Fitted phylogenetic Brownian motion model
Description
A fitted phylogenetic Brownianmotion model object.
Details
The function brown
creates a browntree
object by fitting
a Brownianmotion 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 dataframe viaas(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 sigmasquared matrix itself.
logLik(object,...)

extracts the log likelihood of the fitted model.
update(object, ...)

refits the model.
object
is thebrowntree
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 thebrowntree
object.nboot
is the number of bootstraps.seed
allows one to fix the random seed (seesimulate
below). Additional arguments (in...
) are passed toupdate
. simulate(object, nsim = 1, seed = NULL, ...)

generates random deviates from the fitted model.
object
is thebrowntree
object,nsim
is the desired number of replicates, andseed
is (optionally) the random seed to use.simulate
returns a list of dataframes, each comparable to the original data.
Author(s)
Aaron A. King kingaa at umich dot edu
See Also
ouchtree
, brown
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