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).
coalescent.intervals(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:
A vector with the number of lineages at the start of each coalescent interval.
A vector with the length of each coalescent interval.
The total number of coalescent intervals.
The sum of the lengths of all coalescent intervals.
# 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
# }
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