R: ape/phylobase: unable to convert ultrametric, binary tree to hclust object (warning message)

Question

I've imported a ClustalW2 tree in R using the ape function and read.tree function of the ape package. I estimate molecular ages using the chronopl function, resulting in a ultrametric, binary tree. From which I want to create a R build in dendrogram object.

The tree plots fine, and is a real phylo object. However i'm running into problems when trying to convert it:

Minimal Working Example:

require(ape)
test.tree <- read.tree(file = "testree.phylip", text = NULL, tree.names = NULL, skip = 0,
    comment.char = "#", keep.multi = FALSE)

test.tree.nu <- chronopl(test.tree, 0, age.min = 1, age.max = NULL,
node = "root", S = 1, tol = 1e-8,
CV = FALSE, eval.max = 500, iter.max = 500)

is.ultrametric(test.tree.nu)
is.binary.tree(test.tree.nu)
treeclust <- as.hclust.phylo(test.tree.nu)

The resulting tree "looks" fine, I test to make sure the tree is not ultrametric and binary, and want to convert it into a hclust object, to make eventually a dendrogram object of it.

> is.binary.tree(test.tree.nu)
[1] TRUE
> is.ultrametric(test.tree.nu)
[1] TRUE

After trying to make a hclust object out of the tree, I get an error:

> tree.phylo <- as.hclust.phylo(test.tree.nu)
Error in if (tmp <= n) -tmp else nm[tmp] : 
  missing value where TRUE/FALSE needed
In addition: Warning message:
In nm[inode] <- 1:N :
  number of items to replace is not a multiple of replacement length

I realize this is a very detailed question, and perhaps such questions which are specifically related to certain packages are better asked somewhere else, but I hope someone is able to help me.

All help is much appreciated,

Regards,

File download

The Phylip file can be downloaded here http://www.box.net/shared/rnbdk973ja

Answer 1

I can reproduce this with version 2.6-2 of ape under R 2.12.1 beta (2010-12-07 r53808) on Linux, but your code works in version 2.5-3 of ape.

This would suggest a bug has crept into the package and you should inform the developers of the problem to ask for expert advice. The email address of the maintainer, Emmanuel Paradis, is on the CRAN package for ape

Answer 2

looks like the problem is that chronopl returns a tree which is either unrooted, or has a multifurcating root (depending on how it's interpreted). Also as.hclust.phylo has/had unhelpful error messages.

This:

modded.tree <- drop.tip(test.tree.nu,c(
'An16g06590','An02g12505','An11g00390','An14g01130'))

removes all tips from one of the three clades descending from the root, thus

is.ultrametric(modded.tree)
is.binary.tree(modded.tree)
is.rooted(modded.tree)

all return TRUE, and you can do

treeclust <- as.hclust.phylo(modded.tree)

. Though I think you really want an hclust object representing the multifurcating tree, and though hclust objects can handle those, as.hclust.phylo (from package 'ape') doesn't work on multifurcations for some reason. If you know a way to import newick files into hclust objects, that might be a way forward - ade has write.tree() to generate newick files.