| Add quotes around the string if it contains spaces. | add_quotes_if_has_spaces |
| 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_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 |
| Determines if the two alignments are equal | are_identical_alignments |
| Convert a 'beast2_options' to a table | beast2_options_to_table |
| Creates a beastier report | beastier_report |
| Check if 'BEAST2' is installed properly. | check_beast2 |
| Check if the 'beast2_options' is a valid BEAST2 options object. | check_beast2_options |
| Check if the 'beast2_options', which is a list, has all elements of the right data types | check_beast2_options_data_types |
| Internal function | check_beast2_options_do_not_overwrite_existing_files |
| Check if the filenames in 'beast2_options' differ | check_beast2_options_filenames_differ |
| Check if the 'beast2_options', which is a list, has all the elements needed. | check_beast2_options_names |
| Check if the 'beast2_options' is a valid BEAST2 options object. | check_beast2_optionses |
| Checks the BEAST2 '.jar' path. Will stop if there is a problem with the BEAST2 '.jar' path. | check_beast2_path |
| Internal function | 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 to check if the MCMC's tracelog file can be created. | check_can_create_tracelog_file |
| Internal function | check_can_create_treelog_file |
| Check there are no files in the default beastier folder | check_empty_beastier_folder |
| Check there are no files in the default `beautier` and `beastier` folders | check_empty_beaustier_folders |
| 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. | check_input_filename_validity |
| Check if the input is a valid number of threads. | check_n_threads |
| Checks if the operating system is supported | check_os |
| Check if the input is a valid RNG seed. | check_rng_seed |
| Continue a BEAST2 run | continue_beast2 |
| Creates the terminal command to run BEAST2 from a 'beast2_options' | create_beast2_continue_cmd_from_options |
| Create the folder where the BEAST2 input file will be created | create_beast2_input_file_folder |
| Function to create a set of BEAST2 options. | create_beast2_options |
| Creates the terminal command to run BEAST2 | create_beast2_run_cmd |
| Creates the terminal command to run BEAST2 from a 'beast2_options' | create_beast2_run_cmd_from_options |
| Internal function | create_beast2_screenlog_folder |
| Create the folder where the BEAST2 state output file will be created | create_beast2_state_output_file_folder |
| Internal function | create_beast2_tracelog_folder |
| Internal function | create_beast2_treelog_folder |
| Creates the terminal command to validate a BEAST2 input file | create_beast2_validate_cmd |
| Creates the terminal command to validate a BEAST2 input file using a call to the 'launcher.jar' 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 version a BEAST2 input file | create_beast2_version_cmd |
| Creates the terminal command to version a BEAST2 input file using a call to the 'launcher.jar' 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 |
| Create the temporary folder as used by beastier | create_beastier_tempfolder |
| Create a `beast2_options` structure for the `mcbette` R package | create_mcbette_beast2_options |
| Create a random alignment | create_random_alignment |
| Create a random FASTA file | create_random_fasta |
| Create a random phylogeny | create_random_phylogeny |
| Create a temporary filename for the BEAST2 XML filename | create_temp_input_filename |
| Create a temporary file for the BEAST2 XML output file that stores its state. | create_temp_state_filename |
| This function does nothing. It is intended to inherit is parameters' documentation. | default_params_doc |
| Do a minimal BEAST2 run | do_minimal_run |
| Internal function to extract the screenlog filename for a BEAST2 input file | extract_screenlog_filename_from_beast2_input_file |
| Internal function to extract the tracelog filename for a BEAST2 input file | extract_tracelog_filename_from_beast2_input_file |
| Internal function to extract the treelog filename for a BEAST2 input file | extract_treelog_filename_from_beast2_input_file |
| Get the alignment ID from a file with one alignment | get_alignment_ids_from_xml_filename |
| Get the full path of a BEAST2 example file | get_beast2_example_filename |
| Get a list with the full paths of all BEAST2 example filenames | get_beast2_example_filenames |
| Get the BEAST2 main class name. | get_beast2_main_class_name |
| Extract the filenames from a `beast2_options` | get_beast2_options_filenames |
| Get the BEAST2 version | get_beast2_version |
| Get the path to the beastier temporary files folder | get_beastier_folder |
| Get the full path of a file in the 'inst/extdata' folder | get_beastier_path |
| Get the full paths of files in the 'inst/extdata' folder | get_beastier_paths |
| Get a temporary filename | get_beastier_tempfilename |
| Get the default BEAST2 binary file ('beast', that is) path | get_default_beast2_bin_path |
| Get the default BEAST2 download URL, which depends on the operating system | get_default_beast2_download_url |
| Get the BEAST2 download URL for Linux | get_default_beast2_download_url_linux |
| Get the BEAST2 download URL for Windows | get_default_beast2_download_url_win |
| Get the path to the folder where this package installs BEAST2 by default | get_default_beast2_folder |
| Get the default BEAST2 jar file's path | get_default_beast2_jar_path |
| Get the default BEAST2 path | get_default_beast2_path |
| Get the default BEAST2 version that is used by beastier | get_default_beast2_version |
| Obtains the default path to the Java executable | get_default_java_path |
| Find duplicate 'RealParameter' IDs | get_duplicate_param_ids |
| Get the Java version | get_java_version |
| Get the .trees filenames that BEAST2 will produce | get_trees_filenames |
| Determines if BEAST2 issues a warning when using the BEAST2 XML input file | gives_beast2_warning |
| Determine if the XML text has unique parameter IDs | has_unique_ids |
| Deprecated function to install BEAST2 | install_beast2 |
| Determines if the input is an alignment of type DNAbin | is_alignment |
| Is a file a valid BEAST2 input file? | is_beast2_input_file |
| Checks if BEAST2 is installed | is_beast2_installed |
| Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present | is_bin_path |
| Is the path a path to the BEAST2 jar file? Does not check if the file at that path is present | is_jar_path |
| Deprecated function, use is_on_appveyor | is_on_appveyor |
| Deprecated function, use is_on_ci | is_on_ci |
| Deprecated function, use is_on_travis | is_on_travis |
| Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present | is_win_bin_path |
| Pretty-print a `beast2_options` | print_beast2_options |
| Check there are no files in the default beautier folder | remove_beastier_folder |
| Remove the `beautier` and `beastier` temporary folders | remove_beaustier_folders |
| Remove a file if it is present, will do nothing if it is not. | remove_file_if_present |
| Rename the filenames in the BEAST2 options | rename_beast2_options_filenames |
| Run BEAST2 | run_beast2 |
| Run BEAST2 | run_beast2_from_options |
| Save text (a container of strings) to a file | save_lines |
| Save a NEXUS file as a FASTA file | save_nexus_as_fasta |
| Deprecated function to uninstall BEAST2 | uninstall_beast2 |
| Deprecated function to upgrade BEAST2. | upgrade_beast2 |
