# corBrownian

From ape v2.1-1
by Emmanuel Paradis

##### Brownian Correlation Structure

Expected covariance under a Brownian model (Felsenstein 1985, Martins and Hansen 1997): $$V_{ij} = \gamma \times t_a$$ where $t_a$ is the distance on the phylogeny between the root and the most recent common ancestor of taxa $i$ and $j$ and $\gamma$ is a constant.

- Keywords
- models

##### Usage

```
corBrownian(value=1, phy, form=~1)
## S3 method for class 'corBrownian':
coef(object, unconstrained = TRUE, ...)
## S3 method for class 'corBrownian':
corMatrix(object,
covariate = getCovariate(object), corr = TRUE, ...)
```

##### Arguments

- value
- The $\gamma$ parameter (default to 1)
- phy
- An object of class
`phylo`

representing the phylogeny (with branch lengths) to consider - object
- An (initialized) object of class
`corBrownian`

- corr
- a logical value. If 'TRUE' the function returns the correlation matrix, otherwise it returns the variance/covariance matrix.
- form
- ignored for now.
- covariate
- ignored for now.
- unconstrained
- a logical value. If 'TRUE' the coefficients are returned in unconstrained form (the same used in the optimization algorithm). If 'FALSE' the coefficients are returned in "natural", possibly constrained, form. Defaults to 'TRUE'
- ...
- some methods for these generics require additional arguments. None are used in these methods.

##### Value

- An object of class
`corBrownian`

or coefficient from an object of this class (actually sends`numeric(0)`

!) or the correlation matrix of an initialized object of this class.

##### References

Felsenstein, J. (1985) Phylogenies and the comparative method.
*American Naturalist*, **125**, 1--15.

Martins, E. P. and Hansen, T. F. (1997) Phylogenies and the comparative
method: a general approach to incorporating phylogenetic information
into the analysis of interspecific data. *American Naturalist*,
**149**, 646--667.

##### See Also

*Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)*

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