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Create a strict clock model

Source: R/create_clock_model.R
create_strict_clock_model.Rd

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

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()
}