R: Classical PCA of Spectra Objects

c_pcaSpectra {ChemoSpec} | R Documentation

## Classical PCA of Spectra Objects

### Description

A wrapper which carries out classical PCA analysis on a `Spectra` object. The user can select various options for scaling. There is no normalization by rows - do this manually using `normSpectra`. There is an option to control centering, but this is mainly for compatibility with the `aov_pcaSpectra` series of functions. Centering the data should always be done in PCA and it is the default here.

### Usage

    c_pcaSpectra(spectra, choice = "noscale", cent = TRUE)

### Arguments

`spectra` | An object of S3 class `Spectra`.
`choice` | A character string indicating the choice of scaling. One of `c("noscale"`, `"autoscale"`, `"Pareto")`.
`cent` | Logical: whether or not to center the data. Always center the data unless you know it to be already centered.

### Details

The scale choice `autoscale` scales the columns by their standard deviation. `Pareto` scales by the square root of the standard deviation.

### Value

An object of class `prcomp`, modified to include a list element called `$method`, a character string describing the pre-processing carried out and the type of PCA performed (it appears on plots which you might make).

### Author(s)

Bryan A. Hanson, DePauw University.

### References

K. Varmuza and P. Filzmoser Introduction to Multivariate Statistical Analysis in Chemometrics, CRC Press, 2009.

https://github.com/bryanhanson/ChemoSpec

### See Also

`prcomp` for the underlying function, `r_pcaSpectra` for analogous robust PCA calculations.

For displaying the results, `plotScree`, `plotScores`, `plotLoadings`, `plot2Loadings`, `sPlotSpectra`, `plotScores3D`, `plotScoresRGL`.

### Examples

    data(metMUD1)
    pca <- c_pcaSpectra(metMUD1)
    plotScores(metMUD1, pca, main = "metMUD1 NMR Data",
    	 pcs = c(1,2), ellipse = "cls", tol = 0.05)

[Package ChemoSpec version 4.4.97 Index]