create_strict_clock_model: Create a strict clock model

In beautier: 'BEAUti' from R

Create a strict clock model

Description

Create a strict clock model

Usage

create_strict_clock_model(
  id = NA,
  clock_rate_param = create_clock_rate_param(),
  clock_rate_distr = create_uniform_distr(),
  rate_scaler_factor = 0.75
)

Arguments

id	an alignment's IDs. An ID can be extracted from its FASTA filename with get_alignment_ids_from_fasta_filenames)
clock_rate_param	the clock rate's parameter, a numeric value. For advanced usage, use the structure as created by the create_clock_rate_param function
clock_rate_distr	the clock rate's distribution, as created by a create_distr function
rate_scaler_factor	the strict clock model's operator scaler for the rate. Use an empty string to indicate the default.

Value

a strict clock_model

Note

I am unsure about the relationship between 'clock_rate_param' and 'clock_rate_distr'. Please contact me if you know the most natural architecture

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {
  strict_clock_model <- create_strict_clock_model(
    clock_rate_param = 1.0,
    clock_rate_distr = create_uniform_distr()
  )

  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()
}

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