create_gamma_distr: Create a gamma distribution

In beautier: 'BEAUti' from R

Create a gamma distribution

Description

Create a gamma distribution

Usage

create_gamma_distr(
  id = NA,
  alpha = 0.5396,
  beta = 0.3819,
  value = NA,
  lower = NA,
  upper = NA
)

Arguments

id	the distribution's ID
alpha	the alpha shape parameter, a numeric value. For advanced usage, use the structure as returned by create_alpha_param
beta	the beta shape parameter, a numeric value. For advanced usage, use the structure as returned by create_beta_param
value	the initial value for the MCMC
lower	the lower bound, the lowest possible value
upper	an upper limit of the uniform distribution. If the upper limits needs to be infinity, set upper to Inf.

Value

a gamma distribution

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_distr shows an overview of all supported distributions

Examples

if (is_on_ci()) {

  gamma_distr <- create_gamma_distr(
    alpha = 0.05,
    beta = 10.0
  )

  gtr_site_model <- create_gtr_site_model(
    rate_ac_prior_distr = gamma_distr
  )

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    site_model = gtr_site_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

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