Tuesday, September 11, 2012

Joint estimation of Pagel's λ for multiple characters

In a previous post, I described adding a previously internal function for computing the likelihood of a single value of λ for multiple traits to the NAMESPACE of phytools. This function (likMlambda) can now be used in a very simple way to find the ML joint λ estimate for multiple characters. This is described (if I remember correctly) in Freckleton et al. (2002) and implemented internally in the phytools functions phyl.cca & phyl.pca, but not in any stand alone functions. Here is the function:

  result<-optimize(f=likMlambda,X=X,C=vcv(tree),interval=c(0,1),     maximum=TRUE)

Let's try it out:

> tree<-pbtree(n=100)
> X<-fastBM(lambdaTree(tree,0.7),nsim=10)
> joint.lambda(tree,X)
[1] 0.6722762
[1] -1816.575

Pretty cool.


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