beastier (version 2.5)

run_beast2: Run BEAST2

Description

Run BEAST2

Usage

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

Value

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

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

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()