rln_clock_model_to_xml_prior_distr: Internal function

In beautier: 'BEAUti' from R

Internal function

Description

Internal function to converts a relaxed log-normal clock model to the prior section of the XML as text

Usage

rln_clock_model_to_xml_prior_distr(inference_model)

Arguments

inference_model

a Bayesian phylogenetic inference model. An inference model is the complete model setup in which a site model, clock model, tree prior and more are specified. Use create_inference_model to create an inference model. Use check_inference_model to check if an inference model is valid. Use rename_inference_model_filenames to rename the files in an inference model.

Value

a character vector of XML strings

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

 # <distribution id="posterior" spec="util.CompoundDistribution">
 #     <distribution id="prior" spec="util.CompoundDistribution">
 #       HERE, where the ID of the distribution is 'prior'
 #     </distribution>
 #     <distribution id="likelihood" ...>
 #     </distribution>
 # </distribution>

# Must be an initialized inference model
inference_model <- create_inference_model(
  clock_model = create_rln_clock_model(
    id = "test_output_0",
    ucldstdev_distr = create_gamma_distr(
      id = 0,
      alpha = create_alpha_param(id = 2, value = "0.5396"),
      beta = create_beta_param(id = 3, value = "0.3819")
    ),
    mean_rate_prior_distr = create_uniform_distr(id = 1),
    mparam_id = 1
  )
)

rln_clock_model_to_xml_prior_distr(inference_model)

check_empty_beautier_folder()

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