# vcv

##### 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 phylo
vcv(phy, model = "Brownian", corr = FALSE, ...)
# S3 method for 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

```
# NOT RUN {
tr <- rtree(5)
## all are the same:
vcv(tr)
vcv(corBrownian(1, tr))
vcv(corPagel(1, tr))
# }
```

*Documentation reproduced from package ape, version 5.3, License: GPL (>= 2)*