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
De
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 t
Hey David,
I installed and it is working perfectly! Tried with a couple of big trees
and worked well and fast!
Thank all of you for the help!
Best,
*Gustavo Burin Ferreira, **Msc.*
Instituto de Biociências
Universidade de São Paulo
Tel: (11) 98525-8948
On Wed, Oct 21, 2015 at 2:43 AM, David Ba
Gustavo, all,
I just wanted to let you know that I've integrated Klaus's suggestions
into timeSliceTree, as well as a growing number of additional
functions in paleotree, and these changes are in the current build on
github, which appears to pass all checks as of the moment.
You can install the i
Thanks, Klaus. I was unaware of node.depth.edgelength; I believe I use
dist.nodes to calculate root-to-tip distances in a number of functions
in paleotree, so this could mean improvement potentially to a large
number of functions. I'll have to do a global search for dist.nodes.
Cheers,
-Dave
On T
That's fine with me.
On Tue, Oct 20, 2015 at 3:29 PM, David Bapst wrote:
> Ah, thanks, Klaus! I was is it alright with you if I merge these edits
> into paleotree?
> -Dave
>
> On Tue, Oct 20, 2015 at 1:15 PM, Klaus Schliep
> wrote:
> > Hi Gustavo & David,
> >
> > I attached a file that contains
Hi Gustavo & David,
a tiny improvement I missed another sapply.
You can do the same trick replacing dist.nodes in dropExtinct if needed.
Klaus
On Tue, Oct 20, 2015 at 3:21 PM, Gustavo Burin Ferreira wrote:
> Hi Klaus,
>
> the function works perfectly! Thank you very much!
>
> Best,
>
> *Gustavo
Ah, thanks, Klaus! I was is it alright with you if I merge these edits
into paleotree?
-Dave
On Tue, Oct 20, 2015 at 1:15 PM, Klaus Schliep wrote:
> Hi Gustavo & David,
>
> I attached a file that contains a function timeSliceTree2, which is a
> replacement for timeSliceTree.
> I replaced
> dist.n
Hi Klaus,
the function works perfectly! Thank you very much!
Best,
*Gustavo Burin Ferreira, **Msc.*
Instituto de Biociências
Universidade de São Paulo
Tel: (11) 98525-8948
On Tue, Oct 20, 2015 at 5:15 PM, Klaus Schliep
wrote:
> Hi Gustavo & David,
>
> I attached a file that contains a functio
Hi Gustavo & David,
I attached a file that contains a function timeSliceTree2, which is a
replacement for timeSliceTree.
I replaced
dist.nodes(tree)[, Ntip(tree) + 1]
with
node.depth.edgelength(tree)
dist.nodes computes a matrix (roughly nTips^2 * 4 * 8 bytes which can get
very large for many taxa
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 running
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 tre
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 solutio
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