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Create an NS MCMC object for testing

Source: R/create_test_ns_mcmc.R
create_test_ns_mcmc.Rd

Create an NS MCMC object for testing

Usage

create_test_ns_mcmc(
  chain_length = 2000,
  store_every = 1000,
  pre_burnin = 0,
  n_init_attempts = 3,
  particle_count = 1,
  sub_chain_length = 500,
  epsilon = 1e-12,
  tracelog = create_test_tracelog(),
  screenlog = create_test_screenlog(),
  treelog = create_test_treelog()
)

Arguments

chain_length

upper bound to the 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

particle_count

number of particles

sub_chain_length

sub-chain length

epsilon

epsilon

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 object

See also

Use create_ns_mcmc to create a default nested sampling MCMC

Author

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  mcmc <- create_test_ns_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()
}