Control 'BEAST2'


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Documentation for package ‘babette’ version 2.3

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babette babette: A package for Bayesian phylogenetics.
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