Dear friends,

I used the recluster package to obtain a consensus tree that reflects a
hierarchical cluster of tree species presence and absence from ca 300
distributed through northern Brazil (see code below).

However, I am having a hard time to cut the tree and obtain the resulting
groups. The usual way I do that with simple trees generated by the hclust
package, for instance, is to use the cutree funcion, which yields the group
affiliation of each of the localities.

cutree is also used in a code that calculates the silhouette statistics
used to decide the best number of groups.

However, I can't use cutree with the consensus tree generated by
recluster.cons because it is a phylo and not a hclust class object, and
does not have a merge property.

I have tried the functions as.hclust and as.hclust.phylo, but these
generated messed up trees with no order.

Do you know how to cut a phylo tree and obtain the identities of the
objects included in the resulting groups? Or is it possible to convert a
phylo tree into a hclust one?

Thank you very much for any help,



arvore.upgma = recluster.cons(sp, dist = "simpson", method = "average",
dendro.upgma = as.hclust.phylo(arvore.upgma)

The resulting tree is a total mess!

Dr. Alexandre F. Souza
Professor Adjunto III
Universidade Federal do Rio Grande do Norte
CB, Departamento de Ecologia
Campus Universitário - Lagoa Nova
59072-970 - Natal, RN - Brasil

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