Type:	Package
Title:	Call 'BEAST2'
Version:	2.5.2
Maintainer:	Richèl J.C. Bilderbeek <rjcbilderbeek@gmail.com>
Description:	'BEAST2' (https://www.beast2.org) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is a command-line tool. This package provides a way to call 'BEAST2' from an 'R' function call.
License:	GPL-3
Encoding:	UTF-8
RoxygenNote:	7.3.2
Imports:	ape, beautier (≥ 2.6.11), phangorn, rappdirs, readr, rJava, rlang (≥ 1.1.0), sessioninfo, stringr, tibble, xml2
Suggests:	knitr, rmarkdown, spelling, testthat (≥ 2.1.0), tracerer (≥ 2.2.3)
URL:	https://docs.ropensci.org/beastier/ (website) https://github.com/ropensci/beastier/
BugReports:	https://github.com/ropensci/beastier/issues
Language:	en-US
VignetteBuilder:	knitr
SystemRequirements:	BEAST2 (https://www.beast2.org/)
NeedsCompilation:	no
Packaged:	2024-10-06 14:37:25 UTC; richel
Author:	Richèl J.C. Bilderbeek [aut, cre], Joëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209), David Winter [rev] (David reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209), Jason Griffiths [ctb], Olivier Roy [ctb], Thijs Janzen [ctb]
Repository:	CRAN
Date/Publication:	2024-10-06 15:00:02 UTC

beastier: A package to call BEAST2.

Description

beastier allows to call BEAST2, a popular Bayesian phylogenetics tool, using an R interface. 'beastier' closely follows the interface of BEAST2, including its default settings.

Author(s)

Richèl J.C. Bilderbeek

See Also

These are packages associated with beastier:

• The package beautier can create BEAST2 input files from R

• The package tracerer can parse BEAST2 output files from R

• The package babette combines the functionality of beautier, beastier and tracerer into a single workflow

Examples

check_empty_beaustier_folders()

beast2_options <- create_beast2_options(
  input_filename = get_beastier_path("2_4.xml")
)

if (is_beast2_installed() && beautier::is_on_ci()) {
  run_beast2_from_options(beast2_options)
  file.remove(beast2_options$output_state_filename)
  remove_beaustier_folders()
}

Add quotes around the string if it contains spaces.

Description

Add quotes around the string if it contains spaces. Does nothing if the string contains no spaces. This is used for filenames

Usage

add_quotes_if_has_spaces(filename)

Arguments

Value

a filename. If the filename did not contain spaces, it is returned as-is. If the filename did contain spaces, the filename is surrounded by quotes

Author(s)

Richèl J.C. Bilderbeek

Examples

remove_beaustier_folders()
check_empty_beaustier_folders()

add_quotes_if_has_spaces("x")
add_quotes_if_has_spaces("a b")

check_empty_beaustier_folders()

Would these lines of text, when written to a file, result in a valid BEAST2 input file?

Description

Would these lines of text, when written to a file, result in a valid BEAST2 input file?

Usage

are_beast2_input_lines(
  lines,
  verbose = FALSE,
  method = ifelse(beautier::is_on_ci(), "deep", "fast"),
  beast2_path = get_default_beast2_path()
)

Arguments

Value

TRUE if the text is valid, FALSE if not

Author(s)

Richèl J.C. Bilderbeek

See Also

Use is_beast2_input_file to check a file

Examples

if (is_beast2_installed() && beautier::is_on_ci()) {
  are_beast2_input_lines(get_beastier_path("anthus_2_4.xml"))

  remove_beaustier_folders()
}
check_empty_beaustier_folders()

Would these lines of text, when written to a file, result in a valid BEAST2 input file?

Description

Would these lines of text, when written to a file, result in a valid BEAST2 input file?

Usage

are_beast2_input_lines_deep(
  lines,
  verbose = FALSE,
  beast2_path = get_default_beast2_path()
)

Arguments

Value

TRUE if the text is valid, FALSE if not

Author(s)

Richèl J.C. Bilderbeek

See Also

Use is_beast2_input_file to check a file

Examples

if (is_beast2_installed() && beautier::is_on_ci()) {
  beast2_filename <- get_beastier_path("anthus_2_4.xml")
  text <- readLines(beast2_filename)
  are_beast2_input_lines_deep(text)

  remove_beaustier_folders()
}
check_empty_beaustier_folders()

Would these lines of text, when written to a file, result in a valid BEAST2 input file?

Description

Would these lines of text, when written to a file, result in a valid BEAST2 input file?

Usage

are_beast2_input_lines_fast(lines)

Arguments

Value

TRUE if the text is valid, FALSE if not

Author(s)

Richèl J.C. Bilderbeek

See Also

Use is_beast2_input_file to check a file

Examples

beast2_filename <- get_beastier_path("anthus_2_4.xml")
text <- readLines(beast2_filename)

# TRUE
are_beast2_input_lines_fast(text)
check_empty_beaustier_folders()

Determines if the two alignments are equal

Description

Determines if the two alignments are equal

Usage

are_identical_alignments(p, q)

Arguments

Value

TRUE or FALSE

Author(s)

Richèl J.C. Bilderbeek

Convert a beast2_options to a table

Description

Convert a beast2_options to a table

Usage

beast2_options_to_table(beast2_options)

Arguments

Value

a tibble with two columns, called 'parameter' and 'value'. Each 'parameter' is the name of the element of the 'beast2_options' structure, where the 'value' on the same row holds the value of that parameter

Author(s)

Richèl J.C. Bilderbeek

Examples

beast2_options_to_table(create_beast2_options())

Creates a beastier report

Description

Creates a beastier report, to be used when reporting bugs. Uses message

Usage

beastier_report(
  beast2_folder = get_default_beast2_folder(),
  os = rappdirs::app_dir()$os
)

Arguments

Value

No return value, the information will be shown using message

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

beastier_report()

check_empty_beaustier_folders()

Check if BEAST2 is installed properly.

