create_clock_rate_param: Create a parameter called 'clock_rate', as needed by...

In ropensci/beautier: 'BEAUti' from R

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)

Arguments

value	value of the parameter
estimate	TRUE if this parameter is to be estimated by BEAST2, FALSE otherwise
id	the parameter's ID

Value

a parameter called rate

Note

It cannot be estimated (as a hyper parameter) yet.

Author(s)

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()
}

ropensci/beautier documentation built on July 9, 2024, 6:14 a.m.