[Phylobase-devl] data.frame issue

[François Michonneau]

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
>
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