[R-sig-phylo] annotating tree
Dear List, I have been annotating a target tree with support values from different analyses using the package phyloch. It works great except for the cutoff argument. I ran the examples and this argument also didn't work in them. Any idea how to make this argument work? Thanks in advance! Ricardo Ph.D. Program in Biology The City University of New York New York, NY 10016-4309 The Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies The New York Botanical Garden Bronx, NY 10458-5126 USA [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] annotating tree
Dear Ricardo, There was a line missing in the code; it is fixed now in version 1.4-80 of phyloch. Cheers, Christoph On Nov 8, 2012, at 12:58 PM, Ricardo Kriebel wrote: Dear List, I have been annotating a target tree with support values from different analyses using the package phyloch. It works great except for the cutoff argument. I ran the examples and this argument also didn't work in them. Any idea how to make this argument work? Thanks in advance! Ricardo Ph.D. Program in Biology The City University of New York New York, NY 10016-4309 The Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies The New York Botanical Garden Bronx, NY 10458-5126 USA [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] estimating mutation rate
Hi there, I have a well-supported phylogeny (with branch lengths proportional to absolute time) and I'm interested in estimating the mutation rate of an independently-obtained molecular dataset. Any suggestions? thanks! -john ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] estimating mutation rates
Hi there, I have a well-supported phylogeny (with branch lengths proportional to absolute time) and I'm interested in estimating the mutation rate of an independently-obtained molecular dataset. Any suggestions? thanks! John ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] estimating mutation rates
If you want the branch-specific substitution rate, you could estimate the branch lengths on a topology constrained to match the chronogram, then divide each of the molecular tree's branch lengths by the corresponding chronogram branch lengths to get these rates. If you want a global rate, you might constrain the molecular tree to have the same proportional branch lengths as the chronogram. Look at pml() in phangorn for calculating the likelihoods. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar: http://www.brianomeara.info/calendars/omeara On Thu, Nov 8, 2012 at 12:49 PM, john d dobzhan...@gmail.com wrote: Hi there, I have a well-supported phylogeny (with branch lengths proportional to absolute time) and I'm interested in estimating the mutation rate of an independently-obtained molecular dataset. Any suggestions? thanks! John ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] prop.clades() errors
All, I'm working on some analyses that require comparison of tree structures, and I've bumped into the problem David Bapst posted about back in March: http://www.mail-archive.com/r-sig-phylo@r-project.org/msg01840.html - briefly, prop.clades() is failing to count many clades that are in common. There doesn't seem to be any followup to that post; has anyone made progress figuring it out? I'm currently using ape 3.0-6 and R 2.15.1 on a MacBook running Mountain Lion. thanks, Jeremy Jeremy B. Yoder Postdoctoral Associate Department of Plant Biology University of Minnesota www.jeremybyoder.com (http://www.jeremybyoder.com) jbyo...@gmail.com Sent with Sparrow (http://www.sparrowmailapp.com/?sig) [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Ancestral Reconstruction Giving Identical Values
Hi,
I am attempting to estimate ancestral states using the following methods-
APE::ace, GEIGER::getancstates, as well as this method recommend by Liam Revell
for reconstructing under an OU model:
ou-fitContinuous(tree,data,model=OU)$Trait1
anc.mins-vector()
N-length(tree$tip)
M-tree$Nnode
outree-ouTree(tree,ou$alpha)
for(i in 1:M+N){
anc.mins[i-N]-ace(data,multi2di(root(outree,node=i)),method=pic)$ace[1]
names(anc.mins)[i-N]-i
}
Here are the parameter estimates for one of my traits:
$Lambda
lnl betalambda aic aicc k
1 -121.4771 31.33674 0.4057359 248.9541 250.2173 3
$OU
lnl beta alpha convergence
message k aic aicc
1 -120.7098 281.9509 0.08288029 0 CONVERGENCE: REL_REDUCTION_OF_F =
FACTR*EPSMCH 3 247.4196 248.6828
When I do not transform the tree (i.e. Brownian Motion), the values returned
seem valid. But when I transform the tree using either lambdaTree, ouTree. or
even the exponentialTree, all the values returned are almost identical and when
I plot them on the phylogeny, it is evident that they do not make sense in
regards to the tip values.
Any help on this would be greatly appreciated.
Thank you,
Zac
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