[Phylobase-devl] characters not being read

Conrad Stack stack at psu.edu
Thu Aug 5 21:37:42 CEST 2010


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
> >
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>
>
> --
> Ben Bolker
> *** NEW E-MAIL ADDRESSES:
> ***   bbolker at gmail.com , bolker at mcmaster.ca
> http://www.math.mcmaster.ca/~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
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