Adding a tip at random to a pre-specified clade

Today a user asked how to add a tip randomly within a pre-specified clade.

There is a function that does this in phytools called add.genus.to.species; however, this is hardwired to automatically detect the genus of the tip to be added and the corresponding clade to which it should be attached. Consequently, I thought it would be easier to demonstrate how this can be done using splitTree, add.random, and paste.tree.

Here's an example.

First, our tree.

library(phytools)
plotTree(tree)
nodelabels()

Imagine we want to bind our tip randomly from the clade descended from the node number 45.

(Remember that we can select our node interactively using the function getnode.)

node<-45
tt<-splitTree(tree,split=list(node=node,
    bp=tree$edge.length[which(tree$edge[,2]==node)]))
tt[[2]]<-add.random(tt[[2]],tips="tip to add")
new.tree<-paste.tree(tt[[1]],tt[[2]])
plotTree(new.tree)

Let's repeat this a bunch of times:

foo<-function(tree,node){
    tt<-splitTree(tree,split=list(node=node,
        bp=tree$edge.length[which(tree$edge[,2]==node)]))
    tt[[2]]<-add.random(tt[[2]],tips="tip to add")
    paste.tree(tt[[1]],tt[[2]])
}
new.trees<-replicate(9,foo(tree,node),simplify=FALSE)
class(new.trees)<-"multiPhylo"

We can visualize the result (keeping in mind that the CA of our clade is now node 46, not 45, when we color the clade).

par(mfrow=c(3,3))
nulo<-sapply(new.trees,function(x) plot(paintSubTree(x,45,"2"),
    colors=setNames(c("black","blue"),1:2),fsize=0.6))

That's it.

The tree for this example was simulated as follows:

tree<-pbtree(n=26,tip.label=LETTERS)