Hi Roger and list, Regarding whether I've already written such a thing, no, I tend to not put much emphasis on the graphical side of things (which is partly why the release of strap pleased me greatly) but sampled-ancestor trees are definitely an interest of mine, because of cal3. The '$anag.tips' and '$budd.tips' in cal3 output are just to point out which taxa were inferred to be ancestors (either by anagenesis or budding cladogenesis, respectively). This was necessary as taxa often have stratigraphic durations in cal3. Having durations means they aren't always as easily picked out by having zero-length branches (at least under budding; obviously, anagenetic ancestors should still have zero-length branches).
Thanks for sending along this data file. So, essentially what we'd want here is to first devise some sort of tree-plotter that recognized trees with zero-length terminal branches as 'sampled ancestors' and adjusted them accordingly. Later we can try accounting for the taxa listed in $budd.tips would take a little more work (but properly displaying budding cladogenesis might be a real coding headache!). For a dataset where all taxa are instantaneous populations (and do not have stratigraphic durations), I think the easiest approach would bes to do essentially as you suggest; first-pass run with dropZLB from paleotree, then add them back on as points using the trick that Joseph presents. -Dave On Wed, Dec 9, 2015 at 8:50 AM, Roger Close <roger.cl...@gmail.com> wrote: > Hi Dave, Emmanuel and Joseph, > > Thanks very much for your suggestions. The output of BEAST, at least, is an > ordinary Newick/NEXUS file with ancestors represented as tips on the ends of > zero-length branches (see attached). > > One way to proceed would be to drop the tips that correspond to ancestors > and then add them back on using edge labels. However, I see that paleotree > designates ancestors using $anag.tips; is there a tool for plotting this > type of tree? > > Cheers, > Roger > > > > --- > Roger Close, Postdoctoral Research Associate > Department of Earth Sciences, Oxford University > South Parks Road > Oxford OX1 3AN > United Kingdom > > On 8 December 2015 at 18:56, David Bapst <dwba...@gmail.com> wrote: >> >> Hi Roger, >> >> I'm not aware of any existing solution. Could you send around a small >> example of the data format of an output sampled ancestor tree from >> BEAST or MrBayes? Are they just typical Newick/NEXUS format with >> ancestors indicated tipis with zero-length branches or something more >> complicated? >> >> Remarkably I've not looked at the formatting of one, but obviously >> plotting SA trees is something the community will need in the near >> future. >> >> Cheers, >> -Dave >> >> On Tue, Dec 8, 2015 at 5:46 AM, Roger Close <roger.cl...@gmail.com> wrote: >> > Hi all, >> > >> > Does anyone know of a way to plot sampled-ancestor trees in R such that >> > ancestors lie on branches, rather than being zero-length terminals that >> > follow a bifurcation? >> > >> > Many thanks, >> > Roger >> > >> > --- >> > Roger Close, Postdoctoral Research Associate >> > Department of Earth Sciences, Oxford University >> > South Parks Road >> > Oxford OX1 3AN >> > United Kingdom >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > R-sig-phylo mailing list - R-sig-phylo@r-project.org >> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > Searchable archive at >> > http://www.mail-archive.com/r-sig-phylo@r-project.org/ >> >> >> >> -- >> David W. Bapst, PhD >> Adjunct Asst. Professor, Geology and Geol. Eng. >> South Dakota School of Mines and Technology >> 501 E. St. Joseph >> Rapid City, SD 57701 >> >> http://webpages.sdsmt.edu/~dbapst/ >> http://cran.r-project.org/web/packages/paleotree/index.html > > -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
