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? <div><br></div><div>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). </div>
<div><br></div><div>Thanks!</div><div>Conrad<br><br><div class="gmail_quote">On Thu, Aug 5, 2010 at 8:55 AM, François Michonneau <span dir="ltr"><<a href="mailto:francois.michonneau@gmail.com">francois.michonneau@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Conrad,<br>
<br>
By default, the option "levels.uniform" is set to TRUE and behaves<br>
as you describe. Do you still have the problem if you use<br>
levels.uniform=FALSE?<br>
<br>
That being said, I think it would be better for this option to be<br>
FALSE by default. Any thoughts?<br>
<br>
Cheers,<br>
-- François<br>
<div><div></div><div class="h5"><br>
<br>
<br>
On Thu, Aug 5, 2010 at 02:37, Conrad Stack <<a href="mailto:stack@psu.edu">stack@psu.edu</a>> wrote:<br>
> I'm having a problem where, when reading in variables and state labels, only<br>
> the first N state labels are being used in the resulting data.frame returned<br>
> by readNexus(). For example, if this is part of the CHARACTERS block of my<br>
> nexus file:<br>
> ....<br>
> CHARSTATELABELS<br>
> 1 varX / option1 option2 option3, 2 varY / option4 option5<br>
> option6, 3 varZ / option7 option8;<br>
> MATRIX<br>
> taxa1 121<br>
> taxa2 221<br>
> taxa3 000<br>
> taxa4 000<br>
> taxa5 000<br>
> taxa6 111<br>
> taxa7 111<br>
> ....<br>
><br>
> readNexus returns this:<br>
> ....<br>
> taxa1 option2 option3 option2<br>
> taxa2 option3 option3 option2<br>
> taxa3 option1 option1 option1<br>
> taxa4 option1 option1 option1<br>
> taxa5 option1 option1 option1<br>
> taxa6 option2 option2 option2<br>
> taxa7 option2 option2 option2<br>
> ....<br>
> point being, readNexus doesn't seem to be assigning names to each column<br>
> based on each column's states label, but only on the first N state labels,<br>
> where N is the number of symbols total.<br>
> Thanks!<br>
> Conrad<br>
><br>
><br>
> --<br>
> Conrad Stack<br>
> -----------------------<br>
> PSU Department of Biology<br>
> 208 Mueller Lab<br>
> University Park, PA 16802<br>
> cell: 814.409.8310<br>
> email: <a href="mailto:conrad.stack@gmail.com">conrad.stack@gmail.com</a><br>
><br>
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<br>
</blockquote></div><br><br clear="all"><br>-- <br>Conrad Stack<br>-----------------------<br>PSU Department of Biology<br>208 Mueller Lab <br>University Park, PA 16802<br>cell: 814.409.8310<br>email: <a href="mailto:conrad.stack@gmail.com">conrad.stack@gmail.com</a><br>
</div>