Create a BEAST2 input file

Create a BEAST2 input file

Usage

create_beast2_input_file(
  input_filename,
  output_filename,
  site_model = create_jc69_site_model(),
  clock_model = create_strict_clock_model(),
  tree_prior = create_yule_tree_prior(),
  mrca_prior = NA,
  mcmc = create_mcmc(),
  beauti_options = create_beauti_options(),
  tipdates_filename = NA
)

Arguments

input_filename

A FASTA filename. Use get_fasta_filename to obtain a testing FASTA filename.

output_filename

Name of the XML parameter file created by this function. BEAST2 uses this file as input.

site_model

a site model, as returned by create_site_model

clock_model

a clock model, as returned by create_clock_model

tree_prior

a tree priors, as returned by create_tree_prior

mrca_prior

a Most Recent Common Ancestor prior, as returned by create_mrca_prior

mcmc

one MCMC. Use create_mcmc to create an MCMC. Use create_ns_mcmc to create an MCMC for a Nested Sampling run. Use check_mcmc to check if an MCMC is valid. Use rename_mcmc_filenames to rename the filenames in an MCMC.

beauti_options

one BEAUti options object, as returned by create_beauti_options

tipdates_filename

name of the file containing the tip dates. This file is assumed to have two columns, separated by a tab. The first column contains the taxa names, the second column contains the date.

Value

nothing

See also

Use create_beast2_input_file_from_model to do the same with an inference model. See create_site_model for examples with different site models. See create_clock_model for examples with clock models. See create_tree_prior for examples with different tree priors. See create_mcmc for examples with a different MCMC setup.

Author

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  # Get an example FASTA file
  input_filename <- get_fasta_filename()

  # The file created by beautier, a BEAST2 input file
  output_filename <- get_beautier_tempfilename()

  create_beast2_input_file(
    input_filename,
    output_filename
  )
  file.remove(output_filename)

  remove_beautier_folder()
  check_empty_beautier_folder()
}