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
Sent: January 6, 2017 2:34:49 PM
To: Giulio V. Dalla Riva
Cc: r-sig-phylo@r-projec
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
University
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:
pbtree(n=1
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
4 2987 ext 4869
From: Liam J. Revell
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<-read.nexus("Way
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 mes
P.S. Rumbling on that: a proper answer, however, in a phylogenetic scenario
would also require to try and estimate the evolution of the intralineage trait
variance (an ancestral state reconstruction of the trait mean and variance) as
the hypothesis that it has been constant during long times see
Well, I have the gut that depends also on the adopted units of measure for the
different traits. That is: having only averaged species data, is 1cm of
wingspan increase a greater change than 1kg of bodymass increase?
A solution would be to compare on each tip the inferred traits directional
cha
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
