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babette (version 2.3.3)

Control 'BEAST2'

Description

'BEAST2' () is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2', 'Tracer' and 'DensiTree'. 'babette' provides for an alternative workflow of using all these tools separately. This allows doing complex Bayesian phylogenetics easily and reproducibly from 'R'.

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Version

Install

install.packages('babette')

Monthly Downloads

325

Version

2.3.3

License

GPL-3

Issues

8

Pull Requests

1

Stars

46

Forks

7

Maintainer

Richel Bilderbeek

Last Published

September 27th, 2023

Functions in babette (2.3.3)

plot_densitree

Draw multiple trees on top of one another.
parse_beast2_output_to_ns

Parse BEAST2 NS output
prepare_file_creation

Internal function to prepare for 'BEAST2' creating files
update_babette

Update all babette dependencies, by installing their latest versions
get_alignment_ids_from_xml

Get the alignment IDs from one or more 'BEAST2' XML input files.
bbt_delete_temp_files

Delete all the temporary files created by bbt_run_from_model
bbt_run

Run BEAST2
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.
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
babette-package

babette: A package for Bayesian phylogenetics.
bbt_continue

Continue a BEAST2 run
parse_beast2_output

Process the 'BEAST2' output dependent on 'BEAST2' package specifics
default_params_doc

This function does nothing. It is intended to inherit is parameters' documentation.
bbt_run_from_model

Run BEAST2
bbt_self_test

Do a self test to verify babette that works correctly.
create_test_ns_output

Create NS testing output