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
wrote:
> Hi,
>
> A tree has n terminal nodes (aka tips) and m internal nodes (aka nodes
> simply). In the
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
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
Hey David and Nick,
thanks a lot for the quick responses! I think I wasn't very clear in the
first e-mail. What I get is actually an error from within dist.nodes, not
when calling it.
I've tried to use chainsaw2 and in the beginning it appeared to be working
quite well. However after some
Hi Gustavo,
I'm paleotree's author and maintainer. Just to be clear that I
understand your problem, I believe you are saying that when you use
timeSliceTree, you are getting an error that the internal call to
dist.nodes is failing? Is that right?
The first thought I have is that maybe the
Hi! I re-did chainsaw at some point, now there is chainsaw2. However,
googling that gets you horror movies, so here is a link with example code:
https://groups.google.com/d/msg/biogeobears/Jy9uYckOL7s/XuNZ0B3jAwAJ
(the discussion there points out a rare case where this crashes, but for
most
