Thanks Klaus! I could I've missed them!
Giulio Valentino Dalla Riva
Beaty Biodiversity Research Centre
University of British Columbia
Vancouver, Canada
From: Klaus Schliep <klaus.schl...@gmail.com>
Sent: January 6, 2017 2:34:49 PM
To: Giulio V. Dalla Riva
Dear Phyloers,
Has anybody already implemented a function to convert an igraph graph object
into a phylo object?
(Let's pretend we are in the best of the worlds and the graph object is indeed
a tree and all).
Best,
Giulio Valentino Dalla Riva
Beaty Biodiversity Research Centre
Dear Guangchuang,
Wouldn't that require that the distance between root and current time is, at
most, 0.05 (= 0.1 /2) ?
In that case, I believe you just need to rescale the tree you simulated. That
can be done in a number of way according to which package you use, e.g., in
phytool:
My 2cents on this.
TL;DR: there *may* be good information in the non ultrametric tree, which we
may *not* want to throw away lightheartedly.
Long version: A phylogenetic model variance-covariance matrix is not, in
general, the same thing of the pairwise phylogenetic distance matrix. They are
4869
From: Liam J. Revell <liam.rev...@umb.edu>
Sent: Wednesday, 6 January 2016 12:37 p.m.
To: Giulio V. Dalla Riva; r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] plot trees distribution
Hi Giulio.
You could try something like:
trees<-r
Dear all,
I'm trying to compute the evolutionary distinctiveness of the tips of a tree
```R
tre - collapse.singles(read.newick(tree.phy))
evol.distinct(tre)
```
and I'm getting this error:
```R
Error in while (!(edge %in% root.edge)) { : argument is of length zero
In addition: Warning
Dear Anna,
My first answer would be to insert the individuals in the phylogeny from the
beginning. But: how closely related do you expect the traits of individuals in
the same species to be? If you can't answer soundly to this question, my
approach would be not meaningful.
What PGLS need is a
