R: Outlier Diagnostic Plots for PCA of a Spectra Object

pcaDiag {ChemoSpec} | R Documentation

## Outlier Diagnostic Plots for PCA of a Spectra Object

### Description

A function to carry diagnostics on the PCA results for a `Spectra` object. Basically a wrapper to Filzmoser's `pcaDiagplot` which colors everything according to the scheme stored in the `Spectra` object. Works with PCA results of either class `prcomp` or class `princomp`. Works with either classical or robust PCA results.

### Usage

    pcaDiag(spectra, pca, pcs = 3, quantile = 0.975, plot = c("OD", "SD"),
      use.sym = FALSE, ...)

### Arguments

`spectra` | An object of S3 class `Spectra`.
`pca` | An object of class `prcomp` or `prcomp`, modified to include a character string (`$method`) describing the pre-processing carried out and the type of PCA performed.
`pcs` | As per `pcaDiagplot`. The number of principal components to include.
`quantile` | As per `pcaDiagplot`. The significance criteria to use as a cutoff.
`plot` | A character string, indicating whether to plot the score distances or orthogonal distances, or both. Options are `c("OD", "SD")`.
`use.sym` | logical; if true, the color scheme is change to black and symbols are used for plotting.
`...` | Additional parameters to be passed to the plotting functions.

### Details

If both plots are desired, the output should be directed to a file rather than the screen. Otherwise, the 2nd plot overwrites the 1st in the active graphics window. Alternatively, just call the function twice, once specifying `OD` and once specifying `SD`.

### Value

A list is returned as described in `pcaDiagplot`, so the result must be assigned or it will appear at the console. Side effect is a plot.

### 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

`pcaDiagplot` in package `chemometrics` for the underlying function.

### Examples

    data(SrE.IR)
    res <- c_pcaSpectra(SrE.IR, choice = "noscale")
    temp <- pcaDiag(SrE.IR, res, pcs = 2, plot = "OD")
    temp <- pcaDiag(SrE.IR, res, pcs = 2, plot = "SD")

[Package ChemoSpec version 4.4.97 Index]