create_test_ns_mcmc: Create an NS MCMC object for testing

In ropensci/beautier: 'BEAUti' from R

Create an NS MCMC object for testing

Description

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

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_ns_mcmc to create a default nested sampling MCMC

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()
}

ropensci/beautier documentation built on July 9, 2024, 6:14 a.m.