estcoaltime: Estimate expected time to coalescence for sampled lineages in...
In seedy: Simulation of Evolutionary and Epidemiological Dynamics

Description Usage Arguments Details Value Examples

Estimates the expected time to coalescence for two randomly sampled lineages at a particular time, given the past population dynamics.

1	estcoaltime(bottlesize, popsize, bottletimes, obstime)

`bottlesize`	Effective size of population bottlenecks.
`popsize`	Effective population size between bottlenecks.
`bottletimes`	Vector of bottleneck times.
`obstime`	Time of observation.

Expected coalescent time is calculated under the assumption that population remains constant at popsize, but drops to bottlesize for a single generation at bottleneck times. The probability of coalescence in a particular generation is the reciprocal of the population size at the time.

Returns the expected number of generations since coalescence.