ouch (version 1.0-3)

brown.fit: Brownian-motion model of evolution along a phylogenetic tree

Description

These functions relate to the Brownian motion model for phylogenetic evolution. brown{fits the parameters sigma and theta of this model to given data.} brown.dev{generates simulated data sets.}

Usage

brown.fit(data, topology, times)
brown.dev(n = 1, topology, times, sigma, theta)

Arguments

data

Phenotypic data for extant species, i.e., at the terminal ends of the phylogenetic tree.

topology

Specification of the topology of the phylogenetic tree. This is in the form of a vector of nonnegative integers, one for each node in the tree. The i-th number is that of the ancestor of the i-th node. The root node is distinguished by the

times

A vector of nonnegative numbers, one per node in the tree, specifying the time at which each node is located. The root node should be assigned time 0.

n

the number of simulated data sets to generate.

sigma

the value of sigma to be used in the simulations.

theta

the value of theta to be used in the simulations.

Value

• brown returns a list of the following elements:
• sigma
  Maximum likelihood estimate of sigma.
• theta
  Maximum likelihood estimate of theta.
• u
  -2 log likelihood.
• aic
  Akaike information criterion.
• sic
  Schwartz information criterion (=BIC)
• df
  Number of parameters estimated (= 2).
• brown.dev returns a data frame containing simulated data sets. Each realization is a row.

References

Butler, M.A. and A.A. King (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist, in press.