parse_beast_posterior: Parses BEAST2 output files to a posterior

Description Usage Arguments Value Author(s) See Also Examples

View source: R/parse_beast_posterior.R

Description

Parses BEAST2 output files to a posterior

Usage

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parse_beast_posterior(
  trees_filenames,
  tracelog_filename,
  log_filename = "deprecated"
)

Arguments

trees_filenames

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

tracelog_filename

name of the BEAST2 tracelog .log output file, as can be read using parse_beast_tracelog_file

log_filename

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

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

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trees_filenames <- get_tracerer_path("beast2_example_output.trees")
tracelog_filename <- get_tracerer_path("beast2_example_output.log")
posterior <- parse_beast_posterior(
  trees_filenames = trees_filenames,
  tracelog_filename = tracelog_filename
)

tracerer documentation built on May 30, 2021, 5:06 p.m.