sim.tree: Simulate a Coalescent Tree

In coalesceR: A pedagogical tool to teach the basics of coalescent theory

Description

Simulate a coalescent tree.

Usage

  sim.tree(method,sample,current,ancestral,time)

Arguments

method	simulation method: ‘hudson’ for the continuous time approximations; ‘generations’ for the generation-by-generation algorithm
sample	number of sampled lineages
current	current population size
ancestral	ancestral population size
time	time at which the population changed in size

Details

A coalescent tree is built using either the ‘hudson’'s approximation in continuous time, or a generation-by-generation algorithm. A single population is simulated, and ‘sample’ lineages are simulated. The population is assumed to have a current effective size (‘current’), and an ancestral effective size (‘ancestral’). The change in population size occurred ‘time’ generations in the past

Value

an object of class ‘coalescent’ which is a list with components:

node	the list of nodes (internal and leafs) in the tree
ancestor	the ancestor of each node
label	the label of each leaf
branch.length	the length of the branch above each node

Examples

## This is to simulate a coalescent tree using the Hudson's algorithm, 
## with 20 sampled lineages. In this example, the current population size
## is 100. It was 1000 before a bottleneck that occurred 50 generations ago

tree <- sim.tree(method = "hudson",sample = 20,current = 100,ancestral = 1000,time = 50)

coalesceR documentation built on May 2, 2019, 4:42 p.m.