[Phylobase-devl] characters not being read

[Ben Bolker]

François Michonneau wrote:
> 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

   If we wanted to we could (a) convert spaces back to underscores
ourselves after NCL import (b) disable conversion of spaces to dots by
using check.names=FALSE in the data.frame() call.

   I don't know whether either of these is useful in general, or if we
just need to 'fix' this in the documentation.

  Opinions?

  Ben

> 
> 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
>>
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-- 
Ben Bolker
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