# NPRS.criterion

From ape v2.1-1
by Emmanuel Paradis

##### 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.

##### See Also

##### 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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