Small speed-up for collapseTree plus some other fixes

I just posted a small update to the phytools function collapseTree (demonstrated here), an interactive tree plotted to collapse & expand subtrees.

The update speeds up the animation by calling graphics::points instead of plotrix::draw.circle. Since the 'animation' effect is achieved by each time redrawing the draw from scratch, this small difference seems to have an effect & makes the animation noticeable smoother (if still not perfectly smooth).

Update phytools from GitHub & try it:

library(phytools)
data(anoletree)
obj<-collapseTree(anoletree)

I also fixed some things with documentation & code of cophylo that triggered notes or warnings in Rcmd check.