create_tn93_site_model {beautier} | R Documentation |
Create a TN93 site model
Description
Create a TN93 site model
Usage
create_tn93_site_model(
id = NA,
gamma_site_model = create_gamma_site_model(),
kappa_1_param = create_kappa_1_param(),
kappa_2_param = create_kappa_2_param(),
kappa_1_prior_distr = create_log_normal_distr(m = 1, s = 1.25),
kappa_2_prior_distr = create_log_normal_distr(m = 1, s = 1.25),
freq_equilibrium = "estimated",
freq_param = create_freq_param()
)
Arguments
id |
the IDs of the alignment (can be extracted from
the FASTA filename using |
gamma_site_model |
a gamma site model, as created by create_gamma_site_model |
kappa_1_param |
the 'kappa 1' parameter,
a numeric value.
For advanced usage, use the structure
as returned by |
kappa_2_param |
the 'kappa 2' parameter,
a numeric value.
For advanced usage, use the structure
as returned by |
kappa_1_prior_distr |
the distribution of the kappa 1 prior,
which is a log-normal distribution
(as created by |
kappa_2_prior_distr |
the distribution of the kappa 2 prior,
which is a log-normal distribution
(as created by |
freq_equilibrium |
the frequency in which the rates are at equilibrium
are either |
freq_param |
a 'freq' parameter, as created by create_freq_param |
Value
a TN93 site_model
Author(s)
Richèl J.C. Bilderbeek
Examples
if (is_on_ci()) {
tn93_site_model <- create_tn93_site_model(
kappa_1_param = 2.0,
kappa_2_param = 2.0
)
output_filename <- get_beautier_tempfilename()
create_beast2_input_file(
input_filename = get_fasta_filename(),
output_filename = output_filename,
site_model = tn93_site_model
)
file.remove(output_filename)
remove_beautier_folder()
}