R: Phylogenetic Variance-covariance or Correlation Matrix

vcv {ape} | R Documentation

## Phylogenetic Variance-covariance or Correlation Matrix

### Description

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"`.

### 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.

### Author(s)

Emmanuel Paradis

### 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))

[Package ape version 4.1 Index]