# NPRS.criterion

From ape v2.1-1
0th

Percentile

##### Objective Function Employed in Nonparametric Rate Smoothing

NPRS.criterion computes the objective function to be minimized in the NPRS (nonparametric rate smoothing) algorithm described in Sanderson (1997).

Keywords
manip
##### Usage
NPRS.criterion(phy, chrono, expo = 2, minEdgeLength = 1e-06)
##### Arguments
phy
A non-clock-like phylogenetic tree (i.e. an object of class "phylo"), where the branch lengths are measured in substitutions.
chrono
A chronogram, i.e. a clock-like tree (i.e. an object of class "phylo"), where the branch lengths are measured in absolute time.
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. Note that is is not computationally efficient to optimize the branch lengths in a chronogram by using NPRS.criterion - please use chronogram instead.

##### Value

• NPRS.criterion returns the value of the objective function given a phylogram and a chronogram.

##### 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.

ratogram, chronogram

##### Aliases
• NPRS.criterion
##### Examples
# get tree
data("landplants.newick") # example tree in NH format

# 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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