Re: [R-sig-phylo] Ultrametric tree not recognized

Hi Klaus, I will add an option 'method' to this function so that its definition will be: is.ultrametric(phy, tol = .Machine$double.eps^0.5, option = 1) option = 1 => using the criterion you suggested below option = 2 => using the current 'variance' criterion And other criteria could be

Re: [R-sig-phylo] Ultrametric tree not recognized

Hi Emmanuel, it wasn't so much about the precision, but that it is not invariant against linear transformation of the edge length. At the moment the criterion inside is.ultrametric is the following: var(xx[1:n]) where xx[1:n] is a vector with the tip-to-toot differences. And is.ultrametric

Re: [R-sig-phylo] Ultrametric tree not recognized

Comparing floating point numbers is (at least for me) pretty scary when you get down into it. Here are some more accessible treatments (although Goldberg’s paper seems to be the definitive treatment on the subject): What Every Programmer Should Know About Floating-Point Arithmetic:

Re: [R-sig-phylo] Ultrametric tree not recognized

We should consider to improve is.ultrametric to use as tolerance a certain number significant figures (e.g. 8-10 digits). This way tol would only depend on the tip-to-root distance and not a machine dependent minimal value. I find the use of significant figures suits really well as a stopping

Re: [R-sig-phylo] Ultrametric tree not recognized

Actually I did play around with different tol values and I could get is.ultrametric to recognize my tree. But, exactly as Joseph says, this doesn't really help. Anyway, Liam's suggestion solved the problem. Martin Am 16.08.2016 um 16:22 schrieb Joseph W. Brown: > That�s a good tip, but the

Re: [R-sig-phylo] Ultrametric tree not recognized

That’s a good tip, but the issue here is that many packages use is.ultrametric internally with a hard-coded (likely, default) value of tol. In this case, Martin simply cannot perform the analyses he wants to run because this option is inaccessible. JWB

Re: [R-sig-phylo] Ultrametric tree not recognized

Hello all, this may come be surprising to many, but consulting the manual ?is.ultrametric can be helpful. Why not simply try e.g. is.ultrametric(tree, tol=.01) So in this sense RTFM Regards, Klaus On Aug 16, 2016 9:31 AM, "Martin Dohrmann" wrote: > > Am

Re: [R-sig-phylo] Ultrametric tree not recognized

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

Re: [R-sig-phylo] Ultrametric tree not recognized

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

Re: [R-sig-phylo] Ultrametric tree not recognized

Thanks a lot, that did the trick! (the last line should read "is.ultrametric(nnls)" though) Best wishes, Martin Am 16.08.2016 um 14:53 schrieb Liam J. Revell: > Hi Martin. > > Since you are writing & reading trees to file, my guess is that it has to do > with numerical precision - that is,

Re: [R-sig-phylo] Ultrametric tree not recognized

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