create_rln_clock_model: Create a relaxed log-normal clock model

In ropensci/beautier: 'BEAUti' from R

Create a relaxed log-normal clock model

Description

Create a relaxed log-normal clock model

Usage

create_rln_clock_model(
  id = NA,
  mean_rate_prior_distr = create_uniform_distr(),
  ucldstdev_distr = create_gamma_distr(),
  mparam_id = NA,
  mean_clock_rate = "1.0",
  n_rate_categories = -1,
  normalize_mean_clock_rate = FALSE,
  dimension = NA,
  rate_scaler_factor = 0.75
)

Arguments

id	an alignment's IDs. An ID can be extracted from its FASTA filename with get_alignment_ids_from_fasta_filenames)
mean_rate_prior_distr	the mean clock rate prior distribution, as created by a create_distr function
ucldstdev_distr	the standard deviation of the uncorrelated log-normal distribution, as created by a create_distr function
mparam_id	the ID of the M parameter in the branchRateModel, set to NA to have it initialized
mean_clock_rate	the mean clock rate, 1.0 by default (is called ucld_stdev in XML, where ucld_stdev is always 0.1)
n_rate_categories	the number of rate categories. -1 is default, 0 denotes as much rates as branches
normalize_mean_clock_rate	normalize the mean clock rate
dimension	the dimensionality of the relaxed clock model. Leave NA to let beautier calculate it. Else, the dimensionality of the clock equals twice the number of taxa minus two.
rate_scaler_factor	the strict clock model's operator scaler for the rate. Use an empty string to indicate the default.

Value

a relaxed log-normal clock_model

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  rln_clock_model <- create_rln_clock_model()

  beast2_input_file <- get_beautier_tempfilename()

  create_beast2_input_file(
    get_fasta_filename(),
    beast2_input_file,
    clock_model = rln_clock_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

ropensci/beautier documentation built on April 2, 2024, 5:01 a.m.