create_mrca_prior: Create a Most Recent Common Ancestor prior

In beautier: 'BEAUti' from R

Create a Most Recent Common Ancestor prior

Description

Create a Most Recent Common Ancestor prior

Usage

create_mrca_prior(
  alignment_id = NA,
  taxa_names = NA,
  is_monophyletic = FALSE,
  mrca_distr = NA,
  name = NA,
  clock_prior_distr_id = NA
)

Arguments

alignment_id	ID of the alignment, as returned by get_alignment_id. Keep at NA to have it initialized automatically
taxa_names	names of the taxa, as returned by get_taxa_names. Keep at NA to have it initialized automatically, using all taxa in the alignment
is_monophyletic	boolean to indicate monophyly is assumed in a Most Recent Common Ancestor prior, as returned by create_mrca_prior
mrca_distr	the distribution used by the MRCA prior. Can be NA (the default) or any distribution returned by create_distr
name	the unique name of the MRCA prior, for example a genus, family, order or even class name. Leave at NA to have it named automatically.
clock_prior_distr_id	ID of an MRCA clock model's distribution. Keep at NA to have it initialized automatically

Value

an MRCA prior

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

fasta_filename <- get_beautier_path("anthus_aco.fas")

 # The first two taxa are sister species
 mrca_prior <- create_mrca_prior(
   taxa_names = get_taxa_names(filename = fasta_filename)[1:2]
 )

 # The taxa are monophyletic
 mrca_prior <- create_mrca_prior(
   taxa_names = get_taxa_names(filename = fasta_filename),
   is_monophyletic = TRUE
 )

 # Set the crown age to 10
 mrca_prior <- create_mrca_prior(
   taxa_names = get_taxa_names(fasta_filename),
   mrca_distr = create_normal_distr(mean = 10, sigma = 0.1)
 )

check_empty_beautier_folder()

beautier documentation built on Nov. 2, 2023, 5:08 p.m.