parse_beast_output_files {tracerer}

Parse all BEAST2 output files

Description

Parse all BEAST2 output files

Usage

parse_beast_output_files(log_filename, trees_filenames, state_filename)

Arguments

log_filename

deprecated name of the BEAST2 tracelog .log output file. Use tracelog_filename instead

trees_filenames

the names of one or more a BEAST2 posterior .trees file. Each .trees file can be read using parse_beast_trees

state_filename

name of the BEAST2 state .xml.state output file

Value

a list with the following elements:

itemestimates: parameter estimates item [alignment_id]_trees: the phylogenies in the BEAST2 posterior. [alignment_id] is the ID of the alignment. itemoperators: the BEAST2 MCMC operator acceptances

Author(s)

Richèl J.C. Bilderbeek

See Also

Use remove_burn_ins to remove the burn-in from out$estimates

Examples

trees_filenames <- get_tracerer_path("beast2_example_output.trees")
log_filename <- get_tracerer_path("beast2_example_output.log")
state_filename <- get_tracerer_path("beast2_example_output.xml.state")
parse_beast_output_files(
  log_filename = log_filename,
  trees_filenames = trees_filenames,
  state_filename = state_filename
)