chronogram

0th

Percentile

Chronogram Computed by Nonparametric Rate Smoothing

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

Keywords
manip
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

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.

Aliases
  • chronogram
Examples
# 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
plot(chrono.plants, label.offset = 0.001)

# value of NPRS function for our estimated chronogram
NPRS.criterion(tree.landplants, chrono.plants)
Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)

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