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Create a `beast2_options` structure for the `mcbette` R package

Source: R/create_mcbette_beast2_options.R
create_mcbette_beast2_options.Rd

Create a `beast2_options` structure to be used for the `mcbette` R package, which is a package that allows one to do model comparison. The generated filenames indicating `mcbette` usage, as well as the correct BEAST2 binary/executable type

Usage

create_mcbette_beast2_options(
  input_filename = beastier::create_temp_input_filename(),
  output_state_filename = beastier::create_temp_state_filename(),
  rng_seed = NA,
  n_threads = NA,
  use_beagle = FALSE,
  overwrite = TRUE,
  beast2_bin_path = beastier::get_default_beast2_bin_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_bin_path

name of the BEAST2 binary file (usually simply beast). Use get_default_beast2_bin_path to get the default BEAST binary file's path

verbose

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

Value

a `beast2_options` structure suitable to be used by the `mcbette` R package, which is a list of all function arguments, of which all elements are checked (by check_beast2_options)

See also

to create a regular (that is, not intended for model comparison) BEAST2 options structure, use create_beast2_options

Author

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

create_mcbette_beast2_options()
#> $input_filename
#> [1] "/github/home/.cache/beastier/beast2_71c790274bd.xml"
#> 
#> $output_state_filename
#> [1] "/github/home/.cache/beastier/beast2_71c3a050c1a.xml.state"
#> 
#> $rng_seed
#> [1] NA
#> 
#> $n_threads
#> [1] NA
#> 
#> $use_beagle
#> [1] FALSE
#> 
#> $overwrite
#> [1] TRUE
#> 
#> $beast2_path
#> [1] "/github/home/.local/share/beast/bin/beast"
#> 
#> $verbose
#> [1] FALSE
#> 

check_empty_beaustier_folders()