package: Ornstein-Uhlenbeck methods for comparative phylogenetic...

In ouch: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

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

• Phylogenies in ouch format: ouchtree(), ape2ouch()

• Brownian motion models: brown()

• Ornstein-Uhlenbeck models: hansen(), paint()

• Simulation of models: simulate()

• Display of data: plot()

• Extraction of information from fitted models: summary(), logLik(), coef()

• Example datasets: anolis.ssd, bimac

Citing ouch

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

Author(s)

Aaron A. King

References

\Hansen

1997

\Butler

2004

\Cressler

2015

See Also

Useful links:

• https://kingaa.github.io/ouch/

• Report bugs at https://github.com/kingaa/ouch/issues/

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

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

Other examples: anolis.ssd, bimac, geospiza

ouch documentation built on July 4, 2024, 5:08 p.m.