Function reference • beastier

All functions

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.