brown.fit {ouch} | R Documentation |
These functions relate to the Brownian motion model for phylogenetic evolution.
brown.fit(data, topology, times) brown.dev(n = 1, topology, times, sigma, theta)
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. |
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.
Aaron A. King <king at tiem dot utk dot edu>
Butler, M.A. and A.A. King (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist, in press.