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 localities 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, Sincerely, Alexandre library(recluster) arvore.upgma = recluster.cons(sp, dist = "simpson", method = "average", p=0.5)$cons dendro.upgma = as.hclust.phylo(arvore.upgma) plot(dendro.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 lattes: lattes.cnpq.br/7844758818522706 http://www.docente.ufrn.br/alexsouza [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
