Create a BEAST2 input file

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

# 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)
#> [1] TRUE