ape (version 1.2-5)

chronogram: Chronogram Computed by Nonparametric Rate Smoothing

Description

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

Usage

chronogram(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 inferred chronogram (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 clock-like and scaled so that the root node has age 1 (or the value set by the option scale

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

ratogram, 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 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)