| 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... |
| are_beast2_input_lines_deep | Would these lines of text, when written to a file, result in... |
| are_beast2_input_lines_fast | Would these lines of text, when written to a file, result in... |
| are_identical_alignments | Determines if the two alignments are equal |
| beast2_options_to_table | Convert a 'beast2_options' to a table |
| beastier-package | 'beastier': A package to call BEAST2. |
| beastier_report | Creates a beastier report |
| check_beast2 | Check if 'BEAST2' is installed properly. |
| check_beast2_options | Check if the 'beast2_options' is a valid BEAST2 options... |
| check_beast2_options_data_types | Check if the 'beast2_options', which is a list, has all... |
| check_beast2_options_do_not_overwrite_existing_files | Internal function |
| check_beast2_optionses | Check if the 'beast2_options' is a valid BEAST2 options... |
| 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... |
| check_beast2_path | Checks the BEAST2 '.jar' path. Will stop if there is a... |
| 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... |
| 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... |
| check_input_filename | Checks the input filename. Will stop if there is a problem... |
| check_input_filename_validity | Checks the input filename. Will stop if there is a problem... |
| 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... |
| 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... |
| create_beast2_screenlog_folder | Internal function |
| create_beast2_state_output_file_folder | Create the folder where the BEAST2 state output file will be... |
| 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... |
| create_beast2_validate_cmd_jar | Creates the terminal command to validate a BEAST2 input 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... |
| create_beast2_version_cmd_jar | Creates the terminal command to version a BEAST2 input 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... |
| 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... |
| default_params_doc | This function does nothing. It is intended to inherit is... |
| do_minimal_run | Do a minimal BEAST2 run |
| extract_screenlog_filename_from_beast2_input_file | Internal function to extract the screenlog filename for a... |
| extract_tracelog_filename_from_beast2_input_file | Internal function to extract the tracelog filename for a... |
| extract_treelog_filename_from_beast2_input_file | Internal function to extract the treelog filename for a... |
| 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... |
| 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... |
| 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... |
| 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... |
| has_unique_ids | Determine if the XML text has unique parameter IDs |
| 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... |
| is_jar_path | Is the path a path to the BEAST2 jar file? Does not check if... |
| 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... |
| print_beast2_options | Pretty-print a 'beast2_options' |
| 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 |
| save_lines | Save text (a container of strings) to a file |
| save_nexus_as_fasta | Save a NEXUS file as a FASTA file |
| uninstall_beast2 | Deprecated function to uninstall BEAST2 |
| upgrade_beast2 | Deprecated function to upgrade BEAST2. |