Description

Calls stop if BEAST2 is improperly installed

Usage

check_beast2(beast2_path = get_default_beast2_path())

Arguments

Value

nothing Will stop if BEAST2 is improperly installed

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_beast2_installed()) {
  check_beast2()
}

Check if the beast2_options is a valid BEAST2 options object.

Description

Calls stop if the BEAST2 option object is invalid

Usage

check_beast2_options(beast2_options)

Arguments

Value

nothing Will stop if the BEAST2 option object is invalid

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_beast2_options to create a valid BEAST2 options object

Examples

check_empty_beaustier_folders()

check_beast2_options(create_beast2_options())

check_empty_beaustier_folders()

Check if the beast2_options, which is a list, has all elements of the right data types

Description

Calls stop if not.

Usage

check_beast2_options_data_types(beast2_options)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use check_beast2_options to check the entire beast2_options object

Internal function

Description

Check if the beast2_options will not overwrite existing files, when the 'overwrite' options is set to FALSE.

Usage

check_beast2_options_do_not_overwrite_existing_files(beast2_options)

Arguments

Details

Will stop if a file is threatened to be overwritten

Value

Nothing. Will stop if a file is threatened to be overwritten

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

check_beast2_options_do_not_overwrite_existing_files(
  beast2_options = create_beast2_options()
)

check_empty_beaustier_folders()

Check if the filenames in beast2_options differ

Description

Calls stop if not.

Usage

check_beast2_options_filenames_differ(beast2_options)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use check_beast2_options to check the entire beast2_options object

Check if the beast2_options, which is a list, has all the elements needed.

Description

Calls stop if not.

Usage

check_beast2_options_names(beast2_options)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use check_beast2_options to check the entire beast2_options object

Check if the beast2_options is a valid BEAST2 options object.

Description

Calls stop if the BEAST2 option object is invalid

Usage

check_beast2_optionses(beast2_optionses)

Arguments

Value

Nothing. Will stop if the BEAST2 option object is invalid

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_beast2_options to create a valid BEAST2 options object

Examples

check_empty_beaustier_folders()

check_beast2_optionses(list(create_beast2_options()))

check_empty_beaustier_folders()

Checks the BEAST2 .jar path. Will stop if there is a problem with the BEAST2 .jar path.

Description

Checks the BEAST2 .jar path. Will stop if there is a problem with the BEAST2 .jar path.

Usage

check_beast2_path(beast2_path)

Arguments

Value

nothing. Will call stop if the BEAST2 .jar path has a problem

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed()) {
  beast2_path <- get_default_beast2_jar_path()
  check_beast2_path(beast2_path)
}

check_empty_beaustier_folders()

Internal function

Description

Check if the folder for the state output file can be created. Will stop otherwise

Usage

check_can_create_dir_for_state_output_file(beast2_options)

Arguments

Value

Nothing. Will stop if the folder for the state output file cannot be created

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

check_can_create_dir_for_state_output_file(
  beast2_options = create_beast2_options()
)

check_empty_beaustier_folders()

Internal function

Description

Check that a file can be created at a certain path.

Usage

check_can_create_file(filename, overwrite = TRUE)

Arguments

Details

Will stop if not. Will stop if the file already exists. Does so by creating an empty file at the path, and then deleting it.

Value

Nothing. Will stop if a file cannot be created at a certain path.

Author(s)

Richèl J.C. Bilderbeek

Examples

check_can_create_file("my_local_file.txt")

Internal function

Description

Check if the MCMC's screenlog file can be created. Will stop if not

Usage

check_can_create_screenlog_file(beast2_options)

Arguments

Value

Nothing. Will stop if the MCMC's screenlog file cannot be created.

Author(s)

Richèl J.C. Bilderbeek

Internal function

Description

Check if the state output file can be created. Will stop otherwise

Usage

check_can_create_state_output_file(beast2_options)

Arguments

Value

Nothing. Will stop if the state output file cannot be created.

Author(s)

Richèl J.C. Bilderbeek

Internal function to check if the MCMC's tracelog file can be created.

Description

Check if the MCMC's tracelog file can be created. Will stop if not. If the tracelog file already exists, it is assumed that a new file can be created, by overwriting the existing one.

Usage

check_can_create_tracelog_file(beast2_options)

Arguments

Value

Nothing. Will stop if the MCMC's tracelog file is absent and cannot be created.

Author(s)

Richèl J.C. Bilderbeek

Internal function

Description

Check if the MCMC's treelog file can be created. Will stop if not

Usage

check_can_create_treelog_file(beast2_options)

Arguments

Value

Nothing. Will stop if the MCMC's treelog file is absent and cannot be created.

Author(s)

Richèl J.C. Bilderbeek

Check there are no files in the default beastier folder

Description

Check there are no files in the default beastier folder. The goal is to make sure no temporary files are left undeleted. Will stop if there are files in the beastier folder

Usage

check_empty_beastier_folder(beastier_folder = get_beastier_folder())

Arguments

Value

Nothing. Will stop if there are files in the beastier folder

Author(s)

Richèl J.C. Bilderbeek

Check there are no files in the default 'beautier' and 'beastier' folders

Description

Check there are no files in the default 'beautier' and 'beastier' folders.

Usage

check_empty_beaustier_folders(
  beautier_folder = beautier::get_beautier_folder(),
  beastier_folder = get_beastier_folder()
)

Arguments

Details

The goal is to make sure no temporary files are left undeleted. Will stop if there are files in the beautier of beastier folder.

Value

Nothing. Will stop if there are files in the beautier of beastier folder.

