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]] >> _______________________________________________ >> 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/
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