Control 'BEAST2'
Get the full paths of files in the inst/extdata folder
Parse BEAST2 NS output
Process the 'BEAST2' output dependent on 'BEAST2' package specifics
Draw multiple trees on top of one another.
Get the full path of a file in the inst/extdata folder
babette: A package for Bayesian phylogenetics.
This function does nothing. It is intended to inherit is parameters' d...
Get the alignment IDs from one or more 'BEAST2' XML input files.
Continue a BEAST2 run
Delete all the temporary files created by bbt_run_from_model
Run BEAST2
Run BEAST2
Do a self test to verify babette that works correctly.
Checks if bbt_run has the 'BEAST2' packages needed to process its ar...
Get an example output of bbt_runor bbt_run_from_model.
Create NS testing output
Internal function to prepare for 'BEAST2' creating files
Deprecated function.
'BEAST2' (<https://www.beast2.org>) 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'.
Useful links