[Phylobase-devl] characters not being read

[Brian O'Meara]

Continuous chars still seem to be loaded okay, but standard fails as Conrad indicates.

I'm not sure if this is related to the changes in readNCL/NCL interface code/NCL that might be causing this issue, but phylobase now crashes R if given a poorly-formatted nexus file or given an incorrect path to a nexus file (at least on a Mac OS 10.6.4 with R2.11.1).

Brian

On Aug 3, 2010, at 5:42 PM, Conrad Stack wrote:

> I just upgraded to phylobase 0.6.1 and found that the data in my CHARACTERS blocks are no longer being read in (they show up as blanks in the returned phylo4d object).
> 
> this is from the geospiza.nex dataset:
> 
> BEGIN CHARACTERS;
> 	DIMENSIONS  NCHAR=1;
> 	FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = "  0 1";
> 	MATRIX
> 	fuliginosa    1
> 	fortis        1
> 	magnirostris  0
> 	conirostris   0
> 	scandens      0
> 	difficilis    1
> 	pallida       0
> 	parvulus      0
> 	psittacula    0
> 	pauper        0
> 	Platyspiza    0
> 	fusca         0
> 	Pinaroloxias  0
> 
> ;
> 
> END;
> 
> When it reads in, it shows up like this:
> readNexus("geospiza.nex")
>           label node ancestor edge.length node.type standard_char
> 1    fuliginosa    1       22     0.05500       tip              
> 2        fortis    2       22     0.05500       tip              
> 3  magnirostris    3       21     0.11000       tip              
> 4   conirostris    4       20     0.18333       tip              
> 5      scandens    5       19     0.19250       tip              
> 6    difficilis    6       18     0.22800       tip              
> 7       pallida    7       23     0.08667       tip              
> 8      parvulus    8       25     0.02000       tip              
> 9    psittacula    9       25     0.02000       tip              
> 10       pauper   10       24     0.03500       tip              
> 11   Platyspiza   11       16     0.46550       tip              
> 12        fusca   12       15     0.53409       tip              
> 13 Pinaroloxias   13       14     0.58333       tip              
> 14         <NA>   14        0     0.29744      root          <NA>
> 15         <NA>   15       14     0.04924  internal          <NA>
> 16         <NA>   16       15     0.06859  internal          <NA>
> .......cont....
> 
> Any thoughts?  (I'm using windows 7 32-bit with R 2.11, but the error occurs on my Mac leopard install as well.
> 
> 
> 
> -- 
> Conrad Stack
> -----------------------
> PSU Department of Biology
> 208 Mueller Lab 
> University Park, PA 16802
> cell: 814.409.8310
> email: conrad.stack at gmail.com
> _______________________________________________
> Phylobase-devl mailing list
> Phylobase-devl at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl

________________________________________________
Brian C. O'Meara
Asst. Prof., Dept. of Ecology and Evolutionary Biology
University of Tennessee, Knoxville
http://www.brianomeara.info



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/phylobase-devl/attachments/20100803/2e0c82f1/attachment.htm>