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, ...)
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.
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.