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Create a gamma site model, part of a site model

Source: R/create_gamma_site_model.R
create_gamma_site_model.Rd

Create a gamma site model, part of a site model

Usage

create_gamma_site_model(
  gamma_cat_count = "0",
  gamma_shape = "1.0",
  prop_invariant = "0.0",
  gamma_shape_prior_distr = NA,
  freq_equilibrium = "estimated",
  freq_prior_uniform_distr_id = 1000
)

Arguments

gamma_cat_count

the number of gamma categories, must be an integer with value zero or more

gamma_shape

gamma curve shape parameter

prop_invariant

the proportion invariant, must be a value from 0.0 to 1.0

gamma_shape_prior_distr

the distribution of the gamma shape prior. gamma_shape_prior_distr must be NA for a gamma_cat_count of zero or one. For a gamma_cat_count of two or more, leaving gamma_shape_prior_distr equal to its default value of NA, a default distribution is used. Else gamma_shape_prior_distr must be a distribution, as can be created by create_distr

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_prior_uniform_distr_id

the ID of the `FrequenciesPrior`'s uniform distribution

Value

a gamma site model

See also

Use create_gamma_site_model to create a gamma site model

Author

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  gamma_site_model <- create_gamma_site_model(prop_invariant = 0.5)

  site_model <- create_hky_site_model(gamma_site_model = gamma_site_model)

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

  remove_beautier_folder()
}