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 |
corr |
a logical indicating whether the correlation matrix should
be returned ( |
... |
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))