Create a testing inference model.

Creates a simple inference model with a short MCMC chain, to be used in testing.

Usage

create_test_inference_model(
  site_model = create_jc69_site_model(),
  clock_model = create_strict_clock_model(),
  tree_prior = create_yule_tree_prior(),
  mrca_prior = NA,
  mcmc = create_test_mcmc(),
  beauti_options = create_beauti_options(),
  tipdates_filename = NA
)

Arguments

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

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.

Value

an inference model

See also

Use create_inference_model to create a regular inference model. Use create_test_ns_inference_model to create an inference model to estimate the marginal likelihood with a short MCMC, to be used in testing

Author

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {
  check_empty_beautier_folder()

  inference_model <- create_test_inference_model()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file_from_model(
    get_fasta_filename(),
    beast2_input_file,
    inference_model = inference_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
  check_empty_beautier_folder()
}