ape (version 5.8)

coalescent.intervals: 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)

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.

Arguments

x

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

Author

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