Author(s)

Richèl J.C. Bilderbeek

Checks the input filename. Will stop if there is a problem with the input filename.

Description

Checks the input filename. Will stop if there is a problem with the input filename.

Usage

check_input_filename(input_filename)

Arguments

Value

Nothing. Will stop if the input file is invalid

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

check_input_filename(
  get_beastier_path("beast2_example_output.log")
)

check_empty_beaustier_folders()

Checks the input filename. Will stop if there is a problem with the input filename.

Description

Checks the input filename. Will stop if there is a problem with the input filename.

Usage

check_input_filename_validity(beast2_options)

Arguments

Value

nothing. Will call stop if the input file is invalid

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed()) {
  check_input_filename_validity(
    create_beast2_options(
      input_filename = get_beastier_path("2_4.xml")
    )
  )
}
check_empty_beaustier_folders()

Check if the input is a valid number of threads.

Description

Will stop if not.

Usage

check_n_threads(n_threads)

Arguments

Value

Nothing. Will stop if the number of threads in invalid

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

# Can have 1 or more threads
check_n_threads(1)
check_n_threads(2)
# Can have NA threads
check_n_threads(NA)

check_empty_beaustier_folders()

Checks if the operating system is supported

Description

Checks if the operating system is supported

Usage

check_os(os)

Arguments

Value

Nothing. Will stop if the OS is unsupported

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

check_os("mac")
check_os("unix")
check_os("win")

check_empty_beaustier_folders()

Check if the input is a valid RNG seed.

Description

Will stop if not.

Usage

check_rng_seed(rng_seed)

Arguments

Value

Nothing. Will stop if the RNG seed is invalid

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

# Numbers from 1 and higher are valid RNG seeds
check_rng_seed(1)
check_rng_seed(2)
# Also NA is a valid RNG seed
check_rng_seed(NA)

check_empty_beaustier_folders()

Continue a BEAST2 run

Description

Continue a BEAST2 run

Usage

continue_beast2(beast2_options = create_beast2_options())

Arguments

Value

The text sent to STDOUT and STDERR. It will create the file with name output_state_filenames

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed() && beautier::is_on_ci()) {
  beast2_options <- create_beast2_options(
    input_filename = get_beastier_path("2_4.xml")
  )
  run_beast2_from_options(beast2_options)
  continue_beast2(beast2_options)
  file.remove(beast2_options$output_state_filename)
  remove_beaustier_folders()
}

check_empty_beaustier_folders()

Creates the terminal command to run BEAST2 from a beast2_options

Description

If the BEAST2 input .xml filename or the BEAST2 state .state.xml filename contain spaces, these filenames are quoted, so that the command-line interface to BEAST2 correctly parses its arguments

Usage

create_beast2_continue_cmd_from_options(beast2_options)

Arguments

Value

a character vector with the command and arguments to call BEAST2

Author(s)

Richèl J.C. Bilderbeek

Examples

  if (is_beast2_installed()) {
    create_beast2_continue_cmd_from_options(
      beast2_options = create_beast2_options()
    )
  }

Create the folder where the BEAST2 input file will be created

Description

Create the folder where the BEAST2 input file will be created

Usage

create_beast2_input_file_folder(beast2_options)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

beast2_options <- create_beast2_options()
create_beast2_input_file_folder(beast2_options)

remove_beaustier_folders()
check_empty_beaustier_folders()

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

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()

Creates the terminal command to run BEAST2

Description

Creates the terminal command to run BEAST2

Usage

create_beast2_run_cmd(
  input_filename,
  output_state_filename,
  rng_seed = NA,
  n_threads = NA,
  use_beagle = FALSE,
  overwrite = FALSE,
  beast2_path = get_default_beast2_path(),
  verbose = FALSE
)

Arguments

Value

a character vector with the command and arguments to call BEAST2

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed()) {
  create_beast2_run_cmd(
    input_filename = "input.xml",
    output_state_filename = "output.xml.state",
    beast2_path = get_default_beast2_jar_path()
  )
}

check_empty_beaustier_folders()

Creates the terminal command to run BEAST2 from a beast2_options

Description

Creates the terminal command to run BEAST2 from a beast2_options

Usage

create_beast2_run_cmd_from_options(beast2_options)

Arguments

Value

a character vector with the command and arguments to call BEAST2

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed()) {
  create_beast2_run_cmd_from_options(
    beast2_options = create_beast2_options()
  )
}

check_empty_beaustier_folders()

Internal function

Description

Create the folder for the BEAST2 screenlog file

Usage

create_beast2_screenlog_folder(beast2_options)

Arguments

Author(s)

Richèl J.C. Bilderbeek

Create the folder where the BEAST2 state output file will be created

Description

Create the folder where the BEAST2 state output file will be created

Usage

create_beast2_state_output_file_folder(beast2_options)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

beast2_options <- create_beast2_options()
create_beast2_state_output_file_folder(beast2_options)

remove_beaustier_folders()
check_empty_beaustier_folders()

Internal function

Description

Create the folder for the BEAST2 tracelog file

Usage

create_beast2_tracelog_folder(beast2_options)

Arguments

Author(s)

Richèl J.C. Bilderbeek

Internal function

Description

Create the folder for the BEAST2 treelog file

Usage

create_beast2_treelog_folder(beast2_options)

Arguments

Author(s)

Richèl J.C. Bilderbeek

Creates the terminal command to validate a BEAST2 input file

Description

Creates the terminal command to validate a BEAST2 input file

Usage

create_beast2_validate_cmd(
  input_filename,
  beast2_path = get_default_beast2_path()
)

Arguments

Value

a character vector, of which the first element is the command (java, in this case), and the others are arguments (-jar, in this case, followed by more arguments.

