ouch-package {ouch}R Documentation

Ornstein-Uhlenbeck methods for comparative phylogenetic hypotheses

Description

The ouch package provides facilities for phylogenetic comparative analysis based on Ornstein-Uhlenbeck models of trait evolution along a phylogeny. Multivariate data and complex adaptive hypotheses are supported.

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

Citing ouch

Execute citation("ouch") to view the correct citation for publications.

Author(s)

Aaron A. King

References

T.F. Hansen. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution, 51:1341–1351.

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

Cressler, C. E., Butler, M. A., and King, A. A. 2015. Detecting adaptive evolution in phylogenetic comparative analysis using the Ornstein-Uhlenbeck model. Systematic Biology, 64:953–968.

See Also

Other phylogenetic comparative models: brown(), hansen(), ouchtree, paint()

Other methods for ouch trees: bootstrap(), coef(), logLik, paint(), plot(), print(), simulate(), summary(), update()

Other examples: anolis.ssd, bimac


[Package ouch version 2.17-2 Index]