tipdate.ci: Get coalescent intervals for a tip-dated tree

In phyext: An extension of some of the classes in phylobase. Tree objects now support subnodes on branches

Description

Similar to ape's coalescent intervals, except it works when the tree is not ultrametric. This is being used for now as a helper function for treeHeight

Usage

tipdate.ci(tr, show.plot = F)

Arguments

tr	A tree in phylo format
show.plot	Should a plot be generated highlighting the coalescent events

Details

This is mainly being used with treeHeights for now, but it is a good way to get the coalescent intervals for a tree. Be aware though that the tree needs to be down-convert to ape:::phylo format first.

Value

lineages	The number of extant lineages during this interval
interval.length	The length of each interval
interval.count	The total number of coalescent intervals
total.depth	The height or depth of the tree
I	Indicator for whether or not the event is a coalescent event (1) or a sampling event (0)

Author(s)

J. Conrad Stack

phyext documentation built on May 2, 2019, 5:19 p.m.