Usage
hansen.fit(data, node, ancestor, times, regimes,
guess = 0, interval = c(0.001, 20), tol = 1e-12)
hansen.dev(n = 1, node, ancestor, times, regimes, alpha, sigma, theta)Arguments
data
Phenotypic data for extant species, i.e., at the
terminal ends of the phylogenetic tree.
node
Character vector of names of the nodes.
ancestor
Specification of the topology of the phylogenetic
tree. This is in the form of a character vector of node names, one
for each node in the tree. The i-th name is that of the ancestor of
the i-th node. The root node is distinguished by having
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.
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.