ouch (version 2.7-2)

ouch-deprecated: Deprecated functions in the "ouch" package

Description

These functions are deprecated.

Usage

is.valid.ouch.tree(node, ancestor, times, regimes = NULL)
tree.plot(node, ancestor, times, names = NULL, regimes = NULL)
brown.fit(data, node, ancestor, times)
brown.dev(n = 1, node, ancestor, times, sigma, theta)
hansen.fit(data, node, ancestor, times, regimes = NULL,
           interval = c(0, 100), tol = 1e-12)
hansen.prof(alpha, data, node, ancestor, times, regimes = NULL)
hansen.dev(n = 1, node, ancestor, times, regimes = NULL,
           alpha, sigma, theta)

Arguments

data

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

node

Specification of the 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.

names

Optional vector of species names.

n

Number of pseudorandom data sets to generate.

sigma

the value of $\sigma$ to be used in the simulations.

alpha

Value of selection-strength parameter $\alpha$.

theta

the value of $\theta$ to be used in the simulations.

interval

The interval which will be searched for the optimal $\alpha$. By default, $0 < \alpha < 100$.

tol

Convergence tolerance.

Details

Phylogenetic trees in ouch are now implemented using the S4 class ouchtree. The validity checks formerly implemented by is.valid.ouch.tree are now performed when an ouchtree is contructed; see ouchtree, ouchtree-class. The ouchtree class has a plot method, obviating the need for tree.plot; see ouchtree-class.

Brownian motion (BM) models are now built around the S4 class browntree. Fitting BM models is now accomplished by means of brown; generating random deviates from a fitted model, by the simulate method for browntree-class objects. See browntree-class.

The Ornstein-Uhlenbeck-based Hansen models are now implemented using the S4 class hansentree. They are fit using hansen; see hansentree-class for documentation of the simulate method for this class.

See Also

ouch-package