Dear Enrico/Emmanuel,
Actually, I just realized I need continuous traits, not discrete. Sorry about that. Thanks so much for pointing me towards rTrait(using Cont). Would it be right that a one optima OU model with rTraitCont would have theta set to one single value? And a two optima model would have theta at two possible values for each branch? Etc.? Enrico, thanks very much for that thought. So I am simulating trees and traits on trees, and then calculating K using the phylosignal function. Thus, K is implicitly manipulated, instead of explicitly manipulated. Scott On Monday, January 31, 2011 at 3:28 AM, Enrico Rezende wrote: > Scott, > one important caveat that should be added is that, even when one knows > and controls the parameters of the evolutionary model, the resulting > dataset will have the expected amount of signal only ON AVERAGE, given > the inherent stochasticity of these models. For instance, if you want K > = 1 and assume Brownian motion character evolution on a given tree, you > may still get data that have a K ranging between, say, 0.6 and 1.4 (with > a mean K = 1, of course). Thus, you might want to quantify K after the > simulations to ensure that you're obtaining the amount of signal desired. > > Ah yes, this applies primarily to quantitative traits, for qualitative > characters things change a bit. > > Enrico > > > > Emmanuel Paradis escribió: > > > On Fri, 28 Jan 2011 17:20:57 -0600 Scott Chamberlain > > <myrmecocys...@gmail.com> wrote: > > > > > Dear R community, > > > I would like to simulate discrete characters on a randomly generated > > > tree. However, I would like to create different sets of trees and > > > associated characters at certain levels of phylogenetic signal. > > > > > > > > > > If you know the relationship between phylogenetic signal (Blomberg et > > al's K in your case) and the parameters of the model used to simulate > > the characters, this would be easy. But I don't think this > > relationship is obvious, at least for discrete characters. Keep in > > mind also that, for a given model and parameters of evolution, the > > quantity of phylogenetic signal depends on the tree. > > > > > > > Can someone point me in the right direction? > > > > > > I am familiar with sim.char from geiger package for simulating > > > characters, and rcoal for simulating the ultrametric trees that I > > > want, but I don't know how I could, if at all, simulate characters > > > that have a particular a priori set phylogenetic signal. > > > > > > > > > > BTW, instead of rcoal() you may wish to use rbdtree(). And if you want > > more flexibility for simulating the characters, see rTraitDisc() in ape. > > > > Best, > > > > Emmanuel > > > > > > > As a simple example, the following example gets phylogenetic signal > > > (K) that is all over the map in different runs: > > > > > > > > > q <- list(rbind(c(-.5, .5), c(.5, -.5))) > > > traits <- sim.char(tree, q, model = "discrete", n = 1) > > > traits_ <- as.data.frame(traits[,,1]) > > > traitsvec <- traits_[,1] > > > names(traitsvec) <- rownames(traits_) > > > phylosignal(traitsvec, tree, reps = 100) > > > > > > > > > > > > > > > > > > > > > > > > Sincerely, > > > > > > Scott Chamberlain > > > Rice University, EEB Dept. > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > R-sig-phylo mailing list > > > R-sig-phylo@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > > > > > > > > _______________________________________________ > > R-sig-phylo mailing list > > R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > > > > > -- > ******************************************************************* > Enrico L. Rezende > > Departament de Genètica i de Microbiologia > Facultat de Biociències, Edifici Cn > Universitat Autònoma de Barcelona > 08193 Bellaterra (Barcelona) > SPAIN > > Telephone: +34 93 581 4705 > Fax: +34 93 581 2387 > E-mail: enrico.reze...@uab.cat > > ******************************************************************* > > > [[alternative HTML version deleted]]
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