coalescent.intervals

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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)
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.

Aliases
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
Documentation reproduced from package ape, version 2.7-3, License: GPL (>= 2)

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