\name{chronopl}
\alias{chronopl}
\title{Molecular Dating With Penalized Likelihood}
+\description{
+ 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).
+}
\usage{
chronopl(phy, lambda, age.min = 1, age.max = NULL,
node = "root", S = 1, tol = 1e-8,
algorithm.}
\item{\dots}{further arguments passed to control \code{nlminb}.}
}
-\description{
- 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
formulation where each branch has its own rate, and a nonparametric
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).
+ If two nodes are linked (i.e., one is the ancestor of the other) and
+ have the same values of \code{age.min} and \code{age.max} (say, 10 and
+ 15) this will result in an error because the medians of these values
+ are used as initial times (here 12.5) giving initial branch length(s)
+ equal to zero. The easiest way to solve this is to change slightly the
+ given values, for instance use \code{age.max = 14.9} for the youngest
+ node, or \code{age.max = 15.1} for the oldest one (or similarly for
+ \code{age.min}).
+
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
}
\author{Emmanuel Paradis}
\seealso{
- \code{\link{chronogram}}, \code{\link{ratogram}},
- \code{\link{NPRS.criterion}}, \code{\link{chronoMPL}}
+ \code{\link{chronoMPL}}
}
\keyword{models}