chronogram {ape}R Documentation

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.

Details

Please refer to Sanderson (1997) for mathematical details

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

Author(s)

Gangolf Jobb (http://www.treefinder.de) and Korbinian Strimmer (http://www.stat.uni-muenchen.de/~strimmer/)

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)

[Package ape version 1.7 Index]