ape (version 1.3-1)

ratogram: Ratogram Computed by Nonparametric Rate Smoothing

Description

ratogram computes a ratogram from a phylogram by applying the NPRS (nonparametric rate smoothing) algorithm described in Sanderson (1997).

Usage

ratogram(phy, scale = 1, expo = 2, minEdgeLength = 1e-06)

Arguments

phy

A phylogenetic tree (i.e. an object of class "phylo"), where the branch lengths are measured in substitutions.

scale

Age of the root in the chronogram corresponding to the inferred ratogram(default value: 0).

expo

Exponent in the objective function (default value: 2)

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.

Value

• chronogram returns an object of class "phylo". The branch lengths of this tree will be the absolute rates estimated for each branch.

Details

Please refer to Sanderson (1997) for mathematical details

References

Sanderson, M. J. (1997) A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution, 14, 1218--1231.

See Also

chronogram, NPRS.criterion.

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 ratogram
rato.plants <- ratogram(tree.landplants)

# plot and write to file
plot(rato.plants, label.offset = 0.001)
write.tree(rato.plants, file = "ratogram.phy")