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.<div>
<br></div><div>Thanks!</div><div>-Conrad<br><div><br></div><div><br><br><div class="gmail_quote">On Wed, Aug 4, 2010 at 12:53 PM, 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,<br>
<br>
My last commit should fix the issue Conrad mentioned.<br>
<br>
The problem came from the fact that the nexus file didn't have state<br>
labels and the default option in readNexus was to return them. It<br>
ended up attaching empty labels to the the 0 and 1 which resulted in<br>
the empty column observed. I modified readNexus to (1) return a<br>
warning when state labels are missing and return.labels is TRUE which<br>
leads to ignoring the return.labels option.<br>
<br>
Let me know if you find any other bugs.<br>
<br>
Cheers,<br>
<font color="#888888"> -- François<br>
</font><div><div></div><div class="h5"><br>
On Tue, Aug 3, 2010 at 17:42, Conrad Stack <<a href="mailto:stack@psu.edu">stack@psu.edu</a>> wrote:<br>
> I just upgraded to phylobase 0.6.1 and found that the data in my CHARACTERS<br>
> blocks are no longer being read in (they show up as blanks in the returned<br>
> phylo4d object).<br>
> this is from the geospiza.nex dataset:<br>
> BEGIN CHARACTERS;<br>
> DIMENSIONS NCHAR=1;<br>
> FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";<br>
> MATRIX<br>
> fuliginosa 1<br>
> fortis 1<br>
> magnirostris 0<br>
> conirostris 0<br>
> scandens 0<br>
> difficilis 1<br>
> pallida 0<br>
> parvulus 0<br>
> psittacula 0<br>
> pauper 0<br>
> Platyspiza 0<br>
> fusca 0<br>
> Pinaroloxias 0<br>
> ;<br>
> END;<br>
> When it reads in, it shows up like this:<br>
> readNexus("geospiza.nex")<br>
> label node ancestor edge.length node.type standard_char<br>
> 1 fuliginosa 1 22 0.05500 tip<br>
> 2 fortis 2 22 0.05500 tip<br>
> 3 magnirostris 3 21 0.11000 tip<br>
> 4 conirostris 4 20 0.18333 tip<br>
> 5 scandens 5 19 0.19250 tip<br>
> 6 difficilis 6 18 0.22800 tip<br>
> 7 pallida 7 23 0.08667 tip<br>
> 8 parvulus 8 25 0.02000 tip<br>
> 9 psittacula 9 25 0.02000 tip<br>
> 10 pauper 10 24 0.03500 tip<br>
> 11 Platyspiza 11 16 0.46550 tip<br>
> 12 fusca 12 15 0.53409 tip<br>
> 13 Pinaroloxias 13 14 0.58333 tip<br>
> 14 <NA> 14 0 0.29744 root <NA><br>
> 15 <NA> 15 14 0.04924 internal <NA><br>
> 16 <NA> 16 15 0.06859 internal <NA><br>
> .......cont....<br>
> Any thoughts? (I'm using windows 7 32-bit with R 2.11, but the error occurs<br>
> on my Mac leopard install as well.<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>
</div></div></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></div>