parse_beast_output_files {tracerer} | R Documentation |
Parse all BEAST2 output files
parse_beast_output_files(log_filename, trees_filenames, state_filename)
log_filename |
name of the BEAST2 .log file |
trees_filenames |
name(s) of the BEAST2 .trees file(s) created. BEAST2 will create one .trees file per alignment |
state_filename |
name of the BEAST2 .xml.state file created |
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
Richèl J.C. Bilderbeek
Use remove_burn_ins
to remove the burn-in from
out$estimates
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") out <- parse_beast_output_files( log_filename = log_filename, trees_filenames = trees_filenames, state_filename = state_filename ) testit::assert("estimates" %in% names(out)) testit::assert("beast2_example_output_trees" %in% names(out)) testit::assert("operators" %in% names(out))