Description Details Methods Author(s) See Also
A fitted phylogenetic Brownian-motion model object.
The function brown
creates a browntree
object by fitting
a Brownian-motion model to data.
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.
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.
Aaron A. King kingaa at umich dot edu
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