est_marg_lik: Estimate the marginal likelihood for an inference model.

In mcbette: Model Comparison Using 'babette'

Estimate the marginal likelihood for an inference model.

Description

Estimate the marginal likelihood for an inference model.

Usage

est_marg_lik(
  fasta_filename,
  inference_model = beautier::create_ns_inference_model(),
  beast2_options = beastier::create_mcbette_beast2_options(),
  os = rappdirs::app_dir()$os
)

Arguments

fasta_filename	name of the FASTA file
inference_model	an inference model, as can be created by create_inference_model
beast2_options	a beast2_options structure, as can be created by create_mcbette_beast2_options.
os	name of the operating system, must be unix (Linux, Mac) or win (Windows)

Value

a list showing the estimated marginal likelihoods (and its estimated error), its items are::

• marg_log_lik: estimated marginal (natural) log likelihood

• marg_log_lik_sd: estimated error of marg_log_lik

• esses the Effective Sample Size

Author(s)

Richèl J.C. Bilderbeek

See Also

• can_run_mcbette: see if 'mcbette' can run

• est_marg_liks: estimate multiple marginal likelihoods

Examples

if (can_run_mcbette()) {

  # An example FASTA file
  fasta_filename <- system.file("extdata", "simple.fas", package = "mcbette")

  # A testing inference model with inaccurate (thus fast) marginal
  # likelihood estimation
  inference_model <- beautier::create_ns_inference_model()

  # Shorten the run, by doing a short (dirty, unreliable) MCMC
  inference_model$mcmc <- beautier::create_test_ns_mcmc()

  # Setup the options for BEAST2 to be able to call BEAST2 packages
  beast2_options <- beastier::create_mcbette_beast2_options()

  # Estimate the marginal likelihood
  est_marg_lik(
    fasta_filename = fasta_filename,
    inference_model = inference_model,
    beast2_options = beast2_options
  )

  beastier::remove_beaustier_folders()
}

mcbette documentation built on Sept. 27, 2023, 9:08 a.m.