get_sim_tral_with_uns_nsm_fun: Get a partially evaluated function to simulate a true...

In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny

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

Description

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

Usage

get_sim_tral_with_uns_nsm_fun(
  branch_subst_matrix = rep(1, 6),
  node_subst_matrix = 1,
  branch_mutation_rate = 1,
  node_mutation_rate = 1,
  base_frequencies = rep(0.25, 4),
  node_time = 0.001
)

Arguments

branch_subst_matrix	substitution matrix along the branches. See, among others, sim_unlinked for more details
node_subst_matrix	substitution matrix on the nodes. See, among others, sim_unlinked for more details
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

Value

A partially evaluated function of sim_tral_with_uns_nsm

See Also

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

Examples

f <- get_sim_tral_with_uns_nsm_fun()
check_sim_tral_fun(f)
phylogeny <- ape::read.tree(text = "((A:1, B:1):1, C:2);")
true_alignment <- f(
  true_phylogeny = phylogeny,
  root_sequence = "acgt"
)

richelbilderbeek/pirouette documentation built on Oct. 18, 2023, 3:09 p.m.