[Phylobase-devl] characters not being read

[Conrad Stack]

Looks great.  Two things:  it looks like the warning message about 'state
labels' fires even when labels are found (only when DATATYPE=STANDARD) and,
perhaps relatedly, underscores in CHARSTATELABELS are automatically
converted to periods.

Thanks!
-Conrad



On Wed, Aug 4, 2010 at 12:53 PM, François Michonneau <
francois.michonneau at gmail.com> wrote:

> 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
> >
> >
>
>


-- 
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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