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed() && beautier::is_on_ci()) {
  create_beast2_validate_cmd(
    input_filename = "input.xml"
  )
}

check_empty_beaustier_folders()

Creates the terminal command to validate a BEAST2 input file using a call to the launcher.jar file

Description

Creates the terminal command to validate a BEAST2 input file using a call to the launcher.jar file

Usage

create_beast2_validate_cmd_bin(
  input_filename,
  beast2_bin_path = get_default_beast2_bin_path()
)

Arguments

Value

a character vector, of which the first element is the command (java, in this case), and the others are arguments (-jar, in this case, followed by more arguments.

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed() && beautier::is_on_ci()) {
  create_beast2_validate_cmd_bin(
    input_filename = "input.xml"
  )
}

check_empty_beaustier_folders()

Creates the terminal command to validate a BEAST2 input file using a call to the launcher.jar file

Description

Creates the terminal command to validate a BEAST2 input file using a call to the launcher.jar file

Usage

create_beast2_validate_cmd_jar(
  input_filename,
  beast2_jar_path = get_default_beast2_jar_path()
)

Arguments

Value

a character vector, of which the first element is the command (java, in this case), and the others are arguments (-jar, in this case, followed by more arguments.

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed() && beautier::is_on_ci()) {
  create_beast2_validate_cmd_jar(
    input_filename = "input.xml"
  )
}

check_empty_beaustier_folders()

Creates the terminal command to version a BEAST2 input file

Description

Creates the terminal command to version a BEAST2 input file

Usage

create_beast2_version_cmd(beast2_path = get_default_beast2_path())

Arguments

Value

a character vector, of which the first element is the command (java, in this case), and the others are arguments (-jar, in this case, followed by more arguments.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_beast2_installed()) {
  create_beast2_version_cmd()
}

Creates the terminal command to version a BEAST2 input file using a call to the launcher.jar file

Description

Creates the terminal command to version a BEAST2 input file using a call to the launcher.jar file

Usage

create_beast2_version_cmd_bin(beast2_bin_path = get_default_beast2_bin_path())

Arguments

Value

a character vector, of which the first element is the command (java, in this case), and the others are arguments (-jar, in this case, followed by more arguments.

Author(s)

Richèl J.C. Bilderbeek

Examples

  if (is_beast2_installed() && beautier::is_on_ci()) {
    create_beast2_version_cmd_bin()
  }

Creates the terminal command to version a BEAST2 input file using a call to the launcher.jar file

Description

Creates the terminal command to version a BEAST2 input file using a call to the launcher.jar file

Usage

create_beast2_version_cmd_jar(beast2_jar_path = get_default_beast2_jar_path())

Arguments

Value

a character vector, of which the first element is the command (java, in this case), and the others are arguments (-jar, in this case, followed by more arguments.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_beast2_installed()) {
  create_beast2_version_cmd_jar()
}

Create the temporary folder as used by beastier

Description

Create the temporary folder as used by beastier

Usage

create_beastier_tempfolder()

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

create_beastier_tempfolder()

remove_beaustier_folders()
check_empty_beaustier_folders()

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

Description

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 = create_temp_input_filename(),
  output_state_filename = create_temp_state_filename(),
  rng_seed = NA,
  n_threads = NA,
  use_beagle = FALSE,
  overwrite = TRUE,
  beast2_bin_path = get_default_beast2_bin_path(),
  verbose = FALSE
)

Arguments

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)

Author(s)

Richèl J.C. Bilderbeek

See Also

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

Examples

check_empty_beaustier_folders()

create_mcbette_beast2_options()

check_empty_beaustier_folders()

Create a random alignment

Description

Create a random alignment

Usage

create_random_alignment(n_taxa, sequence_length, rate = 1, taxa_name_ext = "")

Arguments

Value

an alignment of class DNAbin

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

alignment <- create_random_alignment(
  n_taxa = 5,
  sequence_length = 10
)
image(alignment)

remove_beaustier_folders()
check_empty_beaustier_folders()

Create a random FASTA file

Description

Create a random FASTA file

Usage

create_random_fasta(
  n_taxa,
  sequence_length,
  fasta_filename,
  taxa_name_ext = ""
)

Arguments

Value

Nothing, creates a FASTA file

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

fasta_filename <- get_beastier_tempfilename()
create_random_fasta(
  n_taxa = 5,
  sequence_length = 20,
  fasta_filename = fasta_filename
)
file.remove(fasta_filename)

remove_beaustier_folders()
check_empty_beaustier_folders()

Create a random phylogeny

Description

Create a random phylogeny

Usage

create_random_phylogeny(n_taxa, taxa_name_ext = "")

Arguments

Value

a phylogeny of class 'phylo' (which is part of the 'ape' package)

Author(s)

Richèl J.C. Bilderbeek

Examples

create_random_phylogeny(n_taxa = 6)

Create a temporary filename for the BEAST2 XML filename

Description

Create a temporary filename for the BEAST2 XML filename

Usage

create_temp_input_filename()

Value

a temporary filename, that starts with 'beast2_' and has extension '.xml'

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

create_temp_input_filename()

check_empty_beaustier_folders()

Create a temporary file for the BEAST2 XML output file that stores its state.

Description

Create a temporary file for the BEAST2 XML output file that stores its state.

Usage

create_temp_state_filename()

Value

a temporary filename, that starts with 'beast2_' and has extension '.xml.state'

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

create_temp_state_filename()

check_empty_beaustier_folders()

This function does nothing. It is intended to inherit is parameters' documentation.

Description

This function does nothing. It is intended to inherit is parameters' documentation.

