Hi Laura.

I think multi2di also performs random resolutions, so if you wanted to generate, say, 100 random resolutions could you not do:


trees<-replicate(100,multi2di(tree),simplify=FALSE)
class(trees)<-"multiPhylo"

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 12:18 PM, Laura Jackson wrote:
Hi Liam,

I was trying to get this to work on my tree, but it seems that it
doesn't work for larger phylogenies (~1000 tips)? I get the following
error message,..."Error in allTrees(n, TRUE, dd) :
That would generate 7905853580625 trees, and take up more than
7905853581 MB of memory! "

I have attached my phylogeny here. I am trying to get even 10 different
randomly resolved trees. Is this possible with my phylogeny?

Thanks.
-Laura


On Wed, Jun 21, 2017 at 11:08 AM, Laura Jackson
<jacksonlaura...@gmail.com <mailto:jacksonlaura...@gmail.com>> wrote:

    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 <mailto: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-resolutions-of.html
        
<http://blog.phytools.org/2017/06/generating-set-of-random-resolutions-of.html>.

        All the best, Liam

        Liam J. Revell, Associate Professor of Biology
        University of Massachusetts Boston
        web: http://faculty.umb.edu/liam.revell/
        <http://faculty.umb.edu/liam.revell/>
        email: liam.rev...@umb.edu <mailto: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
            <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/
            <http://faculty.umb.edu/liam.revell/>
            email: liam.rev...@umb.edu <mailto: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
            <mailto:R-sig-phylo@r-project.org>
            https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
            <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo>
            Searchable archive at
            http://www.mail-archive.com/r-sig-phylo@r-project.org/
            <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 <mailto:laura.jack...@usd.edu>




--
*/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 <mailto:laura.jack...@usd.edu>

_______________________________________________
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/

Reply via email to