brown.fit {ouch}R Documentation

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 number zero (0).
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.

Author(s)

Aaron A. King <king at tiem dot utk dot edu>

References

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


[Package Contents]