Perform ancestral state reconstruction. These functions are all generic and will dispatch on the class of the given likelihood functions. Currently methods exist for all generics for Mk2, and marginal ancestral state reconstructions are supported for BiSSE.
asr.marginal(lik, pars, nodes=NULL, ...)
asr.joint(lik, pars, n=1, ...)
asr.stoch(lik, pars, n=1, ...) make.asr.marginal(lik, ...)
make.asr.joint(lik, ...)
make.asr.stoch(lik, ...)
The return values of the functions are likely to change in the near future. Watch out!
A likelihood function.
A vector of parameters, suitable for lik.
For asr.marginal only; an optional vector of
nodes to return ancestral states for (using ape's index). By
default, all nodes are returned.
The number of samples to draw from the joint distribution, or number of stochastic reconstructions to make.
Additional arguments passed through to future methods
Richard G. FitzJohn
These three functions compute marginal, joint, and stochastic
ancestral reconstructions. The make versions return functions
that can efficiently be used many times over.
asr.mkn and asr.bisse for methods specific to particular classes, with examples of use.