Just to add to the slew of other good options, I have a small package up on
GitHub (https://github.com/eliotmiller/addTaxa/tree/master/R) that is
basically a big loop around Liam's bind.tip. There are examples included
with the package. The main function you'd be interested in is
randomlyAddTaxa(). It works fairly well last I checked, but there are some
limitations and the package is in need of an overhaul. The main limitation
is when two clades (A and B) are sister to one another and you intend to
add a taxon into the clade (A+B); it's currently impossible to generate the
topology (C,(A,B)), even though that's monophyletic and shouldn't be
prohibited. I aim to fix this at some point within the next month or two if
anyone's interested.

Eliot

On Mon, Jun 19, 2017 at 8:30 AM, Christoph Heibl <christoph.he...@gmx.net>
wrote:

> Another possibility would be addSingleTip() and addTips() from the
> megaptera package (https://github.com/heibl/megaptera). The latter
> function can add any number of tips; the loop that Liam mentioned is
> already build into that function. This is potentially very slow, but for
> your tree size it should work. Note that you have to specify the 'tax'
> argument; it allows you to add tips also to internal nodes of higher rank
> than genera. In your case where you have only genera you can create 'tax'
> easily like this:
>
> ## 'species' is a vector of tip labels that you want to add
> ## will work only if your tip labels are of the form
> "Genus_epithet-or-any-other-string"
> library(megaptera)
> tax <- data.frame(genus = strip.spec(species),
>         species = species,
>         stringsAsFactors = FALSE)
>
>
>
> Christoph Heibl
> An der Weiherleite 3
> 86633 Neuburg an der Donau
> 08431-53 96 534 (Festnetz)
> 0176-23 86 57 92 (Mobil)
> christoph.he...@gmx.net
>
>
> Am 19.06.2017 um 14:06 schrieb Liam Revell:
>
> > The function add.species.to.genus may do what you want. It adds a single
> species to the group defined by the MRCA of members of a genus, according
> to multiple criteria (randomly and so on). It can add only one species at a
> time, so you will need to write a for loop or something to iterate over the
> species that you‚d like to add.
> >
> > --
> > Liam J. Revell, Associate Professor of Biology
> > University of Massachusetts Boston
> > web: http://faculty.umb.edu/liam.revell
> > email: liam.rev...@umb.edu
> >
> > Sent from my Windows 10 phone
> >
> > From: Sergio Ferreira Cardoso<mailto:sergio.
> ferreira-card...@umontpellier.fr>
> > Sent: Monday, June 19, 2017 6:58 AM
> > To: r-sig-phylo<mailto:r-sig-phylo@r-project.org>
> > Subject: [R-sig-phylo] Add terminal branches to tree
> >
> > Hello all,
> >
> > I'm using the package 'phytools' to try to add terminal branches to a
> tree (attached). I tried to use add.everywhere function to add terminal
> branches. I have 167 terminal taxa inside each of the 7 genera on my tree.
> Basically, I just wanted to add some dozens of specimens to the end of each
> branch, but I don't find a way to do it. Is there any tool that would allow
> me to do this? Like adding 30 branches to 'Phal', adding 25 to 'Phat', etc.
> >
> > Thanks in advance.
> >
> >
> >
> > --
> > Institut des Sciences de l'Evolution
> > UMR5554, CNRS, IRD, EPHE
> > Université de Montpellier
> > Place Eugène Bataillon
> > 34095 Montpellier Cedex 05
> > France
> > Email: sergio.ferreira-card...@umontpellier.fr
> > Tel: +33 (4 ) 67 14 46 52
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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>
>
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>
>
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