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Create a Most Recent Common Ancestor prior

Source: R/create_mrca_prior.R
create_mrca_prior.Rd

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

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()