proba.coalescent: Probability of Coalescence

In coalescentMCMC: MCMC Algorithms for the Coalescent

Probability of Coalescence

Description

This function calculates the probability that two lineages coalesce out of a sample of size n in a population of size N after t generations.

Usage

proba.coalescent(t, N = 1e4, n = 2, exact = TRUE)

Arguments

t	a vector of generations (rounded to integers if needed).
N	the size of population (10,000 by default).
n	the sample size (2 by default).
exact	a logical value specifying whether exact calculation should be done or an approximation (Hudson, 1991, eq. 3).

Author(s)

Emmanuel Paradis

References

Hudson, R. R. (1991). Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology, 7, 1–44.

Examples

proba.coalescent(1:10)
## the approximate formula doesn't work well when n is
## not small compared to N:
proba.coalescent(1, 100, 50, exact = FALSE)
proba.coalescent(1, 100, 50)

coalescentMCMC documentation built on April 22, 2022, 5:05 p.m.