[R-sig-phylo] Problem converting phylo to phylo4

Birgit Lemcke birgit.lemcke at systbot.uzh.ch
Thu Mar 26 17:24:28 CET 2009


Sorry for delay

#NEXUS

BEGIN TREES;
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END;

B.
Am 26.03.2009 um 16:41 schrieb Ben Bolker:

>  Could you send/post data (Newick/Nexus) so we can try it out?
>
>  Ben Bolker
>
> Birgit Lemcke wrote:
>> Hello List Members!
>>
>> I tried to convert a tree of class phylo to class phylo4
>>
>> The tree
>> str(tr)
>> List of 5
>>  $ edge       : int [1:591, 1:2] 298 298 298 299 300 300 301 302 303
>> 303 ...
>>  $ Nnode      : int 295
>>  $ tip.label  : chr [1:297] "Baloskion_tetraphyllum"
>> "Sporodanthus_tasmanicus" "Anthochortus_crinalis"
>> "Anthochortus_graminifolius" ...
>>  $ edge.length: num [1:591] 1.598 1.006 0.476 0.524 0.475 ...
>>  $ node.label : chr [1:295] "" "1.00" "1.00" "1.00" ...
>>  - attr(*, "class")= chr "phylo"
>>  - attr(*, "origin")= chr "/Users/birgitlemcke/Job/Doktorarbeit/
>> workspace//Users/birgitlemcke/Desktop/Birgits-folder/
>> ConsAllNodesMrBayes.tre"
>>
>>
>> the error message
>>
>> tr <- as(tr, "phylo4")
>> Fehler in checkTree(object) : All labels must be unique
>> Error in checkTree(object) : All labels must be unique
>>
>> checking tip labels
>>
>> length(unique(tr$tip.label))==length((tr$tip.label))
>> [1] TRUE
>>
>> Does somebody have an idea what the problem is?
>> The weird thing is that I am pretty sure that I did the same already
>> also with the same data.I feel somewhat helpless.
>>
>> Many thanks for answers in advance
>>
>> Cheers
>>
>> Birgit
>>
>> =============================
>> Birgit Lemcke
>> Institut of Systematic Botany
>> University of Zurich
>> Zollikerstrasse 107
>> CH-8008 Zürich
>> Switzerland
>> Ph: +41 (0)44 634 8416		
>> mail: birgit.lemcke at systbot.uzh.ch	
>> =============================
>>
>> _______________________________________________
>> R-sig-phylo mailing list
>> R-sig-phylo at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
>
> -- 
> Ben Bolker
> Associate professor, Biology Dep't, Univ. of Florida
> bolker at ufl.edu / www.zoology.ufl.edu/bolker
> GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
>

=============================
Birgit Lemcke
Institut of Systematic Botany
University of Zurich
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8416		
mail: birgit.lemcke at systbot.uzh.ch	
=============================



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