coalescent.intervals

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.

See Also

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
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 5.3, License: GPL (>= 2)

Community examples

Looks like there are no examples yet.