Hi all,
As a side note to this discussion: ape has now the function
compute.brtime (though it considers only node ages), available on ape's
SVN in R/compute.brtime.R.
Cheers,
Emmanuel
Scott Chamberlain wrote on 14/07/2011 11:15:
Hi Roger,
Can you provide a reproducible example (perhaps a
On 7/14/11 2:45 AM, ppi...@uniroma3.it wrote:
> Thankyou NIck,
> now...I have an error when running it:
>
Oops. Apologies, this stuff is in-house code, I haven't
organized it. Add these to the text file...
===
get_daughters <- function(nodenum, t)
{
daughter_edgenums
The independent contrasts algebra for what Joe is talking about can be found in
these papers:
Garland, T., Jr., P. E. Midford, and A. R. Ives. 1999. An introduction to
phylogenetically based statistical methods, with a new method for confidence
intervals on ancestral values. American Zoologist
Paolo Piras wrote --
Citing
http://www.r-phylo.org/wiki/HowTo/Ancestral_State_Reconstruction:
Using Felsenstein's (1985) phylogenetic independent
contrasts (pic); This is also a Brownian-motion based
estimator, but it only takes descendants of each node
into account in reconstructing the state
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
Hi all,
Citing
http://www.r-phylo.org/wiki/HowTo/Ancestral_State_Reconstruction:
Using Felsenstein's (1985) phylogenetic independent
contrasts (pic); This is also a Brownian-motion based
estimator, but it only takes descendants of each node
into account in reconstructing the state at that node.
Mo
