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.