Re: [R-sig-phylo] Possible Bug in ape::read.tree

2017-09-08 Thread Emmanuel Paradis
Hi George, Nice comparison! It would be interesting to see if the difference between ape and rncl is always in the same direction. It seems that the trees in your test are all relatively small (timings are concentrated around 1 ms). Apparently, read.tree scales a bit better than

Re: [R-sig-phylo] Possible Bug in ape::read.tree

2017-09-07 Thread George Vega Yon
Hi Klaus, Since I'm actually working with the complete PANTHER 11.1 database, I wrote a short document in our project's website comparing both ape and rncl reading ~13,000 trees. ape::read.tree does the job and identifies and reads the singleton as expected. Overall, while I see that the new

Re: [R-sig-phylo] Possible Bug in ape::read.tree

2017-09-05 Thread Klaus Schliep
Dear George & list, you can try install the development version of ape, which can handle singleton nodes: download.packages("ape", ".", repos = "http://ape-package.ird.fr/;) and than install the package from source. See http://ape-package.ird.fr/ape_installation.html for more details. For you tree

Re: [R-sig-phylo] Possible Bug in ape::read.tree

2017-09-05 Thread Liam J. Revell
Hi George. Mario is correct that phytools can read a tree with singleton nodes (if that is indeed your problem), but the name of the function is read.newick. Good luck! - Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web:

Re: [R-sig-phylo] Possible Bug in ape::read.tree

2017-09-05 Thread George Vega Yon
Hi Mario, That sounds great! Thanks, George G. Vega Yon +1 (626) 381 8171 http://cana.usc.edu/vegayon On Tue, Sep 5, 2017 at 2:08 PM, Mario José Marques-Azevedo < mariojm...@gmail.com> wrote: > Hi, George, > > Ape package do not read tree with singletons, yet. New version will read. > You can

Re: [R-sig-phylo] Possible Bug in ape::read.tree

2017-09-05 Thread Mario José Marques-Azevedo
Hi, George, Ape package do not read tree with singletons, yet. New version will read. You can use readTree from phytools package for while. Best regards, Mario On 5 Sep 2017 5:53 p.m., "George Vega Yon" wrote: Hi, When trying to read this tree with the ape::read.tree