4 \title{Chronogram Computed by Nonparametric Rate Smoothing}
6 chronogram(phy, scale = 1, expo = 2, minEdgeLength = 1e-06)
9 \item{phy}{A phylogenetic tree (i.e. an object of class
10 \code{"phylo"}), where the branch lengths are measured in substitutions.}
11 \item{scale}{Age of the root in the inferred chronogram (default value: 0). }
12 \item{expo}{Exponent in the objective function (default value: 2)}
13 \item{minEdgeLength}{Minimum edge length in the phylogram (default
14 value: 1e-06). If any branch lengths are smaller then they will be
18 \code{chronogram} computes a chronogram from a phylogram by applying the NPRS
19 (nonparametric rate smoothing) algorithm described in Sanderson (1997).
22 Please refer to Sanderson (1997) for mathematical details
25 \code{chronogram} returns an object of class \code{"phylo"}. The branch lengths of this
26 tree will be clock-like and scaled so that the root node has age 1 (or the value
27 set by the option \code{scale}
30 Gangolf Jobb (\url{http://www.treefinder.de}) and
31 Korbinian Strimmer (\url{http://www.stat.uni-muenchen.de/~strimmer/})
34 \code{\link{ratogram}}, \code{\link{NPRS.criterion}}.
37 Sanderson, M. J. (1997) A nonparametric approach to estimating
38 divergence times in the absence of rate constancy. \emph{Molecular
39 Biology and Evolution}, \bold{14}, 1218--1231.
43 data("landplants.newick") # example tree in NH format
44 tree.landplants <- read.tree(text = landplants.newick)
48 plot(tree.landplants, label.offset = 0.001)
51 chrono.plants <- chronogram(tree.landplants)
54 plot(chrono.plants, label.offset = 0.001)
56 # value of NPRS function for our estimated chronogram
57 NPRS.criterion(tree.landplants, chrono.plants)