pir_paramsCreate a standard pir_params, as used in Bilderbeek, Laudanno
and Etienne.
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
)a `pir_params`, as can be checked by check_pir_params
name of the main folder
a random number generator seed
the fixed crown age of the posterior. Set to NA to let it be estimated
the length of each DNA sequence in an alignment
the mutation rate per base pair per time unit. Use check_mutation_rate to check if a mutation rate is valid.
name of the operating system, can be mac, unix
or win. Use check_os if the operating system
is valid.
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