Create a TN93 site model

create_tn93_site_model(
  id = NA,
  gamma_site_model = create_gamma_site_model(),
  kappa_1_param = create_kappa_1_param(),
  kappa_2_param = create_kappa_2_param(),
  kappa_1_prior_distr = create_log_normal_distr(m = 1, s = 1.25),
  kappa_2_prior_distr = create_log_normal_distr(m = 1, s = 1.25),
  freq_equilibrium = "estimated"
)

Arguments

id

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

gamma_site_model

a gamma site model, as created by create_gamma_site_model

kappa_1_param

the 'kappa 1' parameter, a numeric value. For advanced usage, use the structure as returned by create_kappa_1_param

kappa_2_param

the 'kappa 2' parameter, a numeric value. For advanced usage, use the structure as returned by create_kappa_2_param

kappa_1_prior_distr

the distribution of the kappa 1 prior, which is a log-normal distribution (as created by create_log_normal_distr) by default

kappa_2_prior_distr

the distribution of the kappa 2 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

a TN93 site_model

Author

Richèl J.C. Bilderbeek

Examples

 tn93_site_model <- create_tn93_site_model(
   kappa_1_param = 2.0,
   kappa_2_param = 2.0
 )

 output_filename <- get_beautier_tempfilename()
 create_beast2_input_file(
   input_filename = get_fasta_filename(),
   output_filename = output_filename,
   site_model = tn93_site_model
 )
file.remove(output_filename)
#> [1] TRUE