coalescent.intervals: Coalescent Intervals
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Value Author(s) See Also Examples

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).

1	coalescent.intervals(x)

`x`	either an ultra-metric phylogenetic tree (i.e. an object of class `"phylo"`) or, alternatively, a vector of interval lengths.

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.

Korbinian Strimmer (http://www.stat.uni-muenchen.de/~strimmer/)

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

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