create_beauti_options: Function to create a set of 'BEAUti' options.

In ropensci/beautier: 'BEAUti' from R

Function to create a set of 'BEAUti' options.

Description

'BEAUti' options are settings that differ between 'BEAUti' version. The use of these options is mostly for testing older versions Whatever option chosen here, the created XML file will be valid.

Usage

create_beauti_options(
  capitalize_first_char_id = FALSE,
  nucleotides_uppercase = FALSE,
  beast2_version = "2.4",
  required = "",
  sequence_indent = 20,
  status = "",
  namespace = get_default_beast_namespace_v2_4()
)

Arguments

capitalize_first_char_id	must the ID of alignment start with a capital? TRUE if yes, FALSE if it can be left lower case (if it is lowercase)
nucleotides_uppercase	must the nucleotides of the DNA sequence be in uppercase?
beast2_version	the BEAST2 version
required	things that may be required, for example BEAST v2.5.0
sequence_indent	the number of spaces the XML sequence lines are indented
status	the BEAUti status
namespace	the 'namespace' XML element in the 'beast' XML tag.

Details

Available BEAUti options are:
* create_beauti_options_v2_4 * create_beauti_options_v2_6

'beautier' uses v2.4 by default, as this is when the first tests were written.

Value

a BEAUti options structure

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  beauti_options <- create_beauti_options_v2_4()
  xml <- create_beast2_input(
    get_fasta_filename(),
    beauti_options = beauti_options
  )

  check_empty_beautier_folder()
}

ropensci/beautier documentation built on July 9, 2024, 6:14 a.m.