[Phylobase-devl] characters not being read

[François Michonneau]

Hi,

  My last commit should fix the issue Conrad mentioned.

  The problem came from the fact that the nexus file didn't have state
labels and the default option in readNexus was to return them. It
ended up attaching empty labels to the the 0 and 1 which resulted in
the empty column observed. I modified readNexus to (1) return a
warning when state labels are missing and return.labels is TRUE which
leads to ignoring the return.labels option.

  Let me know if you find any other bugs.

  Cheers,
  -- François

On Tue, Aug 3, 2010 at 17:42, Conrad Stack <stack at psu.edu> 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
>
>