Re: [R-sig-phylo] Add terminal branches to tree

ell.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

Re: [R-sig-phylo] Add terminal branches to tree

gt; 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 t

Re: [R-sig-phylo] Add terminal branches to tree

" <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 20

Re: [R-sig-phylo] Add terminal branches to tree

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 ( h

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

Re: [R-sig-phylo] Add terminal branches to tree

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

Re: [R-sig-phylo] Add terminal branches to tree

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

Re: [R-sig-phylo] Add terminal branches to tree

Hi Sergio, try ‘bind.tip' and just make a loop to add more. Or ‘bind.tree’ if you want to add a clade. Cheers, Franz > On 19 Jun 2017, at 13:58, Sergio Ferreira Cardoso > wrote: > > Hello all, > > I'm using the package 'phytools' to try to add