create_cbs_tree_prior: Create a Coalescent Bayesian Skyline tree prior

In ropensci/beautier: 'BEAUti' from R

Create a Coalescent Bayesian Skyline tree prior

Description

Create a Coalescent Bayesian Skyline tree prior

Usage

create_cbs_tree_prior(
  id = NA,
  group_sizes_dimension = 5,
  b_pop_sizes_param = create_b_pop_sizes_param(),
  pop_sizes_scaler_scale_factor = ""
)

Arguments

id	an alignment's IDs. An ID can be extracted from its FASTA filename with get_alignment_ids_from_fasta_filenames)
group_sizes_dimension	the group sizes' dimension, as used by the CBS tree prior (see create_cbs_tree_prior)
b_pop_sizes_param	a Bayesian population size parameter, as created by create_b_pop_sizes_param
pop_sizes_scaler_scale_factor	the scale factor used by the population sizes scaler operator

Value

a Coalescent Bayesian Skyline 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()) {

  cbs_tree_prior <- create_cbs_tree_prior()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_beautier_path("test_output_6.fas"),
    beast2_input_file,
    tree_prior = cbs_tree_prior
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

ropensci/beautier documentation built on July 9, 2024, 6:14 a.m.