ape (version 1.2-3)

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)

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:
  • lineagesA vector with the number of lineages at the start of each coalescent interval.
  • interval.lengthA vector with the length of each coalescent interval.
  • interval.countThe total number of coalescent intervals.
  • total.depthThe sum of the lengths of all coalescent intervals.

See Also

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

Examples

Run this code
library(ape)

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

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