Usage

default_params_doc(
  beast2_bin_path,
  beast2_folder,
  beast2_jar_path,
  beast2_options,
  beast2_optionses,
  beast2_path,
  beast2_version,
  beast2_working_dir,
  beastier_folder,
  beautier_folder,
  clock_model,
  clock_models,
  crown_age,
  crown_ages,
  fasta_filename,
  fasta_filenames,
  fixed_crown_age,
  fixed_crown_ages,
  initial_phylogenies,
  input_filename,
  mcmc,
  misc_options,
  n_taxa,
  n_threads,
  os,
  output_filename,
  output_log_filename,
  output_state_filename,
  output_trees_filenames,
  overwrite,
  rename_fun,
  rng_seed,
  sequence_length,
  site_model,
  site_models,
  tree_prior,
  tree_priors,
  use_beagle,
  verbose
)

Arguments

Value

Nothing. This is an internal function that does nothing

Note

This is an internal function, so it should be marked with @noRd. This is not done, as this will disallow all functions to find the documentation parameters

Author(s)

Richèl J.C. Bilderbeek

Do a minimal BEAST2 run

Description

To achieve this, run_beast2_from_options is called.

Usage

do_minimal_run()

Value

The text sent to STDOUT and STDERR. It will create the files with name output_state_filename

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_beast2_installed() && beautier::is_on_ci()) {
  do_minimal_run()
}

Internal function to extract the screenlog filename for a BEAST2 input file

Description

Extract the screenlog filename from a BEAST2 input file

Usage

extract_screenlog_filename_from_beast2_input_file(input_filename)

Arguments

Value

the screenlog filename for a BEAST2 input file

Author(s)

Richèl J.C. Bilderbeek

Internal function to extract the tracelog filename for a BEAST2 input file

Description

Extract the tracelog filename for a BEAST2 input file

Usage

extract_tracelog_filename_from_beast2_input_file(input_filename)

Arguments

Value

the name of the tracelog file

Author(s)

Richèl J.C. Bilderbeek

Examples

if (beautier::is_on_ci())
{

  beast2_input_filename <- get_beastier_tempfilename()
  tracelog_filename <- get_beastier_tempfilename()
  beautier::create_beast2_input_file_from_model(
    input_filename = beautier::get_beautier_path("test_output_0.fas"),
    output_filename = beast2_input_filename,
    inference_model = beautier::create_inference_model(
      mcmc = beautier::create_mcmc(
        tracelog = beautier::create_tracelog(
          filename = tracelog_filename
        )
      )
    )
  )
  extract_tracelog_filename_from_beast2_input_file(
    input_filename = beast2_input_filename
  )
  file.remove(beast2_input_filename)

  remove_beaustier_folders()
}

Internal function to extract the treelog filename for a BEAST2 input file

Description

Extract the treelog filename from a BEAST2 input file

Usage

extract_treelog_filename_from_beast2_input_file(input_filename)

Arguments

Value

the treelog filename for a BEAST2 input file

Author(s)

Richèl J.C. Bilderbeek

Examples

if (beautier::is_on_ci()) {

  beast2_input_filename <- get_beastier_tempfilename()

  beautier::create_beast2_input_file_from_model(
    input_filename = beautier::get_beautier_path("test_output_0.fas"),
    output_filename = beast2_input_filename
  )
  extract_treelog_filename_from_beast2_input_file(
    input_filename = beast2_input_filename
  )
  file.remove(beast2_input_filename)

  remove_beaustier_folders()
}

Get the alignment ID from a file with one alignment

Description

Get the alignment ID from a file with one alignment

Usage

get_alignment_ids_from_xml_filename(xml_filename)

Arguments

Value

one or more alignment IDs

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

# test_output_0
get_alignment_ids_from_xml_filename(get_beastier_path("2_4.xml"))
# c("anthus_aco","anthus_nd2")
get_alignment_ids_from_xml_filename(get_beastier_path("anthus_15_15.xml"))

check_empty_beaustier_folders()

Get the full path of a BEAST2 example file

Description

Will stop if the filename is not a BEAST2 example file

Usage

get_beast2_example_filename(
  filename,
  beast2_folder = get_default_beast2_folder()
)

Arguments

Value

the full path of a BEAST2 example file, will stop if the filename is not a BEAST2 example file

Examples

if (is_beast2_installed()) {
  get_beast2_example_filename("testJukesCantor.xml")
}

Get a list with the full paths of all BEAST2 example filenames

Description

Get a list with the full paths of all BEAST2 example filenames

Usage

get_beast2_example_filenames(beast2_folder = get_default_beast2_folder())

Arguments

Value

a list with the full paths of all BEAST2 example filenames

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_beast2_installed()) {
  get_beast2_example_filenames()
}

Get the BEAST2 main class name.

Description

One way to fix the error no main manifest attribute is to specify the main class name.

Usage

get_beast2_main_class_name()

Value

the BEAST2 main class name

Author(s)

Richèl J.C. Bilderbeek

Examples

get_beast2_main_class_name()

Extract the filenames from a 'beast2_options'

Description

Extract the filenames from a 'beast2_options'

Usage

get_beast2_options_filenames(beast2_options)

Arguments

Value

the filenames from a 'beast2_options'

Author(s)

Richèl J.C. Bilderbeek

Examples

beast2_options <- create_beast2_options()
get_beast2_options_filenames(beast2_options)

Get the BEAST2 version

Description

Get the BEAST2 version

Usage

get_beast2_version(beast2_path = get_default_beast2_path())

Arguments

Value

the BEAST2 version

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed() && beautier::is_on_ci()) {
  get_beast2_version()
}

check_empty_beaustier_folders()

Get the path to the beastier temporary files folder

Description

Get the path to the beastier temporary files folder.

Usage

get_beastier_folder()

Value

the path to the beastier temporary files folder.

