create_std_pir_params: Create a standard 'pir_params'

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

Create a standard pir_params

Description

Create a standard pir_params, as used in Bilderbeek, Laudanno and Etienne.

Usage

create_std_pir_params(
  folder_name = rappdirs::user_cache_dir(),
  rng_seed = 314,
  crown_age = 10,
  sequence_length = 1000,
  mutation_rate = 1/crown_age,
  os = rappdirs::app_dir()$os
)

Arguments

folder_name	name of the main folder
rng_seed	a random number generator seed
crown_age	the fixed crown age of the posterior. Set to NA to let it be estimated
sequence_length	the length of each DNA sequence in an alignment
mutation_rate	the mutation rate per base pair per time unit. Use check_mutation_rate to check if a mutation rate is valid.
os	name of the operating system, can be mac, unix or win. Use check_os if the operating system is valid.

Details

Create a standard pir_params, as used in Bilderbeek, Laudanno and Etienne, by calling create_pir_params with these settings:

• alignment_params default alignment parameters, in which the alignment is simulated using the Jukes-Cantor nucleotide substitution model and a strict clock (as created by create_alignment_params)

• twinning_params default twinning parameters, in which the twin tree is simulated using a Birth-Death process (using get_sim_bd_twin_tree_fun), the twin alignment is simulated using the Jukes-Cantor nucleotide substitution model and a strict clock and has an equal amount of nucleotide substitutions as the true alignment (using get_sim_twal_same_n_muts_fun)

• experiments a list of a generative and multiple candidate models. The generative model is the default generative model, which uses JC69, strict, and Yule, as created by create_gen_experiment. The candidate models are all other (that is, excluding the generative model) birth-death (including Yule) models, which are all nucleotide substitution models (see create_site_models), all clock models (see create_clock_models), and the Yule and BD model (see create_yule_tree_prior and create_bd_tree_prior)

• error_measure_params the default error measurement parameters, (as created by create_error_measure_params) which uses the nLTT statistic to determine the difference between two (or more) trees

Value

a 'pir_params', as can be checked by check_pir_params

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