Usage
hansen.fit(data, topology, times, regimes,
guess = 0, interval = c(0.001, 20), tol = 1e-12)
hansen.dev(n = 1, topology, times, regimes, alpha, 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
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.
regimes
A vector of codes, one for each node in the
tree, specifying the selective regimes hypothesized to have been
operative. Corresponding to each node, enter the code of the regime
hypothesized for the branch segment terminating in that node.
For the
guess
(Optional). An initial guess for the selection
strength parameter alpha. This is used to initialize the
optimization algorithm.
interval
The interval which will be searched for the optimal
alpha. By default, 0.001 < alpha < 20.
tol
Convergence tolerance.
n
Number of pseudorandom data sets to generate.
alpha
Value of alpha to use.
sigma
Value of sigma to use.
theta
Value of theta to use.