create_hky_site_model {beautier}

Create an HKY site model

Description

Create an HKY site model

Usage

create_hky_site_model(
  id = NA,
  kappa = "obsolete",
  kappa_param = create_kappa_param(value = "2.0"),
  gamma_site_model = create_gamma_site_model(),
  kappa_prior_distr = create_log_normal_distr(m = create_m_param(value = "1.0"), s =
    1.25),
  freq_equilibrium = "estimated",
  freq_param = create_freq_param()
)

Arguments

id

the IDs of the alignment (can be extracted from the FASTA filename using get_alignment_id)

kappa

obsoleted parameter. It is the value in the 'kappa_param' argument

kappa_param

a 'kappa' parameter, as created by create_kappa_param

gamma_site_model

a gamma site model, as created by create_gamma_site_model

kappa_prior_distr

the distribution of the kappa prior, which is a log-normal distribution (as created by create_log_normal_distr) by default

freq_equilibrium

the frequency in which the rates are at equilibrium are either estimated, empirical or all_equal. get_freq_equilibrium_names returns the possible values for freq_equilibrium

freq_param

a 'freq' parameter, as created by create_freq_param

Value

an HKY site_model

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  hky_site_model <- create_hky_site_model()
  output_filename <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    output_filename = output_filename,
    site_model = hky_site_model
  )
  file.remove(output_filename)

  remove_beautier_folder()
}