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babette_example_2

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A babette example.

Example #2: fixed crown age

The way to do so, is to date the node of the most recent common ancestor of all taxa:

# Create a FASTA file
fasta_filename <- "primates.fas"
save_nexus_as_fasta(
  nexus_filename = beastier::get_beast2_example_filename("Primates.nex"),
  fasta_filename = fasta_filename
)

inference_results <- bbt_run(
  fasta_filename = fasta_filename
  mrca_prior = create_mrca_prior(
    taxa_names = get_taxa_names(fasta_filename),
    alignment_id = get_alignment_id(fasta_filename),
    is_monophyletic = TRUE,
    mrca_distr = create_normal_distr(
      mean = 15.0,
      sigma = 0.025
    )
  )
)

Here we use an MRCA prior with fixed (non-estimated) values of the mean and standard deviation for the common ancestor node's time.

Result