create_site_model: General function to create a site model.

In beautier: 'BEAUti' from R

General function to create a site model.

Description

General function to create a site model.

Usage

create_site_model(name, id, gamma_site_model = create_gamma_site_model(), ...)

Arguments

name	the site model name. Valid names can be found in get_site_model_names
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
...	specific site model parameters

Value

a site_model

Note

Prefer using the named functions create_gtr_site_model, create_hky_site_model,, create_jc69_site_model, and create_tn93_site_model

Author(s)

Richèl J.C. Bilderbeek

See Also

See create_gtr_site_model for more examples with a GTR site model. See create_hky_site_model for more examples with an HKY site model. See create_jc69_site_model for more examples with a JC69 site model. See create_tn93_site_model for more examples with a TN93 site model

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  input_filename <- get_fasta_filename()
  gtr_site_model <- create_gtr_site_model()
  hk_site_model <- create_hky_site_model()
  jc69_site_model <- create_jc69_site_model()
  tn93_site_model <- create_tn93_site_model()

  # Can use any site model
  output_filename <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = input_filename,
    output_filename = output_filename,
    site_model = jc69_site_model
  )
  file.remove(output_filename)

  remove_beautier_folder()
  check_empty_beautier_folder()
}

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