parse_beast_posterior: Parses BEAST2 output files to a posterior

Description Usage Arguments Value Author(s) See Also Examples

Description

Parses BEAST2 output files to a posterior

Usage

1
parse_beast_posterior(trees_filenames, log_filename)

Arguments

trees_filenames

one or more names of the BEAST2 .trees output files. A BEAST2 run will create as much .trees files as there are alignments

log_filename

name of the BEAST2 .trees 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.

Author(s)

Richèl J.C. Bilderbeek

See Also

Use remove_burn_ins to remove the burn-ins from the posterior's estimates (posterior$estimates)

Examples

1
2
3
4
5
6
7
  trees_filenames <- get_tracerer_path("beast2_example_output.trees")
  log_filename <- get_tracerer_path("beast2_example_output.log")
  posterior <- parse_beast_posterior(
    trees_filenames = trees_filenames,
    log_filename = log_filename
  )
  testit::assert(is_posterior(posterior))

ropensci/tracerer documentation built on May 14, 2019, 8:55 p.m.