get_arg: Get ancestral recombination graph from forward simulations
In nickbrazeau/polySimIBD: Structured Wright Fisher Simulator for Malaria Genetics

get_arg

R Documentation

Get ancestral recombination graph from forward simulations

Description

Given an object swf, which is the result of forward simulation using the function sim_swf(), walk backwards through the ancestry and calculate the coalescent tree at every locus for the specified hosts and/or haplotypes.

Usage

get_arg(swf, host_index = NULL, haplo_index = NULL)

Arguments

`swf`	result of forwards simulation using the function `sim_swf()`
`host_index`	a vector of target hosts. Defaults to all hosts
`haplo_index`	a list of target haplotypes within the hosts specified by `host_index`. Defaults to all haplotypes within the specified hosts.