At the risk of inundating you with options, Henry, there is also expandTaxonTree in the package paleotree (on CRAN) which is similar to the above, but also lets you collapse higher taxa you list as paraphyletic, which can be useful if the taxonomic work of your group has never been concerned with monophyly.
Cheers, -Dave On Tue, Feb 25, 2014 at 3:33 PM, Julien Clavel <julien.cla...@hotmail.fr>wrote: > Hi, > > There is also the stickTip function: > http://rleca.pbworks.com/w/file/fetch/40813743/stickTips_1.2.html > it is possible to tweak the code for more specific things... > > Best, > > Julien > > > From: liam.rev...@umb.edu > > Date: Tue, 25 Feb 2014 10:32:36 -0500 > > To: h.ferguson-...@ucl.ac.uk; r-sig-phylo@r-project.org > > Subject: Re: [R-sig-phylo] utilise more data by making polytomies > > > > Something similar to this is in phytools ( > http://blog.phytools.org/2013/11/new-function-to-add-species-to-genus-in.html), > though not yet on CRAN. Let me know if this is what you're thinking of. > > > > All the best, Liam > > > > Liam J. Revell, Assistant Professor of Biology > > University of Massachusetts Boston > > web: http://faculty.umb.edu/liam.revell/ > > email: liam.rev...@umb.edu > > blog: http://blog.phytools.org > > > > -- > > Sent from Windows Phone > > > > -----Original Message----- > > From: Ferguson-Gow, Henry > > Sent: 2/25/2014 10:23 AM > > To: r-sig-phylo@r-project.org > > Subject: [R-sig-phylo] utilise more data by making polytomies > > > > Hi All > > > > I have a large dataset and a large tree, however the intersection > between them both is quite low. As a supplement to analyses solely on the > species that appear in both the dataset and the tree I thought I could take > the species that are present in the dataset and not the tree, and add those > tips in as a polytomy with their congenerics present on the tree. Is there > a method in R that would help me to do this? > > > > Many thanks > > > > Henry > > > > > > [[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/ > > > > [[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/ > > [[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 [[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/
