create_test_alignment_params: Create testing parameters for the alignment simulation.

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

Create testing parameters for the alignment simulation.

Description

Create testing parameters for the alignment simulation.

Usage

create_test_alignment_params(
  sim_tral_fun = pirouette::sim_tral_with_std_nsm,
  root_sequence = "acgt",
  rng_seed = 0,
  fasta_filename = pirouette::get_temp_fasta_filename()
)

Arguments

sim_tral_fun	function to simulate a true alignment with. This function must have two arguments, called true_phylogeny (which will hold the true phylogeny) and root_sequence (which holds the DNA root sequence). The return type must be DNAbin. Use check_sim_tral_fun to verify if the function has the right signature and output. Some standard functions: Use get_sim_tral_with_std_nsm_fun to get a function (sim_tral_with_std_nsm) the use a standard site model. Use get_sim_tral_with_lns_nsm_fun to get a function (sim_tral_with_lns_nsm) the use a linked node substitution site model. Use get_sim_tral_with_uns_nsm_fun to get a function (sim_tral_with_uns_nsm) the use an unlinked node substitution site model.
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.
rng_seed	a random number generator seed
fasta_filename	name of a FASTA file. Use get_alignment_id to get the ID of the alignment

Value

a list of alignment parameters alignment_params <- create_test_alignment_params() check_alignment_params(alignment_params)

Author(s)

Richèl J.C. Bilderbeek

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