R: Coalescent Intervals

coalescent.intervals {ape} | R Documentation

## Coalescent Intervals

### Description

This function extracts or generates information about coalescent intervals (number of lineages, interval lengths, interval count, total depth) from a phylogenetic tree or a list of internode distances. The input tree needs to be ultra-metric (i.e. clock-like).

### Usage

    coalescent.intervals(x)

### Arguments

`x` | either an ultra-metric phylogenetic tree (i.e. an object of class `"phylo"`) or, alternatively, a vector of interval lengths.

### Value

An object of class `"coalescentIntervals"` with the following entries:

`lineages` | A vector with the number of lineages at the start of each coalescent interval.
`interval.length` | A vector with the length of each coalescent interval.
`interval.count` | The total number of coalescent intervals.
`total.depth` | The sum of the lengths of all coalescent intervals.

### Author(s)

Korbinian Strimmer

### See Also

`branching.times`, `collapsed.intervals`, `read.tree`.

### Examples

    data("hivtree.newick") # example tree in NH format
    tree.hiv <- read.tree(text = hivtree.newick) # load tree
    ci <- coalescent.intervals(tree.hiv) # from tree
    ci
    data("hivtree.table") # same tree, but in table format
    ci <- coalescent.intervals(hivtree.table$size) # from vector of interval lengths
    ci

[Package ape version 5.6 Index]