No problem. Glad someone other than me could make use of my function! Cheers, -Dave
On Tue, Jun 27, 2017 at 4:42 AM, Sergio Ferreira Cardoso <sergio.ferreira-card...@umontpellier.fr> wrote: > 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 -- 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/