Author(s)

Richèl J.C. Bilderbeek

Examples

get_beastier_folder()

Get the full path of a file in the inst/extdata folder

Description

Get the full path of a file in the inst/extdata folder

Usage

get_beastier_path(filename)

Arguments

Value

the full path to the filename. Will stop if the file is absent in the inst/extdata folder

Author(s)

Richèl J.C. Bilderbeek

See Also

for more files, use get_beastier_paths

Examples

get_beastier_path("beast2_example_output.log")
get_beastier_path("beast2_example_output.trees")
get_beastier_path("beast2_example_output.xml")
get_beastier_path("beast2_example_output.xml.state")

Get the full paths of files in the inst/extdata folder

Description

Get the full paths of files in the inst/extdata folder

Usage

get_beastier_paths(filenames)

Arguments

Value

the filenames' full paths. Will stop if a file is absent in the inst/extdata folder

Author(s)

Richèl J.C. Bilderbeek

See Also

for one file, use get_beastier_path

Examples

get_beastier_paths(
  c(
    "beast2_example_output.log",
    "beast2_example_output.trees",
    "beast2_example_output.xml",
    "beast2_example_output.xml.state"
  )
)

Get a temporary filename

Description

Get a temporary filename, similar to tempfile, except that it always writes to a temporary folder named beastier.

Usage

get_beastier_tempfilename(pattern = "file", fileext = "")

Arguments

Value

name for a temporary file

Note

this function is added to make sure no temporary cache files are left undeleted

Author(s)

Richèl J.C. Bilderbeek

Examples

get_beastier_tempfilename()
get_beastier_tempfilename(pattern = "my_pattern_")
get_beastier_tempfilename(fileext = ".ext")

Get the default BEAST2 binary file (beast, that is) path

Description

Get the default BEAST2 binary file (beast, that is) path

Usage

get_default_beast2_bin_path(
  beast2_folder = get_default_beast2_folder(),
  os = rappdirs::app_dir()$os
)

Arguments

Value

the default BEAST2 binary file's path

Author(s)

Richèl J.C. Bilderbeek

See Also

Use get_default_beast2_folder to get the default folder in which BEAST2 is installed. Use install_beast2 with default arguments to install BEAST2 to this location.

Examples

check_empty_beaustier_folders()

if (is_beast2_installed()) {
  get_default_beast2_bin_path()
}

check_empty_beaustier_folders()

Get the default BEAST2 download URL, which depends on the operating system

Description

Get the default BEAST2 download URL, which depends on the operating system

Usage

get_default_beast2_download_url(
  beast2_version = get_default_beast2_version(),
  os = rappdirs::app_dir()$os
)

Arguments

Value

the URL where BEAST2 can be downloaded from

Author(s)

Richèl J.C. Bilderbeek

Examples

get_default_beast2_download_url()

Get the BEAST2 download URL for Linux

Description

Get the BEAST2 download URL for Linux

Usage

get_default_beast2_download_url_linux(
  beast2_version = get_default_beast2_version()
)

Arguments

Value

the URL where BEAST2 can be downloaded from

Author(s)

Richèl J.C. Bilderbeek

Get the BEAST2 download URL for Windows

Description

Get the BEAST2 download URL for Windows

Usage

get_default_beast2_download_url_win(
  beast2_version = get_default_beast2_version()
)

Arguments

Value

the URL where BEAST2 can be downloaded from

Author(s)

Richèl J.C. Bilderbeek

Get the path to the folder where this package installs BEAST2 by default

Description

Get the path to the folder where this package installs BEAST2 by default

Usage

get_default_beast2_folder()

Value

the path to the folder where this package installs BEAST2 by default

Author(s)

Richèl J.C. Bilderbeek

See Also

Use get_default_beast2_jar_path to get the path to the BEAST2 jar file, when installed by this package Use install_beast2 with default arguments to install BEAST2 to this folder.

Examples

check_empty_beaustier_folders()

get_default_beast2_folder()

check_empty_beaustier_folders()

Get the default BEAST2 jar file's path

Description

Get the default BEAST2 jar file's path

Usage

get_default_beast2_jar_path(
  beast2_folder = get_default_beast2_folder(),
  os = rappdirs::app_dir()$os
)

Arguments

Value

the default BEAST2 jar file's path

Author(s)

Richèl J.C. Bilderbeek

See Also

Use get_default_beast2_folder to get the default folder in which BEAST2 is installed. Use install_beast2 with default arguments to install BEAST2 to this location.

Examples

check_empty_beaustier_folders()

get_default_beast2_jar_path()

check_empty_beaustier_folders()

Get the default BEAST2 path

Description

Get the default BEAST2 path

Usage

get_default_beast2_path(
  beast2_folder = get_default_beast2_folder(),
  os = rappdirs::app_dir()$os
)

Arguments

Value

the default BEAST2 path

Author(s)

Richèl J.C. Bilderbeek

See Also

Use get_default_beast2_bin_path to get the default path to the BEAST2 binary file. Use get_default_beast2_jar_path to get the default path to the BEAST2 jar file. Use get_default_beast2_folder to get the default folder in which BEAST2 is installed. Use install_beast2 with default arguments to install BEAST2 to this location.

