create_alignment_params: Create the parameters for the alignment simulation.

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

Create the parameters for the alignment simulation.

Description

These parameters are used in the create_pir_params function

Usage

create_alignment_params(
  root_sequence = pirouette::create_blocked_dna(1000),
  sim_tral_fun = pirouette::sim_tral_with_std_nsm,
  rng_seed = 0,
  fasta_filename = pirouette::get_temp_fasta_filename()
)

Arguments

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.
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.
rng_seed	the random number generator seed as used in the simulation of an alignment
fasta_filename	name of a FASTA file. Use get_alignment_id to get the ID of the alignment

Value

a list of alignment parameters

Author(s)

Richèl J.C. Bilderbeek

Examples

if (beautier::is_on_ci()) {

  # DNA sequence at the root
  n_base_pairs <- 4
  root_sequence <- create_blocked_dna(length = n_base_pairs)

  # Only specify root sequence and mutation rate, use defaults
  alignment_params <- create_alignment_params(
    root_sequence = root_sequence
  )

  # Use defaults explicitly
  alignment_params <- create_alignment_params(
    root_sequence = root_sequence,
    rng_seed = 0
  )

  # Create a pirouette parameter set
  pir_params <- create_test_pir_params(alignment_params = alignment_params)

  # Run pirouette
  if (beautier::is_on_ci() && beastier::is_beast2_installed()) {
    pir_out <- pir_run(
      phylogeny = ape::read.tree(text = "((A:1, B:1):1, C:2);"),
      pir_params = pir_params
    )
    pir_plot(pir_out)
  }
}

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