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
Phylogenies in ouch format:
ouchtree()
,ape2ouch()
Brownian motion models:
brown()
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
T.F. Hansen. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution, 51:1341–1351. 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. 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. doi:10.1093/sysbio/syv043.
See Also
Useful links:
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