create_clock_model: General function to create a clock model

In richelbilderbeek/beastscriptr: 'BEAUti' from R

General function to create a clock model

Description

General function to create a clock model

Usage

create_clock_model(name, id, ...)

Arguments

name	the clock model name. Valid names can be found in get_clock_model_names
id	a clock model's ID
...	specific clock model parameters

Value

a valid clock model

Note

Prefer using the named function create_rln_clock_model and create_strict_clock_model

Author(s)

Richèl J.C. Bilderbeek

See Also

An alignment ID can be extracted from its FASTA filename using get_alignment_id. For more examples about creating a relaxed log-normal clock model, see create_rln_clock_model. For more examples about creating a strict clock model, see create_strict_clock_model.

Examples

if (is_on_ci()) {
  # Can use any of these models
  strict_clock_model <- create_strict_clock_model()
  rln_clock_model <- create_rln_clock_model()

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

  remove_beautier_folder()
}

richelbilderbeek/beastscriptr documentation built on April 9, 2024, 2:28 p.m.