create_beast2_options: Function to create a set of BEAST2 options.

In beastier: Call 'BEAST2'

Function to create a set of BEAST2 options.

Description

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(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

beast2_options <- create_beast2_options()
check_beast2_options(beast2_options)

check_empty_beaustier_folders()

beastier documentation built on Nov. 7, 2023, 5:08 p.m.