sim_tral_with_std_nsm: Adapter function to simulate a twin alignment using a...

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

Adapter function to simulate a twin alignment using a standard site model

Description

Adapter function to simulate a twin alignment using a standard site model

Usage

sim_tral_with_std_nsm(
  true_phylogeny,
  root_sequence,
  mutation_rate = 1,
  site_model = beautier::create_jc69_site_model()
)

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.
mutation_rate	the mutation rate per base pair per time unit. Use check_mutation_rate to check if a mutation rate is valid.
site_model	a nucleotide substitution model, which can be: A standard nucloetide substitution model, as created by create_site_model lns: a linked node-substitution model uns: an unlinked node-substitution model

Value

an alignment

Author(s)

Richèl J.C. Bilderbeek

Examples

# This adapter function must be a sim_true_alignment function
check_sim_tral_fun(
  sim_tral_with_std_nsm
)

# Simulate the true DNA alignment
alignment <- sim_tral_with_std_nsm(
  true_phylogeny = ape::read.tree(text = "((A:1, B:1):2, C:3);"),
  root_sequence = "aaaa",
  mutation_rate = 0.1
)
check_alignment(alignment)

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