4 \title{Ratogram Computed by Nonparametric Rate Smoothing}
6 ratogram(phy, scale = 1, expo = 2, minEdgeLength = 1e-06)
9 \item{phy}{A phylogenetic tree (i.e. an object of class \code{"phylo"}), where
10 the branch lengths are measured in substitutions.}
12 \item{scale}{Age of the root in the chronogram corresponding to the inferred ratogram(default value: 0). }
14 \item{expo}{Exponent in the objective function (default value: 2)}
15 \item{minEdgeLength}{Minimum edge length in the phylogram (default value: 1e-06). If any branch lengths are
16 smaller then they will be set to this value. }
20 \code{ratogram} computes a ratogram from a phylogram by applying the NPRS
21 (nonparametric rate smoothing) algorithm described in Sanderson (1997).
24 Please refer to Sanderson (1997) for mathematical details
27 \code{chronogram} returns an object of class \code{"phylo"}. The branch lengths of this
28 tree will be the absolute rates estimated for each branch.
30 \author{Gangolf Jobb (\url{http://www.treefinder.de}) and
31 Korbinian Strimmer (\url{http://www.stat.uni-muenchen.de/~strimmer/})
34 \code{\link{chronogram}}, \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 rato.plants <- ratogram(tree.landplants)
54 plot(rato.plants, label.offset = 0.001)