coalescent.intervals

From ape v5.3
0th

Percentile

Coalescent Intervals

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).

Keywords
manip
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.

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

Aliases
• coalescent.intervals
• coalescent.intervals.phylo
• coalescent.intervals.default
Examples
# NOT RUN {
data("hivtree.newick") # example tree in NH format