Tuesday, June 28, 2011

Plot stochastic character mapped tree

I just completed a beta version of my plotSimmap() function. I'll post a little more about how this was accomplished tomorrow, but it was fairly straightforward after figuring out how to plot rooted phylograms generally (see previous post here). To check it out, download it (source here), load the source into R, and then run the following code (for example):

> require(geiger)
> require(phytools)
> tree<-drop.tip(birthdeath.tree(b=1,d=0,taxa.stop=21),"21")
> x<-sim.char(tree,model.matrix=list(matrix(c(-1,1,1,-1),2,2)),
model="discrete")[,,1]
> mtree<-make.simmap(tree,x)
> legend<-c("red","yellow"); names(legend)<-c(1,2)
> source("plotSimmap.R")
> plotSimmap(mtree,legend)


It might also be a good to download the latest version of make.simmap() because there may be a bug in the previous version. I'll add these updates to the next version of {phytools}.

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