create_bd_tree_prior: Create a Birth-Death tree prior

In beautier: 'BEAUti' from R

Create a Birth-Death tree prior

Description

Create a Birth-Death tree prior

Usage

create_bd_tree_prior(
  id = NA,
  birth_rate_distr = create_uniform_distr(),
  death_rate_distr = create_uniform_distr()
)

Arguments

id	the ID of the alignment
birth_rate_distr	the birth rate distribution, as created by a create_distr function
death_rate_distr	the death rate distribution, as created by a create_distr function

Value

a Birth-Death tree_prior

Author(s)

Richèl J.C. Bilderbeek

See Also

An alignment ID can be extracted from its FASTA filename using get_alignment_id

Examples

if (is_on_ci()) {

  bd_tree_prior <- create_bd_tree_prior()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = bd_tree_prior
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

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