Unless it does something internally already, you might need to do something
like: options(digits=10) before running the node.depth.edgelength(tree) to
identify your problem.
Yes, I wasn't referring to branching.times. I was talking about various
methods, e.g., BAMM, that don't perform well (or at
Interesting, Rafael. Perhaps it is just barely within tolerance for
force.ultrametric, but not within the zone to avoid issues with
branching.times?
What did
node.depth.edgelength(tree)
return? That should give us an idea how far each tip is from the root.
As a note, Eliot, I don't think I've s
Hi Elliot et al,
Thanks for all the helpful answers, and sorry for my delay in getting back.
min(tree$edge.length) returns a nonzero positive number, but running
force.ultrametric on the tr did not cause that warning message to go away...
*--*
*Rafael Sobral Marcondes*
PhD Candidate (Systematics
I suggest calling min(tree$edge.length) on any tree you plan to use for
comparative methods, including the one you're having trouble with Rafael.
If you get a negative value, then something is really funny and you need to
solve it. If you get a zero then various comparative methods will throw
error
Just to clarify, force.ultrametric is not a formal rate-smoothing method
or anything like that. It is intended only for use to resolve numerical
precision issues such as the one raised in this thread.
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor A
I'll just add that it is always a really good idea to view the trees you
(think you) are using, not just rely on the variance-covariance matrices
derived from them and used in PGLS analyses, etc. Several times when I was
compiling trees and data from the literature authors sent me tree files
(e.g.
I haven't been closing following this thread, so I'm not sure that this
is relevant - but phytools has a function called 'force.ultrametric' (I
believe) that does precisely what its name suggests it might.
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profe
Hmm. I hope that isn't the case - branching.times() is used pretty
widely in ape-dependent packages for getting node ages from dated
ultrametric trees, and if such minimally non-ultrametric trees can
cause branching.times throw negative node ages, then I'm really
concerned what impact that might ha
On Wed, May 2, 2018 at 2:53 PM, David Bapst wrote:
> Given that your tree appears to be non-ultrametric enough to cause
> branching.times to throw some nonsensical node ages, if it is supposed
> to be ultrametric. I recommend checking it carefully to figure out why
> the tips seem to not quite be
Hi Rafael,
I found the source of the error, I think, and filed an issue at github
on the OUwie repo. There are issues with how the code in OUwie handles
non-ultrametric trees if a root.age isn't given by the user, causing
problems for the paleotree function dateNodes, and your tree is
apparently n
Rafael,
That error message is from paleotree's dateNodes function, which is
called as part of OUwie's approach to getting node dates. I think I
see what Elliot is trying to get at, but this might be quicker:
node.depth.edgelength(tree)
That should tell us how far each node, including the tips, a
What does: min(tree$edge.length) say?
Eliot
On Wed, May 2, 2018 at 2:22 PM, Rafael S Marcondes
wrote:
> Here's a little more info that may be relevant: the tree is not supposed to
> have negative dates. Although when I do is.ultrametric(tr) I get FALSE, I
> have always been just ascribing that
Here's a little more info that may be relevant: the tree is not supposed to
have negative dates. Although when I do is.ultrametric(tr) I get FALSE, I
have always been just ascribing that to lack of precision, in part because
it has never been a problem with OUwie().
*--*
*Rafael Sobral Marcondes*
Hi all,
I need some help with a warning message I've been getting when running
parametric bootstrapping in OUwie.
>OUwie.boot(nboot=1, simmap.tree=F...)
Beginning parametric bootstrap -- performing 1 replicates
Warning: Some dates are negative? rootAge may be incorrectly defined or you
are using
14 matches
Mail list logo