Create a strict clock model

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

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

Value

a strict clock_model

Author

Richèl J.C. Bilderbeek

Examples

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)
#> [1] TRUE

strict_clock_model_gamma <- create_strict_clock_model(
  clock_rate_distr = create_gamma_distr()
)

beast2_input_file <- get_beautier_tempfilename()
create_beast2_input_file(
  get_fasta_filename(),
  beast2_input_file,
  clock_model = strict_clock_model_gamma
)
file.remove(beast2_input_file)
#> [1] TRUE