browntree-class: Fitted phylogenetic Brownian motion model

Description Details Methods Author(s) See Also

Description

A fitted phylogenetic Brownian-motion model object.

Details

The function brown creates a browntree object by fitting a Brownian-motion model to data.

Methods

plot()

plots the tree.

print()

prints the tree as a table, along with the coefficients of the fitted model and diagnostic information.

show()

displays the fitted browntree object.

summary()

displays information on the call, the fitted coefficients, and model selection statistics.

coerce

A browntree object can be coerced to a data-frame via as(object,"data.frame").

coef(object,...)

extracts the coefficients of the fitted model. This is a list with three elements:

sigma:

the coefficients of the sigma matrix.

theta:

a list of the estimated optima, one per character.

sigma..sq.matrix:

the sigma-squared matrix itself.

logLik(object,...)

extracts the log likelihood of the fitted model.

update(object, ...)

refits the model. object is the browntree object. Additional arguments (in ...) replace the corresponding arguments in the original call.

bootstrap(object, nboot = 200, seed = NULL, ...)

performs a parametric bootstrap for estimation of confidence intervals. object is the browntree object. nboot is the number of bootstraps. seed allows one to fix the random seed (see simulate below). Additional arguments (in ...) are passed to update.

simulate(object, nsim = 1, seed = NULL, ...)

generates random deviates from the fitted model. object is the browntree object, nsim is the desired number of replicates, and seed is (optionally) the random seed to use. simulate returns a list of data-frames, each comparable to the original data.

Author(s)

Aaron A. King kingaa at umich dot edu

See Also

ouchtree, brown


ouch documentation built on May 19, 2017, 9:22 a.m.

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