[R-sig-phylo] profiles.plot legends
Hi all, I have a very simple question (I'm sure) that I can't quite seem to figure out. I have been trying to plot posterior distributions of parameter estimates from a BiSSE analysis using MCMC in diversitree. I have used the following code to compare the speciation rates between states (cdpostburn is the mcmc object), which generally does what I want. profiles.plot(cdpostburn[c(lambda0,lambda1)],col.line=c(blue, red),las=1,xlab=Speciation rate, legend=topright) The one thing is that the labels in the legend simply say 'lambda0' and 'lambda1', whereas I want them to be a little more informative. Again, I'm sure this is a very simple question but how do I specify the legend labels in the profiles.plot function? Thanks, Kev [[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] profiles.plot legends
Thanks Nick, I am beginning to suspect that adding the legend separately is the way to go. Kev From: Nicholas Crouch [ncro...@uic.edu] Sent: 14 March 2014 14:59 To: Arbuckle, Kevin Subject: Re: [R-sig-phylo] profiles.plot legends Kev, I'm pretty sure that would require going into the BiSSE code. Previously, I have just manually added the legend myself, then you can specify greek letters Nick On Fri, Mar 14, 2014 at 9:49 AM, Arbuckle, Kevin k.arbuc...@liverpool.ac.ukmailto:k.arbuc...@liverpool.ac.uk wrote: Hi all, I have a very simple question (I'm sure) that I can't quite seem to figure out. I have been trying to plot posterior distributions of parameter estimates from a BiSSE analysis using MCMC in diversitree. I have used the following code to compare the speciation rates between states (cdpostburn is the mcmc object), which generally does what I want. profiles.plot(cdpostburn[c(lambda0,lambda1)],col.line=c(blue, red),las=1,xlab=Speciation rate, legend=topright) The one thing is that the labels in the legend simply say 'lambda0' and 'lambda1', whereas I want them to be a little more informative. Again, I'm sure this is a very simple question but how do I specify the legend labels in the profiles.plot function? Thanks, Kev [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.orgmailto: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/ -- Nicholas Crouch Graduate Student Department of Biological Sciences University of Illinois at Chicago [[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] Outgroup with sim.char
Hi R-ers, I am using the discrete argument in sim.char on a preset reference tree, and will eventually be using those simulated characters to re-reconstruct the tree in TNT, which requires a preset outgroup. In this case the outgroup must have all states as plesiomorphic (= state 1 in sim.char). Is the root initially set to all state 1, if root = TRUE? Otherwise, I assume I need to add an outgroup to the reference tree initially and use those states. Thanks! Jo -- Jo Wolfe, Ph.D. Gerstner Scholar/Lerner-Gray Fellow Division of Invertebrate Zoology and Richard Gilder Graduate School American Museum of Natural History Central Park West at 79th St New York, NY 10024 [[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/
