Function to create a set of BEAST2 options.

These BEAST2 options are the R equivalent of the command-line options.

Usage

create_beast2_options(
  input_filename = create_temp_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
)

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

a BEAST2 options structure, which is a list of all function arguments, of which all elements are checked (by check_beast2_options)

Author

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

beast2_options <- create_beast2_options()
check_beast2_options(beast2_options)

check_empty_beaustier_folders()