vcv {ape} | R Documentation |
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"
.
vcv(phy, ...) ## S3 method for class 'phylo' vcv(phy, model = "Brownian", corr = FALSE, ...) ## S3 method for class 'corPhyl' vcv(phy, corr = FALSE, ...)
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. |
a numeric matrix with the names of the tips as colnames and rownames.
Do not confuse this function with vcov
which
computes the variance-covariance matrix among parameters of a fitted
model object.
Emmanuel Paradis
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.
corBrownian
, corMartins
,
corGrafen
, corPagel
,
corBlomberg
, vcv2phylo
tr <- rtree(5) ## all are the same: vcv(tr) vcv(corBrownian(1, tr)) vcv(corPagel(1, tr))