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

To cite the ‘ouch’ package in publications, use: M. A. Butler and A. A. King (2004). Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164:683–695. DOI:10.1086/426002. Additionally, consider citing the package itself: Aaron A. King and Marguerite A. Butler (2021). ouch: Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses. (R package, version 2.17-1). https://kingaa.github.io/ouch/

LaTeX users can obtain BibTeX entries for the above by executing toBibtex(citation("ouch")).

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 2.17-1 Index]