vcv

0th

Percentile

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 "phylo" and "corPhyl".

Keywords
multivariate, manip
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 "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.

Note

Do not confuse this function with vcov which computes the variance-covariance matrix among parameters of a fitted model object.

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

Aliases
  • vcv
  • vcv.phylo
  • vcv.corPhyl
Examples
tr <- rtree(5)
## all are the same:
vcv(tr)
vcv(corBrownian(1, tr))
vcv(corPagel(1, tr))
Documentation reproduced from package ape, version 2.7-3, License: GPL (>= 2)

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