prcomp.phylog: Principal Components Analysis from Simulated Data Sets
In rdiaz02/PHYLOGR: Functions for Phylogenetically Based Statistical Analyses

Description Usage Arguments Value Author(s) References See Also Examples

Performs a principal component analyses on a set of simulated data and return the eigenvalues.

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## S3 method for class 'phylog'
prcomp(x, max.num=0, exclude.tips=NULL, lapply.size=100,
              center=TRUE, scale=TRUE, ...)

`x`	the columns from a data set returned from read.sim.data that you want to use in the PCA. The first column MUST be sim.counter and the second Tips.
`max.num`	if different from 0, the maximum number of simulations to analyze.
`exclude.tips`	an optional vector giving the names of tips to exclude from the analyses.
`lapply.size`	a tuning parameter that can affect the speed of calculations; see Details in phylog.lm.
`center`	should the data be centered before analyses? defaults to yes; see prcomp.
`scale`	should the data be scaled before the analyses? defaults to yes; see prcomp.
`...`	Not used.

A list (of class phylog.prcomp) with components

`call`	the call to the function
`Eigenvalues`	all the eigenvalues from the PCA. The one with sim.counter=0 corresponds to the original (”real”) data.

Ramon Diaz-Uriarte and Theodore Garland, Jr.

Diaz-Uriarte, R., and Garland, T., Jr., in prep. PHYLOGR: an R package for the analysis of comparative data via Monte Carlo simulations and generalized least squares approaches.

Krzanowski, W. J. (1990) Principles of multivariate analysis Oxford University Press.

Morrison, D. F. (1990) Multivariate statistcal methods, 3rd ed. McGraw-Hill.

read.sim.data, summary.phylog.prcomp

data(SimulExample)
ex1.prcomp <- prcomp.phylog(SimulExample[,-11]) # 11th col. is a factor
options(digits=5)
ex1.prcomp
summary(ex1.prcomp)
plot(ex1.prcomp)