Hi Nick, it might be useful to plot the node labels on the tree:
plot(tree, label.offset = .25) tiplabels() nodelabels() Regards, Klaus On Tue, Sep 7, 2021 at 4:56 AM Emmanuel Paradis <emmanuel.para...@ird.fr> wrote: > Hi, > > A tree has n terminal nodes (aka tips) and m internal nodes (aka nodes > simply). In the edge matrix, the tips are numbered 1:n and the nodes are > numbered (n+1):(n+m) (same than n+1:m). n and m can be found with: > > n <- Ntip(tree) # or length(tree$tip.label) > m <- Nnode(tree) # or tree$Nnode > > Details can be found in: > > http://ape-package.ird.fr/misc/FormatTreeR.pdf > > Best, > > Emmanuel > > ----- Le 5 Sep 21, à 21:07, Nick Youngblut nyoun...@gmail.com a écrit : > > For `ape::dist.nodes()`, how can one match the output matrix > rows/columns with > > the node IDs in the tree (eg., the tip.labels)? I cannot just use > > `ape::cophenetic()` in my particular situation. The docs for > > `ape::dist.nodes()` state: > > > > ``` > > … in the case of dist.nodes, the numbers of the tips and the nodes (as > given by > > the element edge). > > ``` > > > > … but tree$edge doesn’t provide any direct info about which nodes are > internal > > vs external and how the external tip labels map to the tree$edge matrix. > > > > Thanks, > > Nick > > _______________________________________________ > > 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/ > > _______________________________________________ > 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/ > -- Klaus Schliep Senior Scientist Institute of Computational Biotechnology TU Graz https://icbt.tugraz.at https://www.phangorn.org/ <http://www.phangorn.org/> [[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/
