\alias{AIC.ace}
\alias{anova.ace}
\title{Ancestral Character Estimation}
+\description{
+ This function estimates ancestral character states, and the associated
+ uncertainty, for continuous and discrete characters.
+
+ \code{logLik}, \code{deviance}, and \code{AIC} are generic functions
+ used to extract the log-likelihood, the deviance, or the Akaike
+ information criterion of a fitted object. If no such values are
+ available, \code{NULL} is returned.
+
+ \code{anova} is another generic function which is used to compare
+ nested models: the significance of the additional parameter(s) is
+ tested with likelihood ratio tests. You must ensure that the models
+ are effectively nested (if they are not, the results will be
+ meaningless). It is better to list the models from the smallest to the
+ largest.
+}
\usage{
ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
model = if (type == "continuous") "BM" else "ER",
information criterion.}
\item{\dots}{further arguments passed to or from other methods.}
}
-\description{
- This function estimates ancestral character states, and the associated
- uncertainty, for continuous and discrete characters.
-
- \code{logLik}, \code{deviance}, and \code{AIC} are generic functions
- used to extract the log-likelihood, the deviance (-2*logLik), or the
- Akaike information criterion of a tree. If no such values are
- available, \code{NULL} is returned.
-
- \code{anova} is another generic function which is used to compare
- nested models: the significance of the additional parameter(s) is
- tested with likelihood ratio tests. You must ensure that the models
- are effectively nested (if they are not, the results will be
- meaningless). It is better to list the models from the smallest to the
- largest.
-}
\details{
If \code{type = "continuous"}, the default model is Brownian motion
where characters evolve randomly following a random walk. This model
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
+ In the default setting (\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. The REML method first estimates the ancestral value
It could be shown that, with a continous character, REML results in
unbiased estimates of the variance of the Brownian motion process
- while ML gives a downward bias. Therefore, the former is recommanded
- over the latter, even though it is not the default.
+ while ML gives a downward bias. Therefore the former is recommanded,
+ even though it is not the default.
For discrete characters (\code{type = "discrete"}), only maximum
likelihood estimation is available (Pagel 1994). The model is
is determined from the data.
}
\value{
- a list with the following elements:
+ an object of class \code{"ace"} with the following elements:
\item{ace}{if \code{type = "continuous"}, the estimates of the
ancestral character values.}
Likelihood of ancestor states in adaptive radiation. \emph{Evolution},
\bold{51}, 1699--1711.
}
-\author{Emmanuel Paradis, Ben Bolker \email{bolker@zoo.ufl.edu}}
+\author{Emmanuel Paradis, Ben Bolker}
\seealso{
\code{\link{corBrownian}}, \code{\link{corGrafen}},
\code{\link{corMartins}}, \code{\link{compar.ou}},