# chronogram

From ape v2.1-1
by Emmanuel Paradis

##### 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

##### 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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