[Phylobase-devl] data.frame issue

[Conrad Stack]

No, no problems, sorry I missed that.  Having it as FALSE by default would
work for most things I do, but perhaps other people might prefer it to be
TRUE?

Also, on an unrelated topic I have been using phylobase for a while now and
thought it would be great if, until multiphylo4(d) is implemented, S4
methods operating on lists of phylo4(d) objects could include generics for
the 'list' datatype (where just the first tree in the list is used).

Thanks!
Conrad

On Thu, Aug 5, 2010 at 8:55 AM, François Michonneau <
francois.michonneau at gmail.com> wrote:

> Hi Conrad,
>
>  By default, the option "levels.uniform" is set to TRUE and behaves
> as you describe. Do you still have the problem if you use
> levels.uniform=FALSE?
>
>  That being said, I think it would be better for this option to be
> FALSE by default. Any thoughts?
>
>  Cheers,
>  -- François
>
>
>
> On Thu, Aug 5, 2010 at 02:37, Conrad Stack <stack at psu.edu> wrote:
> > I'm having a problem where, when reading in variables and state labels,
> only
> > the first N state labels are being used in the resulting data.frame
> returned
> > by readNexus().  For example, if this is part of the CHARACTERS block of
> my
> > nexus file:
> > ....
> >         CHARSTATELABELS
> >                 1 varX /  option1 option2 option3, 2 varY /  option4
> option5
> > option6, 3 varZ / option7 option8;
> >         MATRIX
> > taxa1 121
> > taxa2 221
> > taxa3 000
> > taxa4 000
> > taxa5 000
> > taxa6 111
> > taxa7 111
> > ....
> >
> > readNexus returns this:
> > ....
> > taxa1 option2 option3 option2
> > taxa2 option3 option3 option2
> > taxa3 option1 option1 option1
> > taxa4 option1 option1 option1
> > taxa5 option1 option1 option1
> > taxa6 option2 option2 option2
> > taxa7 option2 option2 option2
> > ....
> > point being, readNexus doesn't seem to be assigning names to each column
> > based on each column's states label, but only on the first N state
> labels,
> > where N is the number of symbols total.
> > Thanks!
> > Conrad
> >
> >
> > --
> > 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
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