parse_beast_posterior {tracerer} | R Documentation |
Parses BEAST2 output files to a posterior
parse_beast_posterior(trees_filenames, log_filename)
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 |
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.
Richèl J.C. Bilderbeek
Use remove_burn_ins
to remove the burn-ins from
the posterior's estimates (posterior$estimates
)
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))