Dears,

I removed ape 4.1 and install 4.0 version and the problem with my tree is
gone. I can extract clade even my tree having singletons. But the problem
still occur in example tree, with new error message. With this tree:

((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),(E1,E2)E)D),(F1)F)R;

or

(((((A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),(F1)F)G)R;

I have this new error:

Error in phy$edge[, 2] : incorrect number of dimensions

And with this tree:

((((((A_1,A_2,)A,(B1,B2,B3)B)C)ABC,((D1,(E1,E2)E)D))DE,(F1)F)G)R;

rsession running infinitely. I need force stop.

Best regards,

Mario



On 1 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 phylocom.
> Then, all node is important, including single one. For this, collapse
> singletons do not work for me. For instance.
>
> This trees:
>
> ((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),(E1,E2)E)D),(F1)F)R;
>
> (((((A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),(F1)F)G)R;
>
> 'collapsed' is:
>
> ((((A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),F1)R;
>
> I lost 'F' node, as I said early. D1 is now in 'right' way.
>
> This tree:
>
> ((((((A_1,A_2,)A,(B1,B2,B3)B)C)ABC,((D1,(E1,E2)E)D))DE,(F1)F)G)R;
>
> 'collapsed' is:
>
> ((((A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D)DE,F1)G;
>
> I lost 'F', 'R' and 'ABC' node.
>
> I have a big tree and some families has polytomies. Then, I extract each
> family (remove tips of this node), resolve plytomies, and I bind families
> tree again. After that, I date tree with phylocon. Phylocon use ages file
> with node age, then each node in my tree is important and collapse
> singletons would be a lost of information.
>
> I created one function to help me with extract node because I have issues
> using drop.tips (https://github.com/MarioJose/
> r-functions/blob/master/drop.clade.label/example.md).
>
> As I said, extract.node was working months ago. I don't know if this error
> is some updated that I did.
>
> Best regards,
>
> Mario
>
>
>
>
> On 1 June 2017 at 11:41, Eliot Miller <eliot.is...@gmail.com> wrote:
>
>> Your Newick string is badly formatted. 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:
>>
>>> Dears,
>>>
>>> I'm using extract.clade from ape package and get some issues. I'm using
>>> phytools package to load tree with single clade like above:
>>>
>>> library(phytools)
>>>
>>> t1 <- read.newick(text='(((((A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)
>>> E)D),(F1)F)G)R;')
>>>
>>> t2 <- read.newick(text='((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),(
>>> E1,E2)E)D),(F1)F)R;
>>>
>>> When I extract 'F' clade, for instance:
>>>
>>> c1 <- extract.clade(t1, 'F')
>>>
>>> or
>>>
>>> c2 <- extract.clade(t2, 'F')
>>>
>>> I have this error:
>>>
>>> Error in prop.part(phy) : attempt to set index 8/8 in SET_VECTOR_ELT
>>>
>>> I have one tree with mode than 300 tips. When I try extract any clade, I
>>> have the same error. If I repeat the command I have this one:
>>>
>>> *** Error in `/usr/lib/rstudio/bin/rsession': malloc(): memory
>>> corruption:
>>> 0x000000000a3aaa40 ***
>>>
>>> My configurations was:
>>>
>>> platform       x86_64-pc-linux-gnu
>>> arch           x86_64
>>> os             linux-gnu
>>> system         x86_64, linux-gnu
>>> language       R
>>> version.string R version 3.3.3 (2017-03-06)
>>>
>>> phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10)
>>>
>>> I try update R to 3.4 and recompile all my packages, but I get the same
>>> error.
>>>
>>> My new configurations:
>>>
>>> platform       x86_64-pc-linux-gnu
>>> arch           x86_64
>>> os             linux-gnu
>>> system         x86_64, linux-gnu
>>> language       R
>>> version.string R version 3.4.0 (2017-04-21)
>>>
>>> phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10)
>>>
>>> I don't know why I have this error if I can extract with the same
>>> commands
>>> some time ago.
>>>
>>> I have the same error if I run in RStudio or in terminal. When I use
>>> RStudio, it abort after the error.
>>>
>>> I try Google, but I don't found nothing that can help me.
>>>
>>> Thank you and best regards,
>>>
>>> Mario
>>>
>>>
>>> ....................................................................
>>> Mario José Marques-Azevedo
>>> Ph.D. Candidate in Ecology
>>> Department of Plant Biology, Institute of Biology
>>> University of Campinas, Campinas, São Paulo, Brazil
>>> https://github.com/mariojose <http://www.github.com/mariojose>
>>>
>>>         [[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-ph...@r-project.org/
>>
>>
>>
>

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