Liam, Thanks so much for your reply and for the blog post, I was able to get it working.
-Laura On Wed, Jun 21, 2017 at 10:35 AM, Liam J. Revell <liam.rev...@umb.edu> wrote: > Dear Laura. > > I also just posted a possible solution to my blog here: > http://blog.phytools.org/2017/06/generating-set-of-random-re > solutions-of.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 > blog: http://blog.phytools.org > > On 6/21/2017 11:02 AM, Liam J. Revell wrote: > >> [This sender failed our fraud detection checks and may not be who they >> appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing] >> >> >> Hi Laura. >> >> The phytools functions resolveNode and resolveAllNodes could be used. >> They resolve either a single node in all possible ways; or all nodes in >> all possible ways, returning a "multiPhylo" object. Note that in the >> latter case the number of trees can be quite large. From the phytools >> doc: "For resolveNode applied to a multifurcation with n descendants, >> the number of resolved trees will be equal to the number of possible >> rooted trees of n taxa. (For instance, three for a trifurcation, 15 for >> a quadrifurcation, and so on.) For resolveAllNodes the number of fully >> resolved trees will be equal to the product of numbers for resolveNode >> applied to each multifurcation separately. (For instance, 45 for a tree >> containing one trifurcation and one quadrifurcation.)" To get a random >> set of resolved trees, rather than all possible trees (because this >> number can be high), you could start with one multifurcating node in the >> tree, resolve it in all ways using resolveNode, pick one of those >> resolutions, then move to the next node & so on. I will try to post a >> formal solution & then share it to the list. >> >> 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 6/21/2017 10:38 AM, Laura Jackson wrote: >> >>> Hi all, >>> >>> I am using the ape package to randomly resolve polytomies using >>> 'multi2di' >>> and wondering if there is a way to use this function to get a single >>> output >>> tree file that contains multiple different randomly resolved trees using >>> some number of resamplings? >>> >>> Thanks, >>> -Laura >>> >>> >> _______________________________________________ >> 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/ >> > -- *Laura M. Jackson* PhD Candidate Department of Biology 185 Churchill Haines University of South Dakota 414 E. Clark St. Vermillion SD 57069-1746 Email: laura.jack...@usd.edu [[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/
