Skip to contents

Create a relaxed log-normal clock model

Source: R/create_clock_model.R
create_rln_clock_model.Rd

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

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()
}