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All functions

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.