Create an MCMC configuration.

Create an MCMC configuration, as in the BEAUti MCMC tab.

Usage

create_mcmc(
  chain_length = 1e+07,
  store_every = -1,
  pre_burnin = 0,
  n_init_attempts = 10,
  sample_from_prior = FALSE,
  tracelog = beautier::create_tracelog(),
  screenlog = beautier::create_screenlog(),
  treelog = beautier::create_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

Details

There are four things that can be saved: * store_every: saves the state of the MCMC to file, as a .state.xml file * tracelog: stores the trace of the state of the MCMC to file. See create_tracelog how to specify the filename * screenlog: stores the screen output to file. See create_screenlog how to specify the filename * treelog: stores the estimated phylogenies to file. See create_treelog how to specify the filename

See also

Use create_test_mcmc to create a short regular MCMC, that can be used for testing runs. 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.

Author

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  # Create an MCMC chain with 50 states
  mcmc <- create_mcmc(chain_length = 50000, store_every = 1000)

  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()
}