\alias{chronopl}
\title{Molecular Dating With Penalized Likelihood}
\usage{
-chronopl(phy, lambda, node.age = 1, node = "root", CV = FALSE)
+chronopl(phy, lambda, age.min = 1, age.max = NULL,
+ node = "root", S = 1, tol = 1e-8,
+ CV = FALSE, eval.max = 500, iter.max = 500, ...)
}
\arguments{
\item{phy}{an object of class \code{"phylo"}.}
- \item{lambda}{value of the smoothng parameter.}
- \item{node.age}{numeric values specifying the fixed node ages.}
+ \item{lambda}{value of the smoothing parameter.}
+ \item{age.min}{numeric values specifying the fixed node ages (if
+ \code{age.max = NULL}) or the youngest bound of the nodes known to
+ be within an interval.}
+ \item{age.max}{numeric values specifying the oldest bound of the nodes
+ known to be within an interval.}
\item{node}{the numbers of the nodes whose ages are given by
- \code{node.age}; \code{"root"} is a short-cut the number of the
- node.}
+ \code{age.min}; \code{"root"} is a short-cut for the root.}
+ \item{S}{the number of sites in the sequences; leave the default if
+ branch lengths are in mean number of substitutions.}
+ \item{tol}{the value below which branch lengths are considered
+ effectively zero.}
\item{CV}{whether to perform cross-validation.}
+ \item{eval.max}{the maximal number of evaluations of the penalized
+ likelihood function.}
+ \item{iter.max}{the maximal number of iterations of the optimization
+ algorithm.}
+ \item{\dots}{further arguments passed to control \code{nlminb}.}
}
\description{
- This function estimates the node ages of a tree using semi-parametric
- method based on penalized likelihood (Sanderson 2002). The branch
- lengths of the input tree are interpreted as (mean) numbers of
- substitutions.
+ This function estimates the node ages of a tree using a
+ semi-parametric method based on penalized likelihood (Sanderson
+ 2002). The branch lengths of the input tree are interpreted as mean
+ numbers of substitutions (i.e., per site).
}
\details{
The idea of this method is to use a trade-off between a parametric
rate for all branches).
\code{lambda} must be given. The known ages are given in
- \code{node.age}, and the correponding node numbers in \code{node}.
+ \code{age.min}, and the correponding node numbers in \code{node}.
These two arguments must obviously be of the same length. By default,
an age of 1 is assumed for the root, and the ages of the other nodes
are estimated.
+ If \code{age.max = NULL} (the default), it is assumed that
+ \code{age.min} gives exactly known ages. Otherwise, \code{age.max} and
+ \code{age.min} must be of the same length and give the intervals for
+ each node. Some node may be known exactly while the others are
+ known within some bounds: the values will be identical in both
+ arguments for the former (e.g., \code{age.min = c(10, 5), age.max =
+ c(10, 6), node = c(15, 18)} means that the age of node 15 is 10
+ units of time, and the age of node 18 is between 5 and 6).
+
+ The input tree may have multichotomies. If some internal branches are
+ of zero-length, they are collapsed (with a warning), and the returned
+ tree will have less nodes than the input one. The presence of
+ zero-lengthed terminal branches of results in an error since it makes
+ little sense to have zero-rate branches.
+
The cross-validation used here is different from the one proposed by
Sanderson (2002). Here, each tip is dropped successively and the
analysis is repeated with the reduced tree: the estimated dates for
with the full phylogeny, \eqn{t_j^{-i}}{tj[-i]} is the estimated date
for the \eqn{j}{j}th node after removing tip \eqn{i}{i} from the tree,
and \eqn{n}{n} is the number of tips.
+
+ The present version uses the \code{\link[stats]{nlminb}} to optimise
+ the penalized likelihood function: see its help page for details on
+ parameters controlling the optimisation procedure.
}
\value{
an object of class \code{"phylo"} with branch lengths as estimated by
- the function. There are two or three further attributes:
+ the function. There are three or four further attributes:
\item{ploglik}{the maximum penalized log-likelihood.}
\item{rates}{the estimated rates for each branch.}
+ \item{message}{the message returned by \code{nlminb} indicating
+ whether the optimisation converged.}
\item{D2}{the influence of each observation on overall date
estimates (if \code{CV = TRUE}).}
}
approach. \emph{Molecular Biology and Evolution}, \bold{19},
101--109.
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
- \code{\link{chronogram}}, \code{\link{ratogram}},
- \code{\link{NPRS.criterion}}, \code{\link{chronoMPL}}
+ \code{\link{chronoMPL}}
}
\keyword{models}
projects / ape.git / blobdiff