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. |