Hi Belinda,
I agree with Brian�s comment. I�d also add the more general point that OU
models don�t really have a clearly interpretable rate parameter in the same way
that BM models do. In BM models, the sigma parameter controls the pace of
trait evolution: the expected change over a given tim
Small follow-up to Liam's suggestion: If you do use an arcsin transformation
for proportional data, the variance of arcsin(sqrt(p)) is approximately 1/(4N),
where p is the proportion and N is sample size. The approximation is good
unless the proportion is very close to 0 or 1.
Best,
Gene
--
The Blomberg et al (2003) randomization test is implemented in the picante
package, with the function phylosignal(). It may be implemented elsewhere
as well.
Best,
Gene
--
Gene Hunt
Curator, Department of Paleobiology
National Museum of Natural History
Smithsonian Institution [NHB, MRC 121]
P.O
Also, the issue of predicting values for unknown tips using data from other
species in the tree is considered in this reference:
Garland, T., and A. R. Ives. 2000. Using the past to predict the present:
confidence intervals for regression equations in phylogenetic comparative
methods. American
Roger,
If you like, go ahead and send me off-list your code and tree file. The
function does not do a lot of error checking, so it is probably hanging on tip
or node names; an incorrect tree structure can flummox it, too. If it is
working ,it shouldn't take more than a few seconds.
Best,
Gen
Alejandro,
Yes, the estimates of beta are reasonable as measures of the rate of evolution,
but they are in the same units of the trait you are analyzing (squared). So,
raw estimates are comparable only if the traits and their units are comparable.
This reasonable for multiple log-transformed
Hi Andy,
Brian Sidlauskas did this in an Evolution paper in 2008 (based on Yang and
Rannala 1997):
Sidlauskas, Brian L. 2008. Continuous and arrested morphological
diversification in sister clades of characiform fishes: a phylomorphospace
approach. Evolution 62(12): 3135-3156.
He had a morpho
Scott,
I have written a function to transform branch lengths on a tree according to
age constraints in the terminal taxa and (optionally) the nodes (attached). If
your phylo object is tr, the command
scalePhylo(tr, tip.ages, node.mins)
will return a phylo object with new branch lengths scaled
Hi,
To Liam's extremely helpful and practical reply, I'd add that one can also use
theory to generate tip data for a trend. For a given tree, all tip values can
be considered a single draw from a multivariate normal distribution, with each
dimension representing a tip taxon. For this MVN, the
