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Run BEAST2

Source: R/bbt_run_from_model.R
bbt_run_from_model.Rd

Do a full run: create a 'BEAST2' configuration file (like 'BEAUti 2'), run 'BEAST2', parse results (like 'Tracer')

Usage

bbt_run_from_model(
  fasta_filename,
  inference_model = beautier::create_inference_model(),
  beast2_options = beastier::create_beast2_options()
)

Arguments

fasta_filename

a FASTA filename

inference_model

a Bayesian phylogenetic inference model, as returned by create_inference_model

beast2_options

'BEAST2' options, as can be created by create_beast2_options

Value

a list with the following elements:

  • estimates: a data frame with 'BEAST2' parameter estimates

  • [alignment_id]_trees: a multiPhylo containing the phylogenies in the 'BEAST2' posterior. [alignment_id] is the ID of the alignment. For example, when running bbt_run_from_model with anthus_aco.fas, this element will have name anthus_aco_trees

  • operators: a data frame with the 'BEAST2' MCMC operator acceptances

  • output: a numeric vector with the output sent to standard output and error streams

  • ns: (optional) the results of a marginal likelihood estimation, will exist only when create_ns_mcmc was used for mcmc. This structure will contain the following elements:

    • marg_log_lik the marginal log likelihood estimate

    • marg_log_lik_sd the standard deviation around the estimate

    • estimates the parameter estimates created during the marginal likelihood estimation

    • trees the trees created during the marginal likelihood estimation

See also

Use remove_burn_ins to remove the burn-ins from the posterior's estimates (posterior$estimates)

Author

Richèl J.C. Bilderbeek

Examples

if (beautier::is_on_ci() && is_beast2_installed()) {
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()

  # Simple short inference
  inference_model <- create_test_inference_model()

  # Default BEAST2 options
  beast2_options <- create_beast2_options()

  bbt_run_from_model(
    fasta_filename = get_babette_path("anthus_aco.fas"),
    inference_model = inference_model,
    beast2_options = beast2_options
  )

  # Cleanup
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()
}