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:
Let's try it out:
Where can I find the likMlambda function?
It is in the current CRAN version of phytools.Delete