retrieve_parent_genetrees: Retrieve all gene trees of the parent tree from a list...

In treeducken: Nested Phylogenetic Tree Simulator

Description

Retrieve all gene trees of the parent tree from a list generated from sim_mlc

Retrieves the gene trees of the child subtrees

Usage

retrieve_parent_genetrees(gene_tree_list)

get_parent_gts(gene_tree_list)

retrieve_child_genetrees(gene_tree_list)

get_child_gts(gene_tree_list)

Arguments

gene_tree_list

A list of length 2: "parent_tree" and "child_trees" both of which are of class "multiPhylo"

Value

A 'multiPhylo' object of only the gene trees generated on the parent subtree

Functions

• retrieve_child_genetrees: Returns a list of objects of class 'multiPhylo'

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 = 2)
parent_trees <- retrieve_parent_genetrees(gene_tree_obj)

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