R: Log likelihood of an one-dimensional Ornstein-Uhlenbeck model

OU1d.loglik {phylolm} | R Documentation

## Log likelihood of an one-dimensional Ornstein-Uhlenbeck model

### Description

computes log likelihood of an one-dimensional Ornstein-Uhlenbeck model with an algorithm that is linear in the number of tips in the tree.

### Usage

    OU1d.loglik(trait, phy, model = c("OUrandomRoot", "OUfixedRoot"), parameters = NULL)

### Arguments

`trait` | a vector of trait values.
`phy` | a phylogenetic tree of type phylo with branch lengths.
`model` | an Ornstein-Uhlenbeck model.
`parameters` | List of parameters for the model

### Author(s)

Lam Si Tung Ho

### Examples

    tr = rtree(100)
    alpha = 1
    sigma2 = 1
    sigma2_error = 0.5
    ancestral.state = 0
    optimal.value = 1

    trait = rTrait(n = 1, tr, model = "OU",
                  parameters = list(ancestral.state=ancestral.state, alpha=alpha,
                                    sigma2=sigma2,sigma2_error=sigma2_error,
                                    optimal.value=optimal.value))
    OU1d.loglik(trait=trait, phy=tr, model="OUfixedRoot",
                parameters=list(ancestral.state=ancestral.state, alpha=alpha,sigma2=sigma2,
                                sigma2_error=sigma2_error,optimal.value=optimal.value))

[Package phylolm version 2.6.2 Index]