Liam, I put the (updated) code up as a gist <https://gist.github.com/josephwb/ad61fd29ed4fb06e712e23d67422c813>. Feel free to use/improve/whatever. Emmanuel sees room for improvement but frankly taking 0.3 seconds to find the MRCA of 5000 taxa on a million-tip tree is good enough for my purposes.
JWB ________________________________________ Joseph W. Brown Post-doctoral Researcher, Smith Laboratory University of Michigan Department of Ecology & Evolutionary Biology Room 2071, Kraus Natural Sciences Building Ann Arbor MI 48109-1079 josep...@umich.edu > On 9 Jun, 2017, at 15:20, Liam J. Revell <liam.rev...@umb.edu> wrote: > > On the other hand, phytools does have a function - the somewhat imprecisely > named fastMRCA - which can find the MRCA of just a pair of species much > faster than getMRCA (however still slower than or only about as fast as > Joseph & Klaus's solutions). > > Liam J. Revell, Associate Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > On 6/9/2017 5:22 AM, Liam J. Revell wrote: >> >> Juan. findMRCA was written before getMRCA existed, but the latter was >> faster so now it just calls getMRCA internally. 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 >> blog: http://blog.phytools.org >> >> On 6/9/2017 1:57 AM, Juan Antonio Balbuena wrote: >>> Package phytools includes a function, findMRCA, that is supposed to work >>> very efficiently with large trees. you may wish to compare it with your >>> function. >>> >>> Cheers >>> >>> Juan >>> >>> -- >>> >>> Dr. Juan A. Balbuena >>> Cavanilles Institute of Biodiversity and Evolutionary Biology >>> University of Valencia >>> http://www.uv.es/~balbuena <http://www.uv.es/%7Ebalbuena> >>> P.O. Box 22085 >>> http://www.uv.es/cophylpaco >>> <http://www.uv.es/cavanilles/zoomarin/index.htm> >>> 46071 Valencia, Spain >>> e-mail: j.a.balbu...@uv.es <mailto:j.a.balbu...@uv.es> tel. +34 963 >>> 543 658 fax +34 963 543 733 >>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> *NOTE!*For shipments by EXPRESS COURIER use the following street address: >>> C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain. >>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> >>> >>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient> >>> >>> Libre de virus. www.avast.com >>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient> >>> >>> >>> >>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >>> >>> >>> _______________________________________________ >>> 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/ >>> >> >> _______________________________________________ >> 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/
