ape (version 5.8)

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

Value

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

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.

Author

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))