create_strict_clock_model: Create a strict clock model

Description Usage Arguments Value Author(s) Examples

Description

Create a strict clock model

Usage

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create_strict_clock_model(id = NA,
  clock_rate_param = create_clock_rate_param(),
  clock_rate_distr = create_uniform_distr())

Arguments

id

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

clock_rate_param

the clock rate's parameter, a numeric value. For advanced usage, use the structure as created by the create_clock_rate_param function

clock_rate_distr

the clock rate's distribution, as created by a create_distr function

Value

a strict clock_model

Author(s)

Richèl J.C. Bilderbeek

Examples

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  strict_clock_model <- create_strict_clock_model(
    clock_rate_param = 1.0,
    clock_rate_distr = create_uniform_distr()
  )

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

  strict_clock_model_gamma <- create_strict_clock_model(
    clock_rate_distr = create_gamma_distr()
  )

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

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