create_gtr_site_model: Create a GTR site model

In beautier: 'BEAUti' from R

Create a GTR site model

Description

Create a GTR site model

Usage

create_gtr_site_model(
  id = NA,
  gamma_site_model = create_gamma_site_model(),
  rate_ac_prior_distr = create_gamma_distr(alpha = 0.05, beta = create_beta_param(value =
    "10.0")),
  rate_ag_prior_distr = create_gamma_distr(alpha = 0.05, beta = create_beta_param(value =
    "20.0")),
  rate_at_prior_distr = create_gamma_distr(alpha = 0.05, beta = create_beta_param(value =
    "10.0")),
  rate_cg_prior_distr = create_gamma_distr(alpha = 0.05, beta = create_beta_param(value =
    "10.0")),
  rate_gt_prior_distr = create_gamma_distr(alpha = 0.05, beta = create_beta_param(value =
    "10.0")),
  rate_ac_param = create_rate_ac_param(),
  rate_ag_param = create_rate_ag_param(),
  rate_at_param = create_rate_at_param(),
  rate_cg_param = create_rate_cg_param(),
  rate_ct_param = create_rate_ct_param(),
  rate_gt_param = create_rate_gt_param(),
  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)
gamma_site_model	a gamma site model, as created by create_gamma_site_model
rate_ac_prior_distr	the AC rate prior distribution, as returned by create_distr
rate_ag_prior_distr	the AG rate prior distribution, as returned by create_distr
rate_at_prior_distr	the AT rate prior distribution, as returned by create_distr
rate_cg_prior_distr	the CG rate prior distribution, as returned by create_distr
rate_gt_prior_distr	the GT rate prior distribution, as returned by create_distr
rate_ac_param	the 'rate AC' parameter, a numeric value. For advanced usage, use the structure as returned by create_rate_ac_param
rate_ag_param	the 'rate AG' parameter, a numeric value. For advanced usage, use the structure as returned by create_rate_ag_param
rate_at_param	the 'rate AT' parameter, a numeric value. For advanced usage, use the structure as returned by create_rate_at_param
rate_cg_param	the 'rate CG' parameter, a numeric value. For advanced usage, use the structure as returned by create_rate_cg_param
rate_ct_param	the 'rate CT' parameter, a numeric value. For advanced usage, use the structure as returned by create_rate_ct_param
rate_gt_param	the 'rate GT' parameter, a numeric value. For advanced usage, use the structure as returned by create_rate_gt_param
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

a GTR site_model

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  gtr_site_model <- create_gtr_site_model(
    rate_ac_param = 1.2,
    rate_ag_param = 2.3,
    rate_at_param = 3.4,
    rate_cg_param = 4.5,
    rate_ct_param = 5.6,
    rate_gt_param = 6.7
  )

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    site_model = gtr_site_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

beautier documentation built on Nov. 2, 2023, 5:08 p.m.