\name{ace}
\alias{ace}
+\alias{print.ace}
\alias{logLik.ace}
\alias{deviance.ace}
\alias{AIC.ace}
ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
model = if (type == "continuous") "BM" else "ER",
scaled = TRUE, kappa = 1, corStruct = NULL, ip = 0.1)
+\method{print}{ace}(x, digits = 4, ...)
\method{logLik}{ace}(object, ...)
\method{deviance}{ace}(object, ...)
\method{AIC}{ace}(object, ..., k = 2)
\method{anova}{ace}(object, ...)
}
\arguments{
- \item{x}{a vector or a factor.}
+ \item{x}{a vector or a factor; an object of class \code{"ace"} in the
+ case of \code{print}.}
\item{phy}{an object of class \code{"phylo"}.}
\item{type}{the variable type; either \code{"continuous"} or
\code{"discrete"} (or an abbreviation of these).}
structure to be used (this also gives the assumed model).}
\item{ip}{the initial value(s) used for the ML estimation procedure
when \code{type == "discrete"} (possibly recycled).}
+ \item{digits}{the number of digits to be printed.}
\item{object}{an object of class \code{"ace"}.}
\item{k}{a numeric value giving the penalty per estimated parameter;
the default is \code{k = 2} which is the classical Akaike
generalized least squares (\code{method = "GLS"}, Martins and Hansen
1997, Cunningham et al. 1998). In the latter case, the specification
of \code{phy} and \code{model} are actually ignored: it is instead
- given through a correlation structure with the option \code{corStruct}.
+ given through a correlation structure with the option
+ \code{corStruct}.
+
+ In the default setting (i.e., \code{method = "ML"} and \code{model =
+ "BM"}) the maximum likelihood estimation is done simultaneously on
+ the ancestral values and the variance of the Brownian motion process;
+ these estimates are then used to compute the confidence intervals in
+ the standard way (see the package \pkg{geiger} for a different
+ implementation). If \code{method = "pic"} or \code{"GLS"}, the
+ confidence intervals are computed using the expected variances under
+ the model, so they depend only on the tree.
For discrete characters (\code{type = "discrete"}), only maximum
likelihood estimation is available (Pagel 1994). The model is
Likelihood of ancestor states in adaptive radiation. \emph{Evolution},
\bold{51}, 1699--1711.
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}, Ben Bolker
-\email{bolker@zoo.ufl.edu}}
+\author{Emmanuel Paradis, Ben Bolker \email{bolker@zoo.ufl.edu}}
\seealso{
\code{\link{corBrownian}}, \code{\link{corGrafen}},
\code{\link{corMartins}}, \code{\link{compar.ou}},