Hi Dave,

Thanks a lot. It was exactly this I was trying to do.
Thank you all for your advice.

Cheers,
Sérgio.

----- Mensagem original -----
> De: "David Bapst" <dwba...@gmail.com>
> Para: "Sergio Ferreira Cardoso" <sergio.ferreira-card...@umontpellier.fr>
> Cc: "Eliot Miller" <et...@cornell.edu>, "r-sig-phylo" 
> <r-sig-phylo@r-project.org>
> Enviadas: Terça-feira, 20 De Junho de 2017 0:11:02
> Assunto: Re: [R-sig-phylo] Add terminal branches to tree

> Hi Sergio,
> 
> Sorry for being late to the party, but maybe expandTaxonTree in
> paleotree does what you're looking for? I wrote it for turning trees
> of genera into trees of species, with the resulting generic polytomies
> collapsed or not (in case we know that the genera is paraphyletic).
> 
> Cheers,
> -Dave
> 
> On Mon, Jun 19, 2017 at 9:36 AM, Sergio Ferreira Cardoso
> <sergio.ferreira-card...@umontpellier.fr> wrote:
>> Thank you all for your suggestions. I guess the more direct way is to use
>> Megaptera. I tried and it worked (I added Man cra1, Man cra2, etc.).
>> However, I wanted it to create a new node that would basically include all
>> these taxa. I sthere any way to merge all the added species in a new node?
>> Thank you all, once again.
>>
>> ________________________________
>>
>> De: "Eliot Miller" <et...@cornell.edu>
>> Para: "Christoph Heibl" <christoph.he...@gmx.net>
>> Cc: "Liam Revell" <liam.rev...@umb.edu>, "r-sig-phylo"
>> <r-sig-phylo@r-project.org>, "Sergio Ferreira Cardoso"
>> <sergio.ferreira-card...@umontpellier.fr>
>> Enviadas: Segunda-feira, 19 De Junho de 2017 14:40:15
>> Assunto: Re: [R-sig-phylo] Add terminal branches to tree
>>
>> 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]]
>>> >
>>> > _______________________________________________
>>> > 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]]
>>>
>>>
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>>
>>
>>
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> 
> 
> 
> --
> David W. Bapst, PhD
> https://github.com/dwbapst/paleotree

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