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]] >> >> >> _______________________________________________ >> 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/ > > > > _______________________________________________ > 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/ -- David W. Bapst, PhD https://github.com/dwbapst/paleotree _______________________________________________ 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/
