Hi Mariana,
extract.clades2 hasn't been well tested. I wrote it for a specific dataset two
years ago and I don't know if someone else has used it successfully. You can
send me your tree off list and I'll see if I can fix it. Alternatively, you can
identify the nodes concerned (?nodelabels, ?noi) and then extract the HPD
values by their node numbers before using extract.clade.
Cheers,
Christoph
On May 2, 2014, at 8:24 PM, Mariana Vasconcellos wrote:
> Hi all:
> I am using the phylock package to read and plot a BEAST tree in R. I want to
> remove outgroups from my plot, therefore I used the extract.clade2() from the
> phylock package. But, when I try to plot the new phylogeny with the extracted
> clade, R quits unexpectedly. I have tried to plot that clade using
> extract.clade() from ape package and it works fine, the problem is that I
> can‚t plot the HPDbars() command doing this way.
>
> What I am doing is more or less like this:
>
> Btree<- read.beast("BEASToutput_logclock.tre‰)
> tree <- extract.clade2(Btree,127)
> plot.phylo(tree, label.offset=0.5, cex=0.7) ## This command cause R to quit
> unexpectedly, but only after the extract.clade2()
>
> Has anyone experienced this problem before? What I need is really simple:
> plot one clade extracted from a BEAST phylogeny with the height_95%_HPD.
> Suggestions?
> Thanks,
>
> ----------------------
> Mariana Mira Vasconcellos
> marian...@utexas.edu
> PhD candidate
> Ecology, Evolution & Behavior
> Integrative Biology
> The University of Texas at Austin
>
>
>
>
>
> [[alternative HTML version deleted]]
>
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