bbt_run_from_model: Run BEAST2

Description Usage Arguments Value Author(s) See Also Examples

View source: R/bbt_run_from_model.R

Description

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

Usage

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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:

Author(s)

Richèl J.C. Bilderbeek

See Also

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

Examples

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if (is_beast2_installed()) {

  # 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
  )
}

richelbilderbeek/rbeast2 documentation built on Oct. 22, 2020, 4:48 a.m.