create_beauti_options_v2_6: Function to create the BEAUti options for version 2.6.

In richelbilderbeek/beastscriptr: 'BEAUti' from R

Function to create the BEAUti options for version 2.6.

Description

Function to create the BEAUti options for version 2.6, by calling create_beauti_options.

Usage

create_beauti_options_v2_6(
  beast2_version = "2.6",
  sequence_indent = 8,
  nucleotides_uppercase = FALSE,
  status = "",
  namespace = get_default_beast_namespace_v2_6(),
  required = ""
)

Arguments

beast2_version	the BEAST2 version
sequence_indent	the number of spaces the XML sequence lines are indented
nucleotides_uppercase	must the nucleotides of the DNA sequence be in uppercase?
status	the BEAUti status
namespace	the 'namespace' XML element in the 'beast' XML tag.
required	things that may be required, for example BEAST v2.5.0

Value

a BEAUti options structure

Author(s)

Richèl J.C. Bilderbeek

See Also

see create_beauti_options_v2_4 for using the older v2.4

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  beauti_options <- create_beauti_options_v2_6()
  xml <- create_beast2_input(
    get_fasta_filename(),
    beauti_options = beauti_options
  )

  check_empty_beautier_folder()
}

richelbilderbeek/beastscriptr documentation built on April 9, 2024, 2:28 p.m.