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

[R-sig-phylo] Nnode not equal to length of node.labels

2017-06-22 Thread Mario José Marques-Azevedo
Dears, I'm studying the structure of phylo object to work it in my functions. I'm using read.newick to read tree with singletons. I do not know why the number of node is not equal to length of node.labels. For instance: I have this tree (the same annexed):

[R-sig-phylo] Function to drop clade

2017-06-06 Thread Mario José Marques-Azevedo
/drop.clade.label.r I leaned a lot working on it! p.s.: drop.tip function remove singletons in the last code. Maybe this behaviour could be optional with a new argument All the best, Mario Mario José Marques-Azevedo Ph.D. Candidate

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

2017-06-01 Thread Mario José Marques-Azevedo
June 2017 at 16:13, Mario José Marques-Azevedo <mariojm...@gmail.com> wrote: > Dear Eliot, > > Thank you for your answer! My tree is ok, but to plot is needed to > collapse singles, as you said. > > I use ape/phytools to manipulate my tree for date it after with ph

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

2017-06-01 Thread Mario José Marques-Azevedo
tted. See: > > plot(t1) > > Error in plot.phylo(t1) : > there are single (non-splitting) nodes in your tree; you may need to use > collapse.singles() > > On Thu, Jun 1, 2017 at 1:31 AM, Mario José Marques-Azevedo < > mariojm...@gmail.com> wrote: > >> De

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

2017-06-01 Thread Mario José Marques-Azevedo
without problem. Maybe some update that I did, but I'm not sure. Thank you again! Best regards, Mario ​ Mario José Marques-Azevedo Ph.D. Candidate in Ecology Department of Plant Biology, Institute of Biology University of Campinas