1 \name{coalescent.intervals}
2 \alias{coalescent.intervals}
3 \alias{coalescent.intervals.phylo}
4 \alias{coalescent.intervals.default}
6 \title{Coalescent Intervals}
8 coalescent.intervals(x)
11 \item{x}{either an ultra-metric phylogenetic tree (i.e. an object of
12 class \code{"phylo"}) or, alternatively, a vector of interval lengths.}
15 This function extracts or generates information about coalescent intervals
16 (number of lineages, interval lengths, interval count, total depth) from
17 a phylogenetic tree or a list of internode distances. The input tree
18 needs to be ultra-metric (i.e. clock-like).
21 An object of class \code{"coalescentIntervals"} with the following entries:
23 \item{lineages}{ A vector with the number of lineages at the start of each coalescent
25 \item{interval.length}{ A vector with the length of each coalescent
27 \item{interval.count}{ The total number of coalescent
29 \item{total.depth}{ The sum of the lengths of all coalescent
33 \code{\link{branching.times}}, \code{\link{collapsed.intervals}},
34 \code{\link{read.tree}}.
37 \author{Korbinian Strimmer (\url{http://www.stat.uni-muenchen.de/~strimmer/})}
40 data("hivtree.newick") # example tree in NH format
41 tree.hiv <- read.tree(text = hivtree.newick) # load tree
43 ci <- coalescent.intervals(tree.hiv) # from tree
46 data("hivtree.table") # same tree, but in table format
47 ci <- coalescent.intervals(hivtree.table$size) # from vector of interval lengths