Examples

if (is_beast2_installed()) {
  get_default_beast2_path()
}

Get the default BEAST2 version that is used by beastier

Description

Get the default BEAST2 version that is used by beastier

Usage

get_default_beast2_version()

Value

the BEAST2 version

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

get_default_beast2_version()

check_empty_beaustier_folders()

Obtains the default path to the Java executable

Description

Obtains the default path to the Java executable

Usage

get_default_java_path(os = rappdirs::app_dir()$os)

Arguments

Value

the default path to the Java executable

Author(s)

Richèl J.C. Bilderbeek

Find duplicate RealParameter IDs

Description

Find duplicate RealParameter IDs

Usage

get_duplicate_param_ids(text)

Arguments

Value

a vector of duplicate IDs, will be empty if all IDs are unique

Author(s)

Richèl J.C. Bilderbeek

See Also

to see if all IDs are unique, use has_unique_ids

Examples

check_empty_beaustier_folders()

line_1 <- "<parameter id=\"RealParameter.1\" ...</parameter>"
line_2 <- "<parameter id=\"RealParameter.2\" ...</parameter>"
# No elements
get_duplicate_param_ids(c(line_1, line_2))

# 'RealParameter.1'
get_duplicate_param_ids(c(line_1, line_1))

# 'RealParameter.2'
get_duplicate_param_ids(c(line_2, line_2))

check_empty_beaustier_folders()

Get the Java version

Description

Get the Java version

Usage

get_java_version()

Value

the Java version

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_beast2_installed() && beautier::is_on_ci()) {
  get_java_version()
}

Get the .trees filenames that BEAST2 will produce

Description

Get the .trees filenames that BEAST2 will produce

Usage

get_trees_filenames(input_filename)

Arguments

Value

character vector with the names of the .trees files that BEAST2 will produce

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

get_trees_filenames(get_beastier_path("2_4.xml"))
get_trees_filenames(get_beastier_path("anthus_2_4.xml"))

check_empty_beaustier_folders()

Determines if BEAST2 issues a warning when using the BEAST2 XML input file

Description

Determines if BEAST2 issues a warning when using the BEAST2 XML input file

Usage

gives_beast2_warning(
  filename,
  verbose = FALSE,
  beast2_path = get_default_beast2_path()
)

Arguments

Value

TRUE if the file produces a BEAST2 warning, FALSE if not

Author(s)

Richèl J.C. Bilderbeek

See Also

Use is_beast2_input_file to check if a file is a valid BEAST2 input file. Use are_beast2_input_lines to check if the text (for example, as loaded from a file) to be valid BEAST2 input.

Examples

if (is_beast2_installed() &&
  beautier::is_on_ci() &&
  rappdirs::app_dir()$os == "unix") {

  # This file is OK for BEAST2, no warning, returns FALSE
  gives_beast2_warning(filename = get_beastier_path("2_4.xml"))

  # BEAST2 will give a warning on this file, returns TRUE
  gives_beast2_warning(
    filename = get_beastier_path("beast2_warning.xml")
  )
}

Determine if the XML text has unique parameter IDs

Description

Determine if the XML text has unique parameter IDs

Usage

has_unique_ids(text)

Arguments

Value

TRUE if all parameter IDs are unique, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

See Also

to obtain the duplicate parameter IDs, use get_duplicate_param_ids

Examples

check_empty_beaustier_folders()

line_1 <- "<parameter id=\"RealParameter.1\" ...</parameter>"
line_2 <- "<parameter id=\"RealParameter.2\" ...</parameter>"
# Unique IDs
has_unique_ids(c(line_1, line_2))
# No unique ID
has_unique_ids(c(line_1, line_1))

check_empty_beaustier_folders()

Deprecated function to install BEAST2

Description

This function is deprecated as it violated CRAN policy.

Usage

install_beast2(
  folder_name = rappdirs::user_data_dir(),
  beast2_version = beastier::get_default_beast2_version(),
  verbose = FALSE,
  os = rappdirs::app_dir()$os
)

Arguments

Details

To install BEAST2 from R, go to https://github.com/richelbilderbeek/beastierinstall.

Value

Nothing. Gives a deprecation message using stop.

Author(s)

Richèl J.C. Bilderbeek

Determines if the input is an alignment of type DNAbin

Description

Determines if the input is an alignment of type DNAbin

Usage

is_alignment(input)

Arguments

Value

TRUE or FALSE

Author(s)

Richèl J.C. Bilderbeek

Is a file a valid BEAST2 input file?

Description

Is a file a valid BEAST2 input file?

Usage

is_beast2_input_file(
  filename,
  show_warnings = FALSE,
  verbose = FALSE,
  beast2_path = get_default_beast2_path()
)

Arguments

Value

TRUE if the file is valid, FALSE if not

Note

this function only works on standard BEAST2 input files: if a BEAST2 input file is modified to use a certain BEAST2 package, this function will label it as an invalid file

Author(s)

Richèl J.C. Bilderbeek

See Also

Use are_beast2_input_lines to check the lines

Examples

check_empty_beaustier_folders()

if (is_beast2_installed() && beautier::is_on_ci()) {

  filename <- get_beastier_path("anthus_2_4.xml")
  # TRUE, this is a BEAST2 input file
  is_beast2_input_file(filename)

  filename <- get_beastier_path("beast2_example_output.log")
  # FALSE, this is not a BEAST2 input file,
  # it is a BEAST2 output log file insteaf
  is_beast2_input_file(filename)
}

check_empty_beaustier_folders()

Checks if BEAST2 is installed

Description

Checks if BEAST2 is installed

Usage

is_beast2_installed(
  folder_name = get_default_beast2_folder(),
  os = rappdirs::app_dir()$os
)

Arguments

Value

TRUE if BEAST2 is installed

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

is_beast2_installed()

check_empty_beaustier_folders()

Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present

Description

Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present

Usage

is_bin_path(path)

Arguments

Value

TRUE if the path is a path to a BEAST2 binary file

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed()) {
  # TRUE
  is_bin_path("beast")
  is_bin_path("BEAST.exe")
  is_bin_path(get_default_beast2_bin_path())
  # FALSE
  is_bin_path("launcher.jar")
  is_bin_path(get_default_beast2_jar_path())
}

check_empty_beaustier_folders()

Is the path a path to the BEAST2 jar file? Does not check if the file at that path is present

Description

Is the path a path to the BEAST2 jar file? Does not check if the file at that path is present

Usage

is_jar_path(path)

