Re: [R-sig-phylo] converting TNT(?) tree to newick tree

Hi Eduardo, Thanks for the link. That did the trick! Chris Law Graduate Student Dept of Ecology & Evolutionary Biology Long Marine Lab - University of California, Santa Cruz cj...@ucsc.edu http://research.pbsci.ucsc.edu/eeb/cjlaw/ On Mon, Feb 27, 2017 at 2:35 PM, Eduardo Ascarrunz

Re: [R-sig-phylo] converting TNT(?) tree to newick tree

Hi Chris, The tntfile2R and tntfile2newick functions from Nick Matzke's package TNTR should help you with that. Here's the link: http://phylo.wdfiles.com/local--files/tntr/tnt_R_utils_v1.R You can also export files in Newick format directly from TNT using the command EXPORT with the flag "=".

Re: [R-sig-phylo] Plotting uncertainty in continuous ASR

Hi Dave. Yes. It is not perfect, but I have shown how to do this here: http://blog.phytools.org/2017/02/more-on-adding-error-bars-to-contmap.html. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/

Re: [R-sig-phylo] Plotting uncertainty in continuous ASR

Hi Kevin. I now show one way to do this here: http://blog.phytools.org/2017/02/more-on-adding-error-bars-to-contmap.html. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu

Re: [R-sig-phylo] Plotting uncertainty in continuous ASR

That's really cool, Liam. Would it also be possible for one to do multiple such error bars per node, for plotting ASRs for multiple traits? -Dave On Mon, Feb 27, 2017 at 12:13 PM, Liam J. Revell wrote: > Hi Kevin. > > This is not automatic - but it is indeed fairly easy to

[R-sig-phylo] Plotting uncertainty in continuous ASR

Hi all, I was wondering about plotting the output of an ancestral state 'reconstruction' of a continuous trait while incorporating at least some of the uncertainty around the estimates. One approach I thought of was to map the ASR onto a tree in a standard way, then at each node have