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beastier (version 2.5)

Call 'BEAST2'

Description

'BEAST2' () 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.

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Install

install.packages('beastier')

Monthly Downloads

368

Version

2.5

License

GPL-3

Issues

Pull Requests

Stars

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Repository

https://docs.ropensci.org/beastier/ (website) https://github.com/ropensci/beastier/

Maintainer

Richel Bilderbeek

Last Published

November 7th, 2023

Functions in beastier (2.5)

check_n_threads

Check if the input is a valid number of threads.

Checks if the operating system is supported

check_beast2_options_data_types

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

check_input_filename_validity

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

check_input_filename

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

create_beast2_run_cmd

Creates the terminal command to run BEAST2

check_can_create_file

Internal function

create_beast2_options

Function to create a set of BEAST2 options.

check_can_create_tracelog_file

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

check_can_create_treelog_file

Internal function

check_can_create_dir_for_state_output_file

Internal function

check_beast2_path

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

create_beast2_treelog_folder

Internal function

continue_beast2

Continue a BEAST2 run

Check if the input is a valid RNG seed.

create_beast2_validate_cmd

Creates the terminal command to validate a BEAST2 input file

check_can_create_screenlog_file

Internal function

check_can_create_state_output_file

Internal function

create_beast2_state_output_file_folder

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

create_random_fasta

Create a random FASTA file

create_beast2_input_file_folder

Create the folder where the BEAST2 input file will be created

create_beast2_continue_cmd_from_options

Creates the terminal command to run BEAST2 from a beast2_options

create_beast2_tracelog_folder

Internal function

create_mcbette_beast2_options

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

check_beast2_options_do_not_overwrite_existing_files

Internal function

create_beast2_version_cmd

Creates the terminal command to version a BEAST2 input file

get_default_beast2_download_url_linux

Get the BEAST2 download URL for Linux

check_empty_beastier_folder

Check there are no files in the default beastier folder

create_random_phylogeny

Create a random phylogeny

get_beast2_example_filenames

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

get_default_beast2_download_url

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

get_beast2_example_filename

Get the full path of a BEAST2 example file

create_temp_input_filename

Create a temporary filename for the BEAST2 XML filename

create_temp_state_filename

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

create_beast2_version_cmd_bin

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

get_default_beast2_download_url_win

Get the BEAST2 download URL for Windows

get_duplicate_param_ids

Find duplicate RealParameter IDs

get_beastier_tempfilename

Get a temporary filename

get_default_beast2_bin_path

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

get_java_version

Get the Java version

check_empty_beaustier_folders

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

get_trees_filenames

Get the .trees filenames that BEAST2 will produce

create_beast2_screenlog_folder

Internal function

extract_screenlog_filename_from_beast2_input_file

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

create_beast2_run_cmd_from_options

Creates the terminal command to run BEAST2 from a beast2_options

extract_tracelog_filename_from_beast2_input_file

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

gives_beast2_warning

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

Deprecated function, use is_on_ci

get_default_beast2_folder

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

save_nexus_as_fasta

Save a NEXUS file as a FASTA file

Save text (a container of strings) to a file

Determines if the input is an alignment of type DNAbin

remove_beastier_folder

Check there are no files in the default beautier folder

is_beast2_installed

Checks if BEAST2 is installed

create_random_alignment

Create a random alignment

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

get_beast2_options_filenames

Extract the filenames from a `beast2_options`

get_beast2_main_class_name

Get the BEAST2 main class name.

remove_beaustier_folders

Remove the `beautier` and `beastier` temporary folders

is_beast2_input_file

Is a file a valid BEAST2 input file?

is_win_bin_path

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

print_beast2_options

Pretty-print a `beast2_options`

create_beast2_validate_cmd_bin

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

Deprecated function, use is_on_travis

Deprecated function to upgrade BEAST2.

rename_beast2_options_filenames

Rename the filenames in the BEAST2 options

uninstall_beast2

Deprecated function to uninstall BEAST2

remove_file_if_present

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

extract_treelog_filename_from_beast2_input_file

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

create_beast2_validate_cmd_jar

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

create_beastier_tempfolder

Create the temporary folder as used by beastier

create_beast2_version_cmd_jar

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

get_beastier_paths

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

get_beastier_path

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

get_default_java_path

Obtains the default path to the Java executable

get_alignment_ids_from_xml_filename

Get the alignment ID from a file with one alignment

get_default_beast2_version

Get the default BEAST2 version that is used by beastier

Determine if the XML text has unique parameter IDs

Deprecated function to install BEAST2

run_beast2_from_options

default_params_doc

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

Do a minimal BEAST2 run

get_beast2_version

Get the BEAST2 version

get_beastier_folder

Get the path to the beastier temporary files folder

get_default_beast2_jar_path

Get the default BEAST2 jar file's path

get_default_beast2_path

Get the default BEAST2 path

Deprecated function, use is_on_appveyor

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

beastier-package

beastier: A package to call BEAST2.

beastier_report

Creates a beastier report

check_beast2_options

Check if the beast2_options is a valid BEAST2 options object.

are_beast2_input_lines_fast

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

add_quotes_if_has_spaces

Add quotes around the string if it contains spaces.

are_beast2_input_lines_deep

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

are_beast2_input_lines

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

are_identical_alignments

Determines if the two alignments are equal

Check if BEAST2 is installed properly.

beast2_options_to_table

Convert a beast2_options to a table

check_beast2_options_filenames_differ

Check if the filenames in beast2_options differ

check_beast2_options_names

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

check_beast2_optionses

Check if the beast2_options is a valid BEAST2 options object.