings | Plot aovPCA Loadings of a Spectra Object
aovPCAscores | Conduct PCA and plot aovPCA Scores of a Spectra Object
avgFacLvls | Average levels of a factor in a data matrix
baselineSpec | Carry out baseline correction on a Spectra object
binBuck | Bin or Bucket a Spectra Object
binData | Bin or Bucket Data
calcSN | Calculate the signal-to-noise ratio of a peak in a spectrum.
check4Gaps | Check for Missing Values (Gaps)
ChemoSpec | Exploratory Chemometrics for Spectroscopy
chkSpectra | Verify the Integrity of a Spectra Object
classPCA | Classical PCA of Spectra Objects
clupaSpectra | Conduct Hierarchical Cluster-Based Peak Alignment on a Spectra Object
colLeaf | Color the Leaves of a Dendrogram
colorSymbol | Colors and Symbols in ChemoSpec and Spectra Objects
conColScheme | Change the Color Scheme of a Spectra Object
coordProjCS | Modified Version of coordProj from mclust
CuticleIR | IR Spectra of Plant Cuticles by Genotype and Treatment
evalClusters | Evaluate or Compare the Quality of Clusters Quantitatively
files2SpectraObject | Merge Files in a Directory into a Spectra Object
findTMS | Find the TMS/TSP Peak in an NMR Spectrum.
groupNcolor | Assign Group Membership and Colors for a Spectra Object
hcaScores | HCA on PCA scores from a Spectra Object
hcaSpectra | Plot HCA Results of a Spectra Object
hmapSpectra | Create a Seriated Heat Map Comparing Samples and Spectral Data for a Spectra Object
hypTestScores | Conduct MANOVA using PCA Scores and Factors in a Spectra Object
isWholeNo | Determine if a Number is a Whole Number
labelExtremes | Label Extreme Values in a 2D Data Set
labelExtremes3d | Identify Extreme Values in 3D
LoopThruSpectra | Display the spectra in a Spectra object one at a time
makeEllipsoid | Create Ellipsoid
mclust3D | mclust Analysis in 3D
mclust3dSpectra | mclust Analysis of a Spectra Object in 3D
mclustSpectra | mclust Analysis of a Spectra Object PCA Results
normSpectra | Normalize a Spectra Object
normVec | Normalize a Vector to range -1 to +1
pcaBoot | Cross-Validation of Classical PCA Results for a Spectra Object
pcaDiag | Outlier Diagnostic Plots for PCA of a Spectra Object
plot2Loadings | Plot PCA Loadings from a Spectra object Against Each Other
plotHCA | Plot Dendrogram for Spectra Object
plotLoadings | Plot PCA Loadings for a Spectra Object
plotScores | Plot PCA Scores of a Spectra Object
plotScores3D | 3D PCA Score Plot for a Spectra Object
plotScoresCor | Compute Confidence Ellipses
plotScoresDecoration | Decorate PCA Score Plot of a Spectra Object
plotScoresRGL | Interactive 3D Score Plot of a Spectra Object
plotScree | Scree Plots of PCA Results for a Spectra Object
plotScree2 | Scree Plots of PCA Results for a Spectra Object
plotSpectra | Plot Spectra Object
q2rPCA | Conversion Between PCA Classes
r2qPCA | Conversion Between PCA Classes
readBrukerAscii | Read and process a Bruker NMR spectrum saved using Topspin
readBrukerTxt | Read and process a Bruker NMR spectrum saved using Topspin
readJDX | Read and process a JCAMP-DX file.
removeFreq | Remove Frequencies from a Spectra Object
removeGroup | Remove Samples or Groups from a Spectra Object
removeSample | Remove Samples or Groups from a Spectra Object
robPCA | Robust PCA of a Spectra Object
rowDist | Compute Distance Between Rows of a Matrix
seX | Functions to Compute Measures of Central Tendency and Spread. seX!
seXy | Functions to Compute Measures of Central Tendency and Spread. seX!
seXy95 | Functions to Compute Measures of Central Tendency and Spread. seX!
seXyIqr | Functions to Compute Measures of Central Tendency and Spread. seX!
seXyMad | Functions to Compute Measures of Central Tendency and Spread. seX!
shrinkLeaf | Shrink the Leaves of a Dendrogram
specSurvey | Plot Measures of Central Tendency and Spread for a Spectra Object
Spectra | Spectra Objects
splitSpectraGroups | Create New Groups from an Existing Spectra Object
sPlotSpectra | s-Plot of Spectra Data Post PCA
SrE.IR | IR and NMR Spectra of Serenoa repens (Saw Palmetto) Oil Extracts and Reference Oils
SrE.NMR | IR and NMR Spectra of Serenoa repens (Saw Palmetto) Oil Extracts and Reference Oils
sumGroups | Summarize the Group Parameters of a Spectra Object
sumSpectra | Summarize a Spectra Object