Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi Santiago. This is identical to my suggestion, except that the pooled variance is a weighted mean in which weights (for better or worse) are proportional to the sample size of each species. If the variances are indeed homogeneous, this should be preferred because it gives greater weight to

Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi Rafael, Your method would underestimate the error associated with values derived from single specimens because those values would have the highest errors, not average errors. What I have done in such cases is to estimate an average standard deviation across species and use that average

Re: [R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi Rafael. What I would recommend in the case where you have relatively small samples per species is to compute a pooled within-species variance (https://en.wikipedia.org/wiki/Pooled_variance). This is effectively equivalent to assuming that the within-species variances are relatively

[R-sig-phylo] Measurement error for tips with only 1 measured specimen (OUwie)

Hi all, I’m using OUwie to fit multi-optima OU models and I have a question about incorporating measurement error into my analyses. I’m running my models with known measurement error (mserr=‘known’) and using the standard error (std.error()) as an estimate of it, as recommended by Ives et al

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

[R-sig-phylo] How to contribute?

Hi everyone, I would like to try to contribute to ape. Where can I find how to do so? Sure, I've searched the ape homepage ( ) and checked if Emmanuel Paradis has a GitHub hosting the ape code (as he does with pegas), but I could not find a place where the code is