# Exploratory Chemometrics for Spectroscopy

## Documentation for package ‘ChemoSpec’ version 4.3.17

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

## Help Pages

ChemoSpec-package | Exploratory Chemometrics for Spectroscopy
alignMUD | Made Up NMR Data Sets
aovPCAloadings | Plot aovPCAscores Loadings of a Spectra Object
aovPCAscores | Plot ANOVA-PCA Scores from a Spectra Object
aov_pcaSpectra | ANOVA-PCA Analysis of Spectra Data
avgFacLvls | Average Levels of a Factor in a Data Matrix
baselineSpectra | Baseline Correction of a Spectra Object
binData | Bin or Bucket Data
binSpectra | Bin or Bucket a Spectra Object
check4Gaps | Check for Missing Values (Gaps)
ChemoSpec | Exploratory Chemometrics for Spectroscopy
chkSpectra | Verify the Integrity of a Spectra Object
clupaSpectra | Conduct Hierarchical Cluster-Based Peak Alignment on a Spectra Object
colLeaf | Color the Leaves of a Dendrogram Based on a Spectra Object
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
cv_pcaSpectra | Cross-Validation of Classical PCA Results for a Spectra Object
c_pcaSpectra | Classical PCA of Spectra Objects
evalClusters | Evaluate or Compare the Quality of Clusters Quantitatively
files2SpectraObject | Merge Files in a Directory into a Spectra Object
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
metMUD1 | Made Up NMR Data Sets
metMUD2 | Made Up NMR Data Sets
normSpectra | Normalize a Spectra Object
normVec | Normalize a Vector to range -1 to +1
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
plotSpectraDist | Plot the Distance Between Spectra in a Spectra Object
plotSpectraJS | Plot a Spectra Object Interactively
q2rPCA | Conversion Between PCA Classes
r2qPCA | Conversion Between PCA Classes
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
rowDist | Compute Distance Between Rows of a Matrix
r_pcaSpectra | Robust PCA of a Spectra Object
sampleDistSpectra | Compute the Distance Between Samples in a Spectra Object
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!
sgfSpectra | Apply Savitzky-Golay filters to a Spectra object
shrinkLeaf | Shrink the Leaves of a Dendrogram Based on 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
surveySpectra | Plot Measures of Central Tendency and Spread for a Spectra Object
surveySpectra2 | Plot Measures of Central Tendency and Spread for a Spectra Object