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)
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.

Aliases
  • coalescent.intervals
  • coalescent.intervals.phylo
  • coalescent.intervals.default
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 3.2, License: GPL (>= 2)

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