R: Call 'BEAST2'

# Call 'BEAST2'

## Documentation for package ‘beastier’ version 2.5.2

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

A B C D E G H I P R S U

## -- 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.