create_test_mcmc {beautier}R Documentation

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()
}

[Package beautier version 2.6.11 Index]