[Phylobase-devl] characters not being read

[François Michonneau]

Hi again Conrad,

  In the file you sent me there were no state labels (just
charstatelabels), so the warning is normal.

  For the underscore issue, there isn't much we can do about. NCL
converts underscores to spaces because there is no way to
differentiate them in newick strings for instance. Then when the name
is assigned to the column name in R, the space is converted to a dot.

  Cheers,
  -- François

On Wed, Aug 4, 2010 at 22:31, Conrad Stack <stack at psu.edu> wrote:
> 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
>> >
>> > _______________________________________________
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>> > 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
>