Thursday, January 30, 2014

New version of ancThresh for λ model

The current version of ancThresh (for ancestral character estimation under the threshold model; see Revell In press) permits a Brownian or Ornstein-Uhlenbeck model for the evolution of the liabilities. I just added a 3rd model, the λ model of Pagel (1999). The code for this version is here; but since it uses some functions internally that have also been updated, the best thing to do is to update phytools to the latest version.

I'm not a huge fan of the λ model in general, since it is not clear what biological process it is meant to approximate; however under some circumstances it could be a useful model for traits that evolve on the tree (and thus have phylogenetic covariance), but are also affected by contemporary factors that are not necessarily phylogenetically correlated. This is how I am using this model in the empirical study for which I have added this feature to ancThresh.

At the moment it is largely untested - so if you run into any problems, please let me know.

No comments:

Post a Comment