pirouette (version 1.6.9)

get_sim_tral_with_lns_nsm_fun: Get a partially evaluated function to simulate a true alignment with a linked node substitution site model.

Description

Get a partially evaluated function to simulate a true alignment with a linked node substitution site model.

Usage

get_sim_tral_with_lns_nsm_fun(
  subst_matrix = rep(1, 6),
  branch_mutation_rate = 1,
  node_mutation_rate = 1,
  base_frequencies = rep(0.25, 4),
  node_time = 0.001
)

Value

A partially evaluated function of sim_tral_with_lns_nsm

Arguments

subst_matrix

nucleotide substitution matrix

branch_mutation_rate

mutation rate along the branch. See, among others, sim_unlinked for more details

node_mutation_rate

mutation rate on the node. See, among others, sim_unlinked for more details

base_frequencies

the four base frequencies (a, c, g, t) to be specified to create the rate matrix (i.e. Q matrix) used to simulate alignments

node_time

amount of time spent at the nodes. See, among others, sim_unlinked for more details

See Also

Use get_sim_tral_with_uns_nsm_fun to get a partially evaluated function to simulate a true alignment with an unlinked node substitution site model.

Examples

# Create a valid 'check_sim_tral_fun'
f <- get_sim_tral_with_lns_nsm_fun()
check_sim_tral_fun(f)

# Simulate a true alignment
phylogeny <- ape::read.tree(text = "((A:1, B:1):1, C:2);")
true_alignment <- f(
  true_phylogeny = phylogeny,
  root_sequence = "acgt"
)