Call 'BEAST2'

Documentation for package ‘beastier’ version 2.5.1

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-- A --

add_quotes_if_has_spaces	Add quotes around the string if it contains spaces.
are_beast2_input_lines	Would these lines of text, when written to a file, result in a valid BEAST2 input file?
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_fast	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

-- B --

beast2_options_to_table	Convert a 'beast2_options' to a table
beastier_report	Creates a beastier report

-- C --

check_beast2	Check if 'BEAST2' is installed properly.
check_beast2_options	Check if the 'beast2_options' is a valid BEAST2 options object.
check_beast2_optionses	Check if the 'beast2_options' is a valid BEAST2 options object.
check_beast2_options_data_types	Check if the 'beast2_options', which is a list, has all elements of the right data types
check_beast2_options_do_not_overwrite_existing_files	Internal function
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_path	Checks the BEAST2 '.jar' path. Will stop if there is a problem with the BEAST2 '.jar' path.
check_can_create_dir_for_state_output_file	Internal function
check_can_create_file	Internal function
check_can_create_screenlog_file	Internal function
check_can_create_state_output_file	Internal function
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_empty_beastier_folder	Check there are no files in the default beastier folder
check_empty_beaustier_folders	Check there are no files in the default 'beautier' and 'beastier' folders
check_input_filename	Checks the input filename. Will stop if there is a problem with the input filename.
check_input_filename_validity	Checks the input filename. Will stop if there is a problem with the input filename.
check_n_threads	Check if the input is a valid number of threads.
check_os	Checks if the operating system is supported
check_rng_seed	Check if the input is a valid RNG seed.
continue_beast2	Continue a BEAST2 run
create_beast2_continue_cmd_from_options	Creates the terminal command to run BEAST2 from a 'beast2_options'
create_beast2_input_file_folder	Create the folder where the BEAST2 input file will be created
create_beast2_options	Function to create a set of BEAST2 options.
create_beast2_run_cmd	Creates the terminal command to run BEAST2
create_beast2_run_cmd_from_options	Creates the terminal command to run BEAST2 from a 'beast2_options'
create_beast2_screenlog_folder	Internal function
create_beast2_state_output_file_folder	Create the folder where the BEAST2 state output file will be created
create_beast2_tracelog_folder	Internal function
create_beast2_treelog_folder	Internal function
create_beast2_validate_cmd	Creates the terminal command to validate a BEAST2 input file
create_beast2_validate_cmd_bin	Creates the terminal command to validate a BEAST2 input file using a call to the 'launcher.jar' 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_beast2_version_cmd	Creates the terminal command to version a BEAST2 input file
create_beast2_version_cmd_bin	Creates the terminal command to version a BEAST2 input file using a call to the 'launcher.jar' file
create_beast2_version_cmd_jar	Creates the terminal command to version a BEAST2 input file using a call to the 'launcher.jar' file
create_beastier_tempfolder	Create the temporary folder as used by beastier
create_mcbette_beast2_options	Create a 'beast2_options' structure for the 'mcbette' R package
create_random_alignment	Create a random alignment
create_random_fasta	Create a random FASTA file
create_random_phylogeny	Create a random phylogeny
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.

-- D --

default_params_doc	This function does nothing. It is intended to inherit is parameters' documentation.
do_minimal_run	Do a minimal BEAST2 run

-- E --

extract_screenlog_filename_from_beast2_input_file	Internal function to extract the screenlog filename for a BEAST2 input file
extract_tracelog_filename_from_beast2_input_file	Internal function to extract the tracelog filename for a BEAST2 input file
extract_treelog_filename_from_beast2_input_file	Internal function to extract the treelog filename for a BEAST2 input file

-- G --

get_alignment_ids_from_xml_filename	Get the alignment ID from a file with one alignment
get_beast2_example_filename	Get the full path of a BEAST2 example file
get_beast2_example_filenames	Get a list with the full paths of all BEAST2 example filenames
get_beast2_main_class_name	Get the BEAST2 main class name.
get_beast2_options_filenames	Extract the filenames from a 'beast2_options'
get_beast2_version	Get the BEAST2 version
get_beastier_folder	Get the path to the beastier temporary files folder
get_beastier_path	Get the full path of a file in the 'inst/extdata' folder
get_beastier_paths	Get the full paths of files in the 'inst/extdata' folder
get_beastier_tempfilename	Get a temporary filename
get_default_beast2_bin_path	Get the default BEAST2 binary file ('beast', that is) path
get_default_beast2_download_url	Get the default BEAST2 download URL, which depends on the operating system
get_default_beast2_download_url_linux	Get the BEAST2 download URL for Linux
get_default_beast2_download_url_win	Get the BEAST2 download URL for Windows
get_default_beast2_folder	Get the path to the folder where this package installs BEAST2 by default
get_default_beast2_jar_path	Get the default BEAST2 jar file's path
get_default_beast2_path	Get the default BEAST2 path
get_default_beast2_version	Get the default BEAST2 version that is used by beastier
get_default_java_path	Obtains the default path to the Java executable
get_duplicate_param_ids	Find duplicate 'RealParameter' IDs
get_java_version	Get the Java version
get_trees_filenames	Get the .trees filenames that BEAST2 will produce
gives_beast2_warning	Determines if BEAST2 issues a warning when using the BEAST2 XML input file

-- H --

has_unique_ids

Determine if the XML text has unique parameter IDs

-- I --

install_beast2	Deprecated function to install BEAST2
is_alignment	Determines if the input is an alignment of type DNAbin
is_beast2_input_file	Is a file a valid BEAST2 input file?
is_beast2_installed	Checks if BEAST2 is installed
is_bin_path	Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present
is_jar_path	Is the path a path to the BEAST2 jar file? Does not check if the file at that path is present
is_on_appveyor	Deprecated function, use is_on_appveyor
is_on_ci	Deprecated function, use is_on_ci
is_on_travis	Deprecated function, use is_on_travis
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

-- P --

print_beast2_options

Pretty-print a 'beast2_options'

-- R --

remove_beastier_folder	Check there are no files in the default beautier folder
remove_beaustier_folders	Remove the 'beautier' and 'beastier' temporary folders
remove_file_if_present	Remove a file if it is present, will do nothing if it is not.
rename_beast2_options_filenames	Rename the filenames in the BEAST2 options
run_beast2	Run BEAST2
run_beast2_from_options	Run BEAST2

-- S --

save_lines	Save text (a container of strings) to a file
save_nexus_as_fasta	Save a NEXUS file as a FASTA file

-- U --

uninstall_beast2	Deprecated function to uninstall BEAST2
upgrade_beast2	Deprecated function to upgrade BEAST2.