Create an HKY site model

create_hky_site_model(
  id = NA,
  kappa = "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"
)

Arguments

id

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

kappa

the kappa

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

Value

an HKY site_model

Author

Richèl J.C. Bilderbeek

Examples

 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)
#> [1] TRUE