Arguments

Value

TRUE if the path is a path to a BEAST2 jar file

Author(s)

Richèl J.C. Bilderbeek

Examples

# Returns TRUE
is_jar_path("beast.jar")
is_jar_path("launcher.jar")
is_jar_path(get_default_beast2_jar_path())
# Returns FALSE
is_jar_path("beast")
is_jar_path(get_default_beast2_bin_path())

Deprecated function, use is_on_appveyor

Description

Deprecated function, use is_on_appveyor

Usage

is_on_appveyor()

Value

TRUE if run on AppVeyor, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Deprecated function, use is_on_ci

Description

Deprecated function, use is_on_ci

Usage

is_on_ci()

Value

TRUE if run on AppVeyor or Travis CI, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Deprecated function, use is_on_travis

Description

Deprecated function, use is_on_travis

Usage

is_on_travis()

Value

TRUE if run on Travis CI, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present

Description

Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present

Usage

is_win_bin_path(path)

Arguments

Value

TRUE if the path is a path to a BEAST2 binary file

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

# TRUE
is_win_bin_path("BEAST.exe")
# FALSE
is_win_bin_path("beast")
is_win_bin_path("launcher.jar")

check_empty_beaustier_folders()

Pretty-print a 'beast2_options'

Description

Pretty-print a 'beast2_options'

Usage

print_beast2_options(beast2_options)

Arguments

Value

Nothing. Will display the 'beast2_options' using cat.

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

print_beast2_options(create_beast2_options())

check_empty_beaustier_folders()

Check there are no files in the default beautier folder

Description

Check there are no files in the default beautier folder. The goal is to make sure no temporary files are left undeleted. Will stop if there are files in the beautier folder.

Usage

remove_beastier_folder()

Value

Nothing.

Author(s)

Richèl J.C. Bilderbeek

See Also

use remove_beautier_folder to remove the default 'beautier' folder

Examples

check_empty_beastier_folder()

remove_beastier_folder()

check_empty_beastier_folder()

Remove the 'beautier' and 'beastier' temporary folders

Description

Remove the 'beautier' and 'beastier' temporary folders

Usage

remove_beaustier_folders()

Value

Nothing.

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

remove_beaustier_folders()

check_empty_beaustier_folders()

Remove a file if it is present, will do nothing if it is not.

Description

Remove a file if it is present, will do nothing if it is not.

Usage

remove_file_if_present(filename)

Arguments

Value

Nothing. Will remove the file if it is presented, will do nothing if it is not.

Author(s)

Richèl J.C. Bilderbeek

Examples

filename <- tempfile()
file.create(filename)
remove_file_if_present(filename)
remove_file_if_present(filename)

Rename the filenames in the BEAST2 options

Description

Rename the filenames in the BEAST2 options

Usage

rename_beast2_options_filenames(beast2_options, rename_fun)

Arguments

Value

a 'beast2_options' with the filenames it contains renamed

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

# beast2_options with local filenames
beast2_options <- create_beast2_options(
  input_filename = "my.fas",
  output_state_filename = "my_state.xml.state"
)
# Rename filenames to be in /my/new/folder
rename_beast2_options_filenames(
  beast2_options = beast2_options,
  rename_fun = beautier::get_replace_dir_fun("/my/new/folder")
)

check_empty_beaustier_folders()

Run BEAST2

Description

Run BEAST2

Usage

run_beast2(
  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

Value

The text sent to STDOUT and STDERR. It will create the file with name output_state_filenames

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed() && beautier::is_on_ci()) {

  output_state_filename <- create_temp_state_filename()

  run_beast2(
    input_filename = get_beastier_path("2_4.xml"),
    output_state_filename = output_state_filename

  )
  file.remove(output_state_filename)
  remove_beaustier_folders()
}

check_empty_beaustier_folders()

Run BEAST2

Description

Run BEAST2

Usage

run_beast2_from_options(beast2_options = create_beast2_options())

Arguments

Value

The text sent to STDOUT and STDERR. It will create the file with name output_state_filenames

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beaustier_folders()

if (is_beast2_installed() && beautier::is_on_ci()) {
  beast2_options <- create_beast2_options(
    input_filename = get_beastier_path("2_4.xml")
  )
  run_beast2_from_options(beast2_options)
  file.remove(beast2_options$output_state_filename)
  remove_beaustier_folders()
}
check_empty_beaustier_folders()

Save text (a container of strings) to a file

Description

Save text (a container of strings) to a file

Usage

save_lines(filename, lines)

Arguments

Value

Nothing. Will save the lines to file

Author(s)

Richèl J.C. Bilderbeek

Examples

text <- c("hello", "world")
filename <- get_beastier_tempfilename()
save_lines(filename = filename, lines = text)
file.remove(filename)

remove_beaustier_folders()

Save a NEXUS file as a FASTA file

Description

Save a NEXUS file as a FASTA file

Usage

save_nexus_as_fasta(nexus_filename, fasta_filename)

Arguments

Value

nothing. The NEXUS file will be saved as a FASTA file

Deprecated function to uninstall BEAST2

Description

Deprecated function to uninstall BEAST2

Usage

uninstall_beast2(
  folder_name = rappdirs::user_data_dir(),
  os = rappdirs::app_dir()$os,
  verbose = FALSE
)

Arguments

Value

Nothing. A deprecation message using stop will be triggered

Author(s)

Richèl J.C. Bilderbeek

Deprecated function to upgrade BEAST2.

Description

Deprecated function to upgrade BEAST2.

Usage

upgrade_beast2(
  folder_name = rappdirs::user_data_dir(),
  os = rappdirs::app_dir()$os
)

Arguments

Value

Nothing. A deprecation message using stop will be triggered

Author(s)

Richèl J.C. Bilderbeek