[R-sig-phylo] Hillis & Huelsenbeck 1992 g1 test?

Hi all, has anyone implemented Hillis and Huelsenbeck’s g1 test for phylogenetic signal? ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at

Re: [R-sig-phylo] Easiest way to get the stem age of a clade?

: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 2/13/2014 12:16 AM, Simon Greenhill wrote: Hi all, What's the easiest way to get the stem age of a given clade of a tree? Many thanks, Simon

[R-sig-phylo] Easiest way to get the stem age of a clade?

Hi all, What's the easiest way to get the stem age of a given clade of a tree? Many thanks, Simon ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at

[R-sig-phylo] Lineages Through Time Plot with Confidence / HPD Interval

Hi all, Does anyone know of a good implementation of an LTT plot that can draw a Confidence Interval or HPD interval from a set of trees? I've seen things like `ltt` in phytools that can draw one line for each tree in the sample. However, this can look a bit messy, and I'd ideally love to just

[R-sig-phylo] apTreeshape and odd Colless scores

Hi all, I've noticed that apTreeshape's _colless_ and _colless.test_ functions can give normalised/standardised Ic values outside the expected range of 0-1. For example, getcolless - function(tips) { # randomly generate a tree, and get the normalized Colless score.

[R-sig-phylo] Best way to summarize a tree balance statistic over a posterior tree distribution?

Hi all, What's the best way to summarise a tree balance statistic (e.g. Colless Ic, or Fusco and Cronk's Iw) over a posterior tree distribution? I'm a bit concerned that running e.g. apTreeshape's colless.test or caper's fusco.test on, say, 1000 trees will give me a massive false positive

Re: [R-sig-phylo] birthdeath {ape} fails every time.

Hi all, Thanks for the quick replies, workarounds and bugfixes! Plenty for me to go on with! Simon ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

[R-sig-phylo] birthdeath {ape} fails every time.

Morning all, Whenever I try to use ape's (v 3.0-2) birthdeath function e.g. birthdeath(rcoal(sample(10:100, 1))) I get the following error: Error in while (foo(up) 0) up - up + inc : missing value where TRUE/FALSE needed The warnings all appear to be this sort of thing: 1: In log(1 - a)

Re: [R-sig-phylo] Convert instantaneous transition rate to time

Hi Cecile, Brian, Thanks for these suggestions. I was hoping there'd be something nice and simple! I'll investigate these ideas and see what I come up with. Many thanks, Simon ___ R-sig-phylo mailing list R-sig-phylo@r-project.org

[R-sig-phylo] Convert instantaneous transition rate to time.

Hi all, What is the best way to convert an instantaneous transition rate (such as that given by geiger's `fitDiscrete` method) into a measure of stability over time? So, I have a set of traits with a small number of states. I want to fit these onto a set of trees with branches proportional to