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.
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.
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
Execute citation("ouch") to view the correct citation for publications.
Aaron A. King
T.F. Hansen. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution, 51:1341--1351. tools:::Rd_expr_doi("10.1111/j.1558-5646.1997.tb01457.x").
Butler, M.A. and A.A. King. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164:683--695. tools:::Rd_expr_doi("10.1086/426002").
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. tools:::Rd_expr_doi("10.1093/sysbio/syv043").