S3 methods for phyl.pca

This morning Joan Maspons kindly supplied code for several S3 methods that can be used with the phytools function phyl.pca to return results via print, summary, and biplot that are similar to the equivalent S3 methods for objects of class prcomp. After a few minor tweaks (source code here) I have added these methods to the phytools package. The object returned by phyl.pca is in no way changed (it's merely been assigned the class attribute "phyl.pca"), so any prior functions designed to work with phyl.pca should still function. The updates are in a new minor phytools release phytools 0.3-74.

Here's a quick demo:

> library(phytools)
Loading required package: ape
Loading required package: maps
Loading required package: rgl
> packageVersion("phytools")
[1] ‘0.3.74’
> ## simulate tree
> tree<-pbtree(n=26,scale=1,tip.label=LETTERS)
> ## simulate data
> X<-fastBM(tree,nsim=4)
> ## phylogenetic PCA
> pca<-phyl.pca(tree,X,mode="cov")
> ## S3 print method
> pca
Phylogenetic pca
Starndard deviations:
      PC1       PC2       PC3       PC4
1.1851495 1.1200792 0.9641014 0.4812711
Loads:
            PC1        PC2         PC3        PC4
[1,] -0.1915766  0.9282404  0.15015897 -0.2812837
[2,]  0.9346040 -0.2431641 -0.03290792 -0.2574947
[3,]  0.4657425  0.5602278 -0.65456104  0.2019371
[4,]  0.5296652  0.3231947  0.74759143  0.2368691
> summary(pca)
Importance of components:
                         PC1   PC2   PC3   PC4
Standard deviation     1.185 1.120 0.964 0.481
Proportion of Variance 0.368 0.328 0.243 0.060
Cumulative Proportion  0.368 0.696 0.939 1.000
> biplot(pca)