Re: [R-sig-phylo] Adding random branches to tree recursively

Thank you very much Liam, You are always so helpful.  I tried you code and get this warning: Warning message: In bind.tree(tree, tip, where = where, position = pp) : one tree has no branch lengths, they have been ignored After adding edge.length=

Re: [R-sig-phylo] Error message when running gls with estimated lambda

dear all, like kari allen in june 2011, i am trying to "to run Pagels GLS in R and I have consistently encountered an error message (see script and error message below). When I fix the lambda value to 0 or 1, I do get a result, but when I let lambda vary (ie. set "fixed=F" instead of "fixed=T"),

Re: [R-sig-phylo] simulate Ne changes on a given phylogeny

Hi Jake, Weighing in late here, and just with an opinion on your last question. In my opinion, it is unlikely that the mutation probability per generation would change very rapidly. On the assumption that it is already somewhere near some limit (e.g. the drift barrier that Lynch proposed, or