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

2017-06-19 Thread Sergio Ferreira Cardoso
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?

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

2017-06-19 Thread David Bapst
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

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

2017-06-19 Thread f.k...@mailbox.org
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

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

2017-06-19 Thread 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

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

2017-06-19 Thread Sergio Ferreira Cardoso
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

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

2017-06-19 Thread Christoph Heibl
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

2017-06-19 Thread Eliot Miller
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