[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
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>>
>>
>>
>> --
>> 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
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