create_beast2_input: Create a BEAST2 XML input text

In beautier: 'BEAUti' from R

Create a BEAST2 XML input text

Description

Create a BEAST2 XML input text

Usage

create_beast2_input(
  input_filename,
  tipdates_filename = NA,
  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()
)

Arguments

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

Value

a character vector of XML strings

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_beast2_input_from_model to create the BEAST2 XML input text from an inference model Use create_beast2_input_file to also save it to file.

create_beast2_input_file shows more examples

Examples

if (is_on_ci()) {
  create_beast2_input(
    input_filename = get_fasta_filename()
  )
}

beautier documentation built on Nov. 2, 2023, 5:08 p.m.