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]] >>> >>> >>> _______________________________________________ >>> 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/