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Create a GTR site model

Source: R/create_site_model.R
create_gtr_site_model.Rd

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

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()
}