[Phylobase-devl] characters not being read

Ben Bolker bolker at ufl.edu
Mon Aug 9 03:09:10 CEST 2010


  I don't have a strong opinion on this.
   In the meantime I committed a documentation patch that at least notes
the issue.  Feel free to change it for reasons of style or accuracy.

  Ben



François Michonneau wrote:
> Hi,
> 
>   I feel there are 2 different issues here.
> 
>   For the tip labels, I feel it would be best to keep the labels as they
> are returned from NCL to stay consistant.
> 
>   For the CHARSTATELABELS we can add the option check.names to
> readNexus.
> 
>   Cheers,
>   -- François 
> 
> On Thu, 2010-08-05 at 15:37 -0400, Conrad Stack wrote:
>> What about, since phylobase requires ape, importing the checkLabel
>> function from ape and filtering all tip label through that function?
>>
>>
>> -conrad
>>
>> On Thu, Aug 5, 2010 at 10:00 AM, Ben Bolker <bolker at ufl.edu> wrote:
>>         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
>>         >>>>
>>         >>>> _______________________________________________
>>         >>>> 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
>>         >>
>>         > _______________________________________________
>>         > 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
>>         
>>         
>>         --
>>         
>>         Ben Bolker
>>         *** NEW E-MAIL ADDRESSES:
>>         ***   bbolker at gmail.com , bolker at mcmaster.ca
>>         http://www.math.mcmaster.ca/~bolker
>>         GPG key:
>>         http://www.math.mcmaster.ca/~bolker/benbolker-publickey.asc
>>         
>>
>>
>>
>> -- 
>> Conrad Stack
>> -----------------------
>> PSU Department of Biology
>> 208 Mueller Lab 
>> University Park, PA 16802
>> cell: 814.409.8310
>> email: conrad.stack at gmail.com
>>


-- 
Ben Bolker
*** NEW E-MAIL ADDRESSES:
***   bbolker at gmail.com , bolker at mcmaster.ca
http://www.math.mcmaster.ca/~bolker
GPG key: http://www.math.mcmaster.ca/~bolker/benbolker-publickey.asc

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 261 bytes
Desc: OpenPGP digital signature
URL: <http://lists.r-forge.r-project.org/pipermail/phylobase-devl/attachments/20100808/f111270c/attachment.pgp>


More information about the Phylobase-devl mailing list