# vcv

From ape v3.2
by Emmanuel Paradis

##### Phylogenetic Variance-covariance or Correlation Matrix

This function computes the expected variances and covariances of a continuous trait assuming it evolves under a given model.

This is a generic function with methods for objects of class
`"phylo"`

and `"corPhyl"`

.

- Keywords
- multivariate, manip

##### Usage

```
vcv(phy, ...)
## S3 method for class 'phylo':
vcv(phy, model = "Brownian", corr = FALSE, ...)
## S3 method for class 'corPhyl':
vcv(phy, corr = FALSE, ...)
```

##### Arguments

- phy
- an object of the correct class (see above).
- model
- a character giving the model used to compute the
variances and covariances; only
`"Brownian"`

is available (for other models, a correlation structure may be used). - corr
- a logical indicating whether the correlation matrix should
be returned (
`TRUE`

); by default the variance-covariance matrix is returned (`FALSE`

). - ...
- further arguments to be passed to or from other methods.

##### Value

- a numeric matrix with the names of the tips as colnames and rownames.

##### Note

Do not confuse this function with `vcov`

which
computes the variance-covariance matrix among parameters of a fitted
model object.

##### References

Garland, T. Jr. and Ives, A. R. (2000) Using the past to predict the
present: confidence intervals for regression equations in phylogenetic
comparative methods. *American Naturalist*, **155**, 346--364.

##### See Also

`corBrownian`

, `corMartins`

,
`corGrafen`

, `corPagel`

,
`corBlomberg`

, `vcv2phylo`

##### Examples

```
tr <- rtree(5)
## all are the same:
vcv(tr)
vcv(corBrownian(1, tr))
vcv(corPagel(1, tr))
```

*Documentation reproduced from package ape, version 3.2, License: GPL (>= 2)*

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