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
vcv(phy, ...) ## S3 method for class 'phylo': vcv(phy, model = "Brownian", corr = FALSE, ...) ## S3 method for class 'corPhyl': vcv(phy, corr = FALSE, ...)
- an object of the correct class (see above).
- 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).
- a logical indicating whether the correlation matrix should
be returned (
TRUE); by default the variance-covariance matrix is returned (
- further arguments to be passed to or from other methods.
- a numeric matrix with the names of the tips as colnames and rownames.
Do not confuse this function with
computes the variance-covariance matrix among parameters of a fitted
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.
tr <- rtree(5) ## all are the same: vcv(tr) vcv(corBrownian(1, tr)) vcv(corPagel(1, tr))