One of the utilities of the function
multiOU that I posted yesterdy featuring a difference equation
approximation of the OU model is that it can easily be used to visualize the evolutionary process by permitting
the user to easily retain the states simulated for internal nodes.
A limitation of this is that the evolution along internal edges can include multiple, different regimes.
In the following, I show how to simulate & visualize multi-regime OU in which the regime changes along edges through the use of singleton nodes. With singleton nodes we can break edges of the tree into a set of new edges, each of which has only one regime. I'll use semi-transparent colors to make it easier to visualize the evolutionary process using our traitgram projection.
library(phytools) set.seed(100) cols<-setNames(sapply(c("#e41a1c","#377eb8","#4daf4a"), make.transparent,alpha=0.6),letters[1:3]) tree<-pbtree(n=60,scale=2) Q<-matrix(c(-1,1,0,1,-2,1,0,1,-1),3,3, dimnames=list(letters[1:3],letters[1:3])) tree<-sim.history(tree,Q,anc="a")
## Done simulation(s).
plot(tree,colors=cols,ftype="off",lwd=2) tmp<-markChanges(tree,plot=FALSE) ## for later add.simmap.legend(colors=cols,prompt=FALSE,x=0.05,y=60)
Next, convert our object to a tree with singletons. To that object, we will also add some elements & a class
attribute so that
multiOU will know how to treat the object:
obj<-map.to.singleton(tree) obj$maps<-as.list(obj$edge.length) for(i in 1:length(obj$maps)) names(obj$maps[[i]])<-names(obj$maps)[i] class(obj)<-c("simmap","phylo") ## here's our tree with singletons par(cex=0.6) plotTree.singletons(obj) ## the colors are different
OK, now let's simulate on the tree with singletons:
sig2<-setNames(c(1,1,1),letters[1:3]) alpha<-setNames(c(2,2,2),letters[1:3]) theta<-setNames(c(10,0,-10),letters[1:3]) x<-multiOU(obj,alpha,sig2,theta,internal=TRUE,dt=1/10000*2) phenogram(obj,x,ftype="off",colors=cols,ylim=c(-11,11), xlim=c(0,2),lwd=3) abline(h=c(10,0,-10),lty="dashed",col=cols,lwd=3,lend=2) abline(v=tmp[,"x"],lwd=1,lty="dashed",col=make.transparent("grey",0.2)) add.simmap.legend(colors=cols,prompt=FALSE,x=0,y=-5)
Obviously, what's cool about this is that we can see the direction of evolution change along edges at the point that a regime change has been simulated. Neat.
Is there a way you could insert more singleton nodes on the tree, to break up those straight lines on the resulting phenogramReplyDelete