Ornstein-Uhlenbeck methods for comparative phylogenetic hypotheses

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Description

The ouch package provides facilities for Ornstein-Uhlenbeck based methods of phylogenetic comparative analysis.

Classes

The basic class, ouchtree, is provided to encode a phylogenetic tree. Plot and print methods are provided.

The class browntree derives from class ouchtree and encodes the results of fitting a Brownian Motion model to data.

The class hansentree derives from class ouchtree and encodes the results of fitting a Hansen model to data.

Detailed Documentation

ouchtree

ouchtree

Brownian motion methods

brown, browntree-class

Ornstein-Uhlenbeck methods

hansen, hansentree-class

simulate methods

simulate-browntree, simulate-hansentree

plot methods

plot-browntree, plot-hansentree

ape2ouch

Convert a tree in ape format to ouch format. See ape2ouch

Author(s)

Aaron A. King (kingaa at umich dot edu)

References

Butler, M.A. and A.A. King (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164:683–695.