Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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 &

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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,

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

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

[R-sig-phylo] Problem with negative ages in OUwie.boot?

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