sim_multilocus_coal: Simulates multi-locus coalescent on a given locus tree

In treeducken: Nested Phylogenetic Tree Simulator

Description

separates a locus tree into loci broken up by duplications and simulates the coalescent on each loci.

Usage

sim_multilocus_coal(
  locus_tree,
  effective_pop_size,
  generation_time = 1,
  mutation_rate = 1e-06,
  num_reps
)

sim_mlc(
  locus_tree,
  effective_pop_size,
  generation_time = 1,
  mutation_rate = 1e-06,
  num_reps
)

Arguments

locus_tree	a locus tree from 'sim_ltBD' of class 'phy'
effective_pop_size	the effective population size
generation_time	unit time per generation (default 1 year per generation)
mutation_rate	number of mutations per unit time
num_reps	number of coalescent simulations per locus

Details

This simulation follows the algorithm given in Rasmussen and Kellis 2012. The locus tree is scaled into coalescent units prior to being used. The generation_time parameter default assumes 1 generation per year if the units of the tree are in millions of years. The mutation_rate parameter is by default set to 1e-6 mutations per year (this is totally arbitrary). Also note that the return type is a list of many trees so for sufficiently complicated locus trees with 'num_reps' set to a larger value may slow things considerably so use with caution.

Value

A list of list of gene trees of length 'num_reps' simulated along each locus. The first member of the list is the parent tree, all others are child trees

Examples

# first simulate a species tree
mu <- 0.5
lambda <- 1.0
nt <- 6
tr <- sim_stBD(sbr = lambda, sdr = mu, numbsim = 1, n_tips = nt)
# for a locus tree with 100 genes sampled per locus tree
gene_br <- 0.1
gene_dr <- 0.02
transfer_rate <- 0.2
locus_tree <- sim_ltBD(species_tree = tr[[1]],
                  gbr = gene_br,
                  gdr = gene_dr,
                  lgtr = transfer_rate,
                  num_loci = 1)
effect_popsize <- 1e6
gene_tree_obj <- sim_mlc(locus_tree[[1]],
                                      effect_popsize,
                                      num_reps = 20)

treeducken documentation built on March 3, 2021, 1:11 a.m.