# cutPhylo: Cut the phylogeny at a given age or node In RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies

 cutPhylo R Documentation

## Cut the phylogeny at a given age or node

### Description

The function cuts all the branches of the phylogeny which are younger than a specific age or node (i.e. the age of the node).

### Usage

```cutPhylo(tree,age=NULL,node=NULL,keep.lineage=TRUE)
```

### Arguments

 `tree` a phylogenetic tree. The tree needs not to be ultrametric and fully dichotomous. `age` the age (in terms of time distance from the recent) at which the tree must be cut `node` the node whose age must be used as cutting limit. `keep.lineage` logical specifying whether lineages with no descendant tip must be retained (see example below). Default is `TRUE`.

### Details

When an entire lineage is cut (i.e. one or more nodes along a path) and `keep.lineages = TRUE`, the leaves left are labeled as "l" followed by a number.

### Value

The function returns the cut phylogeny and plots it into the graphic device. The time axis keeps the root age of the original tree. Note, tip labels are ordered according to their position in the tree.

### Author(s)

Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto

### Examples

```## Not run:
library(ape)

set.seed(22)
rtree(100)->tree
3->age

cutPhylo(tree,age=age)->t1
cutPhylo(tree,age=age,keep.lineage=FALSE)->t1
cutPhylo(tree,node=151)->t2
cutPhylo(tree,node=151,keep.lineage=FALSE)->t2

## End(Not run)
```

RRphylo documentation built on May 9, 2022, 9:08 a.m.