create_rln_clock_model: Create a relaxed log-normal clock model

Description Usage Arguments Value Author(s) Examples

Description

Create a relaxed log-normal clock model

Usage

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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)

Arguments

id

an alignment's IDs. An ID can be extracted from its FASTA filename with get_alignment_ids)

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.

Value

a relaxed log-normal clock_model

Author(s)

Richèl J.C. Bilderbeek

Examples

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  rln_clock_model <- create_rln_clock_model()

  beast2_input_file <- tempfile(fileext = ".xml")
  create_beast2_input_file(
    get_fasta_filename(),
    beast2_input_file,
    clock_model = rln_clock_model
  )
  testit::assert(file.exists(beast2_input_file))

  rln_clock_model_exp <- create_rln_clock_model(
    mean_rate_prior_distr = create_exp_distr()
  )

  beast2_input_file <- tempfile(fileext = ".xml")
  create_beast2_input_file(
    get_fasta_filename(),
    beast2_input_file,
    clock_model = rln_clock_model_exp
  )
  testit::assert(file.exists(beast2_input_file))

ropensci/beautier documentation built on May 14, 2019, 8:52 p.m.