cv_pcaSpectra

This function carries out classical PCA on the data in a
<code>Spectra</code> object using a cross-validation method. A simple
re-write of Peter Filzmoser's <code>pcaCV</code> method
with some small plotting changes.

multivariate

A collection of functions for top-down exploratory data analysis
of spectral data including nuclear magnetic resonance (NMR), infrared (IR),
Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy.
Includes functions for plotting and inspecting spectra, peak alignment,
hierarchical cluster analysis (HCA), principal components analysis (PCA) and
model-based clustering. Robust methods appropriate for this type of
high-dimensional data are available. ChemoSpec is designed for structured
experiments, such as metabolomics investigations, where the samples fall into
treatment and control groups. Graphical output is formatted consistently for
publication quality plots. ChemoSpec is intended to be very user friendly and
to help you get usable results quickly. A vignette covering typical operations
is available.

Bryan Hanson

ChemoSpec

Exploratory Chemometrics for Spectroscopy

Bryan A. Hanson

Mike Bostock

Matt Keinsley

Tejasvi Gupta

cv_pcaSpectra function

<dl><dt>spectra</dt>
<dd>An object of S3 class <code>Spectra</code>.</dd>
<dt>pcs</dt>
<dd>As per <code>pcaCV</code> where it is called amax;
an integer giving the number of PC scores to include.</dd>
<dt>choice</dt>
<dd>A character string indicating the choice of scaling. One of
<code>c("noscale"</code>, <code>"autoscale"</code>, <code>"Pareto")</code>.</dd>
<dt>repl</dt>
<dd>As per <code>pcaCV</code>; the number of
replicates to perform.</dd>
<dt>segments</dt>
<dd>As per <code>pcaCV</code>.</dd>
<dt>segment.type</dt>
<dd>As per <code>pcaCV</code>.</dd>
<dt>length.seg</dt>
<dd>As per <code>pcaCV</code>.</dd>
<dt>trace</dt>
<dd>As per <code>pcaCV</code>.</dd>
<dt>...</dt>
<dd>Parameters to be passed to the plotting routines.</dd></dl>

Arguments

Bryan A. Hanson, DePauw University. Derived from <code>pcaCV</code>.

Author

Cross-Validation of Classical PCA Results for a Spectra Object — cv_pcaSpectra

<dl>

<dt>spectra</dt>
<dd>An object of S3 class <code>Spectra</code>.</dd>


<dt>pcs</dt>
<dd>As per <code>pcaCV</code> where it is called amax;
an integer giving the number of PC scores to include.</dd>


<dt>choice</dt>
<dd>A character string indicating the choice of scaling. One of
<code>c("noscale"</code>, <code>"autoscale"</code>, <code>"Pareto")</code>.</dd>


<dt>repl</dt>
<dd>As per <code>pcaCV</code>; the number of
replicates to perform.</dd>


<dt>segments</dt>
<dd>As per <code>pcaCV</code>.</dd>


<dt>segment.type</dt>
<dd>As per <code>pcaCV</code>.</dd>


<dt>length.seg</dt>
<dd>As per <code>pcaCV</code>.</dd>


<dt>trace</dt>
<dd>As per <code>pcaCV</code>.</dd>


<dt>...</dt>
<dd>Parameters to be passed to the plotting routines.</dd>

</dl>

cv_pcaSpectra: Cross-Validation of Classical PCA Results for a Spectra Object

Description

Usage

Value

Arguments

Author

References

See Also

Examples