Am 16.08.2016 um 15:20 schrieb Joseph W. Brown:
I agree that it is almost certainly numerical precision, as rescaling
the tree fixes things:
is.ultrametric(phy);
[1] FALSE
fie <- phy;
fie$edge.length <- fie$edge.length * 0.1;
is.ultrametric(fie);
[1] TRUE
I’ve also tested the ultrametricity(?) with a non-R program and the
results are the same. So can we assume this is not a PhyloBayes issue, and
rather an unavoidable problem with large, old trees? But the fact that
MrBayes trees are ultrametric is confusing; does MrBayes use less precise
edge lengths?
Actually the MrBayes branch lengths appear to be MORE precise.
Martin
On 16 Aug, 2016, at 08:53, Liam J. Revell <liam.rev...@umb.edu> wrote:
Hi Martin.
Since you are writing & reading trees to file, my guess is that it has
to do with numerical precision - that is, the rounding of your edge lengths
when they are written to file.
Does your tree look ultrametric when plotted in R? If so, this is
probably the case.
My recommendation is that you use phangorn to compute the non-negative
least-squares edge lengths with the condition that the tree is ultrametric.
This will give you the edge lengths that result in the distances between
taxa with minimum sum of squared differences from the distances implied by
your input tree, under the criterion that the resulting tree is ultrametric.
To do this you need to merely run:
library(phytools)
library(phangorn)
is.ultrametric(tree) ## fails
plotTree(tree,ftype="off") ## does my tree look ultrametric?
nnls<-nnls.tree(cophenetic(tree),tree,rooted=TRUE)
is.ultrametric(tree) ## should pass
Let us know if this works. All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 8/16/2016 6:41 AM, Martin Dohrmann wrote:
Hi,
I want to do some diversification pattern analyses with various R
packages. I'm using a time-calibrated tree produced by PhyloBayes. Branch
lengths are in millions of years and all taxa are extant, so the tree
should be ultrametric. However, when I call "is.ultrametric", it returns
"FALSE".
Has anybody encountered something like this? Any ideas about what's
going on/how to solve this?
Some further information:
I also tried other PhyloBayes time trees, with the same result. In
contrast, MrBayes time trees I tried for comparison are recognized as
ultrametric. Regarding my diversification analyses, TESS would not run,
telling me "The likelihood function is only defined for ultrametric
trees!". On the other hand, BAMMtools doesn't seem to have a problem with
my tree. I haven't tried other packages yet, but I suspect RPANDA, TreePar
etc. might also have issues if they don't recognize my tree as ultrametric.
I'd appreciate any help!
Best wishes,
Martin
Dr. Martin Dohrmann
Ludwig-Maximilians-University Munich
Dept. of Earth & Environmental Sciences
Palaeontology & Geobiology
Molecular Geo- & Palaeobiology Lab
Richard-Wagner-Str. 10
80333 Munich, Germany
Phone: +49-(0)89-2180-6593
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Dr. Martin Dohrmann
Ludwig-Maximilians-University Munich
Dept. of Earth & Environmental Sciences
Palaeontology & Geobiology
Molecular Geo- & Palaeobiology Lab
Richard-Wagner-Str. 10
80333 Munich, Germany
Phone: +49-(0)89-2180-6593
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