Function reference • babette

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(): Update all babette dependencies, by installing their latest versions