# Control 'BEAST2'

## Documentation for package ‘babette’ version 2.3.4

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

bbt_continue | Continue a BEAST2 run
bbt_delete_temp_files | Delete all the temporary files created by bbt_run_from_model
bbt_run | Run BEAST2
bbt_run_from_model | Run BEAST2
bbt_self_test | Do a self test to verify babette that works correctly.
check_beast2_pkgs | Checks if 'bbt_run' has the 'BEAST2' packages needed to process its arguments. Will stop if not.
create_test_bbt_run_output | Get an example output of 'bbt_run' or 'bbt_run_from_model'.
create_test_ns_output | Create NS testing output
default_params_doc | This function does nothing. It is intended to inherit is parameters' documentation.
get_alignment_ids_from_xml | Get the alignment IDs from one or more 'BEAST2' XML input files.
get_babette_path | Get the full path of a file in the 'inst/extdata' folder
get_babette_paths | Get the full paths of files in the 'inst/extdata' folder
parse_beast2_output | Process the 'BEAST2' output dependent on 'BEAST2' package specifics
parse_beast2_output_to_ns | Parse BEAST2 NS output
plot_densitree | Draw multiple trees on top of one another.
prepare_file_creation | Internal function to prepare for 'BEAST2' creating files
update_babette | Deprecated function.