create_test_mcmc: Create an MCMC configuration for testing.

In beautier: 'BEAUti' from R

Create an MCMC configuration for testing.

Description

Create an MCMC configuration for testing.

Usage

create_test_mcmc(
  chain_length = 3000,
  store_every = 1000,
  pre_burnin = 0,
  n_init_attempts = 10,
  sample_from_prior = FALSE,
  tracelog = create_test_tracelog(),
  screenlog = create_test_screenlog(),
  treelog = create_test_treelog()
)

Arguments

chain_length	length of the MCMC chain
store_every	number of states the MCMC will process before the posterior's state will be saved to file. Use -1 or NA to use the default frequency.
pre_burnin	number of burn in samples taken before entering the main loop
n_init_attempts	number of initialization attempts before failing
sample_from_prior	set to TRUE to sample from the prior
tracelog	a tracelog, as created by create_tracelog
screenlog	a screenlog, as created by create_screenlog
treelog	a treelog, as created by create_treelog

Value

an MCMC configuration

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_mcmc to create a default BEAST2 MCMC

Examples

if (is_on_ci()) {

  # Create an MCMC chain with 50 states
  mcmc <- create_test_mcmc()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    get_fasta_filename(),
    beast2_input_file,
    mcmc = mcmc
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

beautier documentation built on Nov. 2, 2023, 5:08 p.m.