[Phylobase-devl] characters not being read

[Conrad Stack]

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
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