drop.tip method for object of class "contMap"; and code to specify internal node values using contMap

A phytools user recently asked me if it is possible to specify the values at some or all internal nodes using the phytools function contMap.

Actually, upon further discussion, what it turns out that she really wanted to do is estimate ancestral states for a larger tree, and then supply those states to contMap.

In either case, it turns out, the easiest way to do this is by first writing a drop.tip method for an object of class "contMap". (I'm using method in the general, not S3 R sense). Then what we're going to do is attach our internal node values as leaves of zero length to internal nodes and run drop.tip.contMap to prune them.

First, this is our drop.tip.conMap function.

drop.tip.contMap<-function(x,tip){
    x$tree<-drop.tip.simmap(x$tree,tip)
    x
}

Now let's simulate some data & plot the simulated (rather than estimated) states at internal nodes.

library(phytools)
tree<-pbtree(n=26,tip.label=LETTERS[26:1])
x<-fastBM(tree,internal=TRUE)

Finally, let's see how we can use drop.tip.contMap to set values at internal nodes:

## all the nodes in our tree
nodes<-1:tree$Nnode+Ntip(tree)
tt<-tree
## go through all nodes & attach a zero-length leaf
## to each node
for(i in 1:length(nodes)){
    M<-matchNodes(tt,tree)
    ii<-M[which(M[,2]==nodes[i]),1]
    tt<-bind.tip(tt,nodes[i],edge.length=0,where=ii)
}
## here is our tree with zero-length edges
## normally we would turn off plotting
obj<-contMap(tt,x)

## now drop these tips
obj<-drop.tip.contMap(obj,as.character(nodes))
plot(obj)

This can, of course, be modified to set only some internal nodes.

Let's also try it with the practical case in which we have a nested subtree that we want to use for contMap, but we would like to use ancestral state estimates obtained for the full tree. This is even easier, because now we just use contMap on the full tree and then drop the tips not in our subtree of interest:

set.seed(7)
tree<-pbtree(n=50)
plotTree(tree,node.numbers=TRUE,fsize=0.8)

x<-fastBM(tree)
obj<-contMap(tree,x,plot=FALSE)
obj<-drop.tip.contMap(obj,
    setdiff(tree$tip.label,extract.clade(tree,77)$tip.label))
plot(obj)

That's all there is to it. I will add drop.tip.contMap to future versions of phytools.