create_m_param: Create a parameter called m

In ropensci/beautier: 'BEAUti' from R

Create a parameter called m

Description

Create a parameter called m

Usage

create_m_param(id = NA, estimate = FALSE, lower = NA, upper = NA, value = 0)

Arguments

id	the parameter's ID
estimate	TRUE if this parameter is to be estimated by BEAST2, FALSE otherwise
lower	lowest possible value of the parameter. If the parameter is estimated, lower must be less than value
upper	upper value of the parameter
value	value of the parameter

Value

a parameter called m

Note

this parameter is used in a log-normal distribution (as returned by create_log_normal_distr) 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()) {

  # Create the parameter
  m_param <- create_m_param()

  # Use the parameter in a distribution
  log_normal_distr <- create_log_normal_distr(
    m = m_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,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = log_normal_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()

}

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