https://github.com/cran/ape
Tip revision: f68e51c050f9ec5cc674d158fc58a0835198d441 authored by Emmanuel Paradis on 19 December 2005, 00:00:00 UTC
version 1.8
version 1.8
Tip revision: f68e51c
NPRS.criterion.Rd
\name{NPRS.criterion}
\alias{NPRS.criterion}
\title{Objective Function Employed in Nonparametric Rate Smoothing}
\usage{
NPRS.criterion(phy, chrono, expo = 2, minEdgeLength = 1e-06)
}
\arguments{
\item{phy}{A non-clock-like phylogenetic tree (i.e. an object of class
\code{"phylo"}), where the branch lengths are measured in
substitutions.}
\item{chrono}{A chronogram, i.e. a clock-like tree (i.e. an object of
class \code{"phylo"}), where the branch lengths are measured in
absolute time.}
\item{expo}{Exponent in the objective function (default value: 2)}
\item{minEdgeLength}{Minimum edge length in the phylogram (default
value: 1e-06). If any branch lengths are smaller then they will be
set to this value.}
}
\description{
\code{NPRS.criterion} computes the objective function to be minimized
in the NPRS (nonparametric rate smoothing) algorithm described in
Sanderson (1997).
}
\details{
Please refer to Sanderson (1997) for mathematical details. Note that
is is not computationally efficient to optimize the branch lengths in
a chronogram by using \code{NPRS.criterion} - please use
\code{\link{chronogram}} instead.
}
\value{
\code{NPRS.criterion} returns the value of the objective function given
a phylogram and a chronogram.
}
\author{Gangolf Jobb (\url{http://www.treefinder.de}) and Korbinian
Strimmer (\url{http://www.stat.uni-muenchen.de/~strimmer/})
}
\seealso{
\code{\link{ratogram}}, \code{\link{chronogram}}
}
\references{
Sanderson, M. J. (1997) A nonparametric approach to estimating
divergence times in the absence of rate constancy. \emph{Molecular
Biology and Evolution}, \bold{14}, 1218--1231.
}
\examples{
library(ape)
# get tree
data("landplants.newick") # example tree in NH format
tree.landplants <- read.tree(text = landplants.newick)
# plot tree
tree.landplants
plot(tree.landplants, label.offset = 0.001)
# estimate chronogram
chrono.plants <- chronogram(tree.landplants)
# plot and write to file
plot(chrono.plants, label.offset = 0.001)
write.tree(chrono.plants, file = "chronogram.phy")
# value of NPRS function for our estimated chronogram
NPRS.criterion(tree.landplants, chrono.plants)
}
\keyword{manip}