beautier (version 2.6.12)

create_clock_rate_param: Create a parameter called clock_rate, as needed by create_strict_clock_model

Description

Create a parameter called clock_rate, as needed by create_strict_clock_model

Usage

create_clock_rate_param(value = "1.0", estimate = FALSE, id = NA)

Value

a parameter called rate

Arguments

value

value of the parameter

estimate

TRUE if this parameter is to be estimated by BEAST2, FALSE otherwise

id

the parameter's ID

Author

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  clock_rate_param <- create_clock_rate_param(
    id = "anthus_aco", value = 1.0
  )

  # Use the parameter in a clock model
  strict_clock_model <- create_strict_clock_model(
    clock_rate_param = clock_rate_param
  )

  # Use the distribution to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    clock_model = strict_clock_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}