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Documentation for package ‘beastier’ version 2.4.8

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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 '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 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_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_beautier_tempfolder Create the temporary folder as used by beautier
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 Determines if the environment is AppVeyor
is_on_ci Determines if the environment is a continuous integration service
is_on_travis Determines if the environment is Travis CI
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_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.