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Creates the terminal command to run BEAST2

Source: R/create_beast2_run_cmd.R
create_beast2_run_cmd.Rd

Creates the terminal command to run BEAST2

Usage

create_beast2_run_cmd(
  input_filename,
  output_state_filename,
  rng_seed = NA,
  n_threads = NA,
  use_beagle = FALSE,
  overwrite = FALSE,
  beast2_path = 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 BEAST2 output file that stores the state (usually has a .xml.state 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

a character vector with the command and arguments to call BEAST2

Author

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed()) {
  create_beast2_run_cmd(
    input_filename = "input.xml",
    output_state_filename = "output.xml.state",
    beast2_path = get_default_beast2_jar_path()
  )
}

check_empty_beaustier_folders()