params_process: Create an object params_process

In PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

Create an object params_process

Description

params_process creates or extracts a set of parameters of class params_process.

Usage

params_process(x, ...)

Arguments

x	an S3 object.
...	further arguments to be passed to the specific method.

Value

An S3 object of class params_process. This is essentially a list containing the following entries:

process

The model used. One of "BM" (for a full BM model, univariate or multivariate); "OU" (for a full OU model, univariate or multivariate); or "scOU" (for a "scalar OU" model).

p

Dimension of the trait.

root.state

List describing the state of the root, with:

random

random state (TRUE) or deterministic state (FALSE)

value.root

if deterministic, value of the character at the root

exp.root

if random, expectation of the character at the root

var.root

if random, variance of the character at the root (pxp matrix)

shifts

List with position and values of the shifts:

edges

vector of the K id of edges where the shifts are

values

matrix p x K of values of the shifts on the edges (one column = one shift)

relativeTimes

vector of dimension K of relative time of the shift from the parent node of edges

variance

Variance-covariance matrix size p x p.

selection.strength

Matrix of selection strength size p x p (OU).

optimal.value

Vector of p optimal values at the root (OU).

See Also

params_process.character, params_process.PhyloEM, params_BM, params_OU simul_process.params_process

PhylogeneticEM documentation built on Aug. 31, 2022, 9:16 a.m.