create_mrca_prior {beautier} | R Documentation |
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 |
taxa_names |
names of the taxa,
as returned by |
is_monophyletic |
boolean to indicate monophyly is assumed in
a Most Recent Common Ancestor prior,
as returned by |
mrca_distr |
the distribution used by the MRCA prior.
Can be NA (the default) or any distribution
returned by |
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 |
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()