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
beast2_options_to_table
                        Convert a 'beast2_options' to a table
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 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_optionses
                        Check if the 'beast2_options' is a valid BEAST2
                        options object.
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.
default_params_doc      This function does nothing. It is intended to
                        inherit is parameters' documentation.
do_minimal_run          Do a minimal BEAST2 run
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
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
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 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
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.
