Hello, 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 = "G:/ape/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.ultrametrictest.tree.nu) is.binary.treetest.tree.nu) treeclust <- as.hclust.phylo(tree.phylo)
The resulting tree "looks" fine, I test to make sure the tree is ultrametric and binary, and want to convert it into a hclust object, to make eventually a dendrogram object of it.
> is.binary.treetest.tree.nu)  TRUE > is.ultrametrictest.tree.nu)  TRUE
After trying to make a hclust object out of the tree, I get an error:
> tree.phylo <- as.hclust.phylotest.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,
File download The Phylip file can be downloaded here