ouch-package {ouch} | R Documentation |
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()
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.
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.
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