[Phylobase-devl] characters not being read

[François Michonneau]

Hi,

  I just committed a change to phylobase that should fix the issue Brian
described.

  I'll let you know when the other issue raised by Conrad is fixed.

  Cheers,
  -- François 

On Tue, 2010-08-03 at 18:35 -0400, Brian O'Meara wrote:
> 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
> 
> 
> 
> 
> 
> 
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