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Estimate the marginal likelihoods for one or more inference models

Source: R/est_marg_liks.R
est_marg_liks.Rd

Estimate the marginal likelihoods (aka evidence) for one or more inference models, based on a single alignment. Also, the marginal likelihoods are compared, resulting in a relative weight for each model, where a relative weight of a model close to 1.0 means that that model is way likelier than the others.

Usage

est_marg_liks(
  fasta_filename,
  inference_models = list(beautier::create_inference_model(mcmc =
    beautier::create_ns_mcmc())),
  beast2_optionses = rep(list(beastier::create_mcbette_beast2_options()), times =
    length(inference_models)),
  verbose = FALSE,
  os = rappdirs::app_dir()$os
)

Arguments

fasta_filename

name of the FASTA file

inference_models

a list of one or more inference models, as can be created by create_inference_model

beast2_optionses

list of one or more beast2_options structures, as can be created by create_mcbette_beast2_options. Use of reduplicated plural to achieve difference with beast2_options

verbose

if TRUE show debug output

os

name of the operating system, must be unix (Linux, Mac) or win (Windows)

Value

a data.frame showing the estimated marginal likelihoods (and its estimated error) per combination of models. Columns are:

  • site_model_name: name of the site model

  • clock_model_name: name of the clock model

  • tree_prior_name: name of the tree prior

  • marg_log_lik: estimated marginal (natural) log likelihood

  • marg_log_lik_sd: estimated error of marg_log_lik

  • weight: relative model weight, a value from 1.0 (all evidence is in favor of this model combination) to 0.0 (no evidence in favor of this model combination)

  • ess: effective sample size of the marginal likelihood estimation

Details

In the process, multiple (temporary) files are created (where [x] denotes the index in a list)

  • beast2_optionses[x]$input_filename path to the the BEAST2 XML input file

  • beast2_optionses[x]$output_state_filename path to the BEAST2 XML state file

  • inference_models[x]$mcmc$tracelog$filename path to the BEAST2 trace file with parameter estimates

  • inference_models[x]$mcmc$treelog$filename path to the BEAST2 trees file with the posterior trees

  • inference_models[x]$mcmc$screenlog$filename path to the BEAST2 screen output file

These file can be deleted manually by bbt_delete_temp_files, else these will be deleted automatically by the operating system.

See also

  • can_run_mcbette: see if 'mcbette' can run

  • est_marg_liks: estimate multiple marginal likelihood of a single inference mode

Author

Richèl J.C. Bilderbeek

Examples

if (can_run_mcbette()) {

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

  # Create two inference models
  inference_model_1 <- beautier::create_ns_inference_model(
    site_model = beautier::create_jc69_site_model()
  )
  inference_model_2 <- beautier::create_ns_inference_model(
    site_model = beautier::create_hky_site_model()
  )

  # Shorten the run, by doing a short (dirty, unreliable) MCMC
  inference_model_1$mcmc <- beautier::create_test_ns_mcmc()
  inference_model_2$mcmc <- beautier::create_test_ns_mcmc()

  # Combine the inference models
  inference_models <- list(inference_model_1, inference_model_2)

  # Create the BEAST2 options, that will write the output
  # to different (temporary) filanems
  beast2_options_1 <- beastier::create_mcbette_beast2_options()
  beast2_options_2 <- beastier::create_mcbette_beast2_options()

  # Combine the two BEAST2 options sets,
  # use reduplicated plural
  beast2_optionses <- list(beast2_options_1, beast2_options_2)

  # Compare the models
  marg_liks <- est_marg_liks(
    fasta_filename,
    inference_models = inference_models,
    beast2_optionses = beast2_optionses
  )

  # Interpret the results
  interpret_marg_lik_estimates(marg_liks)

  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()
}