Dear Agustín,
the nexus file on dropbox does not contain any trees.
If you open it in an editor you see this:
#NEXUS
[Tree distribution from: The global diversity of birds in space and time;
W. Jetz, G. H. Thomas, J. B. Joy, K. Hartmann, A. O. Mooers
doi:10.1038/nature11631]
[Subsampled and pruned from birdtree.org on 2018-02-13T21:49:59Z ]
[Data: "Hackett All Species" (see Jetz et al. 2012 supplement for details)]
BEGIN TREES;
TREE tree_4104 =
TREE tree_9438 =
...
TREE tree_1868 =
TREE tree_0011 =
END;
Looks like your download did not work and the error message from read.nexus
could improve.
Cheers,
Klaus
On Tue, Feb 13, 2018 at 5:11 PM, Agus Camacho <agus.cama...@gmail.com>
wrote:
> Dear list,
>
> I am puzzled with this error when importing a bird tree subset from
> https://birdtree.org/subsets/ .
>
> The subset is supposed to be in nexus format. However,
>
> trees<-read.nexus("output.nex")
>
> Error in if (tp[3] != "") obj$node.label <- tp[3] :
>
> missing value where TRUE/FALSE needed
>
>
> read.tree gives the same error
> read.newick gets stuck, it never ends reading in the tree
>
> I tried scanning the file and then several notes appear before the actual
> trees Thus, I tried read.annotated.nexus from OutbreakTools.
> But it gives another error:
>
> Error in read.annotated.nexus("C:/Users/agusc/Dropbox/output.nex") :
> .annotated.clado.build is not yet implemented.
>
>
> I tried with several different subsets from different backbones and none
> worked.
> Here is one: https://www.dropbox.com/s/037u6pjr4006o6r/output.nex?dl=0
>
> Somebody has reported this error previously in the internet, but it still
> seems to be unsolved.
>
> Thanks in advance and best regards.
> Agus
>
>
> --
> Agustín Camacho Guerrero.
> http://www.agustincamacho.com
> Doutor em Zoologia.
> Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
> Biociências, USP.
> Rua do Matão, trav. 14, nº 321, Cidade Universitária,
> São Paulo - SP, CEP: 05508-090, Brasil.
>
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>
> _______________________________________________
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>
--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/
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