sim_tral_with_uns_nsm: Adapter function to simulate an alignment with the...

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

Adapter function to simulate an alignment with the linked_node_sub (lns) site model.

Description

Adapter function to simulate an alignment with the linked_node_sub (lns) site model.

Usage

sim_tral_with_uns_nsm(
  true_phylogeny,
  root_sequence,
  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

true_phylogeny	the true phylogeny; the actual evolutionary history of the species, of class phylo
root_sequence	the DNA sequence at the root of the phylogeny. By default, this will consist out of an equal amount of each letter Use check_root_sequence to check if a root sequence is valid.
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

an alignment of type DNAbin

Author(s)

Richèl J.C. Bilderbeek

See Also

Use sim_tral_with_lns_nsm to simulate the true alignment with a linked node substitution model. Use sim_twal_with_uns_nsm to simulate the twin alignment with an unlinked node substitution model. Use get_sim_tral_with_uns_nsm_fun to get a partially evaluated unary function.

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