Run BEAST2

Run BEAST2

Usage

run_beast2(
  input_filename,
  output_state_filename = beastier::create_temp_state_filename(),
  rng_seed = NA,
  n_threads = NA,
  use_beagle = FALSE,
  overwrite = TRUE,
  beast2_path = beastier::get_default_beast2_path(),
  verbose = FALSE
)

Arguments

input_filename

the name of a BEAST2 input XML file. This file usually has an .xml extension. Use create_temp_input_filename to create a temporary filename with that extension.

output_state_filename

name of the .xml.state file to create. Use create_temp_state_filename to create a temporary filename with that extension.

rng_seed

the random number generator seed of the BEAST2 run. Must be a non-zero positive integer value or NA. If rng_seed is NA, BEAST2 will pick a random seed

n_threads

the number of computational threads to use. Use NA to use the BEAST2 default of 1.

use_beagle

use BEAGLE if present

overwrite

if TRUE: overwrite the .log and .trees files if one of these exists. If FALSE, BEAST2 will not be started if

• the .log file exists

• the .trees files exist

• the .log file created by BEAST2 exists

• the .trees files created by BEAST2 exist

beast2_path

name of either a BEAST2 binary file (usually simply beast) or a BEAST2 jar file (usually has a .jar extension). Use get_default_beast2_bin_path to get the default BEAST binary file's path Use get_default_beast2_jar_path to get the default BEAST jar file's path

verbose

if TRUE, additional information is displayed, that is potentially useful in debugging

Value

The text sent to STDOUT and STDERR. It will create the file with name output_state_filenames

Author

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed() && beautier::is_on_ci()) {

  output_state_filename <- create_temp_state_filename()

  run_beast2(
    input_filename = get_beastier_path("2_4.xml"),
    output_state_filename = output_state_filename

  )
  file.remove(output_state_filename)
  remove_beaustier_folders()
}

check_empty_beaustier_folders()