treesim {popgen}R Documentation

Standard neutral coalescent simulator

Description

Generates a sample from the standard neutral coalescent model.

Usage

treesim(n, Sn, theta, rho.vec, mutations = FALSE, sample = FALSE)

Arguments

n The number of alleles to generate.
Sn The number of sites between which recombination can occur.
theta The mutation rate (= 2Nu where u is the mutation rate per gene per generation)
rho.vec Cumulative recombination rate over the Sn sites.
mutations Logical flag indicating whether the relative positions of the mutations should be returned.
sample Logical flag indicating whether the sample of alleles should be returned.

Value

A list with components

nss The number of segregating sites in the sample.
tree.time The total time on the tree (measured in units of 2N generations)
total.time The total time on the tree (measured in units of 2N generations)
mutations A vector containing the positions of the mutations in the range [0, 1].
sample A (n x nss) matrix containing the sample of alleles.

Author(s)

Jonathan Marchini

References

Hudson, R, R. (1990) Gene genealogies and the coalescent process. In Oxford Surveys in Evolutionary Biology, Vol. 7, pages 1–43, OUP, Oxford.

Examples


 ## No recombination

 n <- 20
 Sn <- 1000
 theta <- 5
 rho.vec <- rep(0, Sn)
 a <- treesim(n, Sn, theta, rho.vec, mutations = TRUE, sample = TRUE)
 mat <- LDmat(a$sample, typ = "haplotype", pos = a$mutations)

 ## 2 hotspots of recombination

 n <- 20
 Sn <- 1000
 theta <- 20
 rho.vec <- c(rep(0, 200), rep(2000, 500), rep(4000, 300))
 a <- treesim(n, Sn, theta, rho.vec, mutations = TRUE, sample = TRUE)
 mat <- LDmat(a$sample, typ = "haplotype", pos = a$mutations)


[Package popgen version 0.0-4 Index]