diversitree (version 0.7-2)

asr: Ancestral State Reconstruction

Description

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.

Usage

asr.marginal(lik, pars, nodes=NULL, ...)
asr.joint(lik, pars, n=1, simplify=TRUE, ...)
asr.stoch(lik, pars, n=1, ...) 
make.asr.marginal(lik, ...)
make.asr.joint(lik, ...)
make.asr.stoch(lik, ...)

Arguments

lik

A likelihood function.

pars

A vector of parameters, suitable for lik.

nodes

For asr.marginal only; an optional vector of nodes to return ancestral states for (using ape's index). By default, all nodes are returned.

n

The number of samples to draw from the joint distribution, or number of stochastic reconstructions to make.

simplify

For asr.joint, return a vector of states when n=1? Otherwise leaves as a one row matrix.

...

Additional arguments passed through to future methods

Value

• The return values of the functions are likely to change in the near future. Watch out!

Details

These three functions compute marginal, joint, and stochastic ancestral reconstructions. The make versions return functions that can efficiently be used many times over.

See Also

asr.mkn and asr.bisse for methods specific to particular classes, with examples of use.