Cody,
Have you taken care to scale your data so that they have approximately the
same means and variances? Sometimes numerical issues arise due to a
mismatch of scales? What are your variables? If you plot one against the
other, what do you see?
Regarding the interpretations: a good deal
Hi Aaron and Julien,
Thanks for the responses. I will try different methods for computing the
log-likelihood and will report back on the list (they take a while to
run...).
The traits are a continuous plumage ornamentation score for male and female
passerines. They way they are calculated is a
Hi Cody,
Maybe in your case you are rather interested in testing whether there is
significant interaction in the selection strength (i.e. you constrain the
alpha matrix but not the sigma matrix) than testing for significant
correlations between traits?
e.g.
mvOU(tree, data, model=OU1,
Hi Julien and Aaron,
Thank to you both for your suggestions.
Julien, yes I think that is more what I am interested in, but I was
(probably incorrectly) worried that an unconstrained sigma matrix might
scoop up some of the signal that is actually due to an interaction in
'selection', and would
Hi Cody,
I remember a similar discussion with Aaron some time ago. It seems difficult to
interpret negative eigenvalues in the multivariate Ornstein-Uhlenbeck process,
excepted maybe in some particular situations. Adaptation should result in
positive values. Krzysztof Bartoszek writes a bit on
Dear comparative phylogeneticists community,
The Phylogenetic Comparative Methods wiki at http://www.r-phylo.org/,
which is an outcome of the same venerable hackathon in 2007 that
resulted in the founding of this list, has been hosted by NESCent. As
you may be aware, NESCent is closing this
On 5/6/15, 4:56 PM, Hilmar Lapp wrote:
If we do not hear expressions of interest in transfer of hosting before
May 22 2015, then the wiki will have to be taken offline when NESCent
closes. An XML dump of the wiki contents will be placed in the NESCent
digital archive with Duke Libraries, but
Hi all,
I think the best solution would be to transfer the how-to material to
Wikibooks, which is run by the same people that run Wikipedia. The
current Phylogenetics book is pretty sparse. I'd be willing to take
some time to organize and transfer the text.
Hi!
I used phytools to perform a stochastic character mapping on a list of
phylogenetic trees (make.simmap function). Does phytools include a function
somehow analogous to the densiTree function of the R package phangorn that
allows superimposing in a single plot the graphical outputs of the
For a reduced dataset (~2500 species) comparing
M1-mvOU(tree, data, model=OU1, param=list(alpha=constraint,
sigma=constraint))
M2-mvOU(tree, data, model=OU1, param=list(decomp=symmetricPositive))
I got the following parameters (both successfully converged)
M1$AIC
33842.8
M1$alpha
fem
Josef - this is awesome. I tried it out. Very cool. I don't know if my
brain is able to parse the mixtures of colors along edges into
probabilities of being in each state, but nonetheless - super cool.
Marina - there is also a function in phytools that does this for a two
state character.
Marina,
I actually wrote a function to do this the other day. Hope it's helpful:
densiMap - function(simmap.trees, pal=rainbow, alpha=10, ...){
# Palette is the color palette to draw from, alpha is the
transparency of each plot. ... passed to plotSimmap.
states -
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