[R-sig-phylo] generate liability/threshold plot from ancThresh
Hi folks, I'm trying to generate the thresholds and liabilities plot, including the posterior support values, from Revell (2014) Evolution 68(3), Figure 6B. Does anybody have a script for this? I see the liabilities output from ancThresh(), but no thresholds. Thanks! ~John John S. S. Denton, Ph.D. Department of Vertebrate Paleontology American Museum of Natural History www.johnssdenton.com ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] generate liability/threshold plot from ancThresh
Hi John. The posterior sample of the relative positions of the thresholds (if there is more than one) are output in the matrix par, i.e.: mcmc-ancThresh(...) mcmc$par ## contains the posterior sample of the thresholds To get a visualization of the posterior density you can, for instance, use stats function density with the column of interest from par as input. Is that helpful? I hope a little bit. All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 5/2/2014 9:26 AM, John Denton wrote: Hi folks, I'm trying to generate the thresholds and liabilities plot, including the posterior support values, from Revell (2014) Evolution 68(3), Figure 6B. Does anybody have a script for this? I see the liabilities output from ancThresh(), but no thresholds. Thanks! ~John John S. S. Denton, Ph.D. Department of Vertebrate Paleontology American Museum of Natural History www.johnssdenton.com ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] problem with phylock package
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 cant 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]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] problem with phylock package
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]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
