parse_beast_state_operators: Parses a BEAST2 .xml.state output file to get only the...

In beast-dev/RBeast: Create BEAST and BEAST2 input files and parse their output

Description

Parses a BEAST2 .xml.state output file to get only the operators acceptances

Usage

parse_beast_state_operators(filename = system.file("extdata",
  "beast2_example_output.xml.state", package = "RBeast"))

Arguments

filename

name of the BEAST2 .xml.state output file

Value

data frame with all the operators' success rates

Author(s)

Richel J.C. Bilderbeek

Examples

  xml_state_filename <- system.file(
    "extdata", "beast2_example_output.xml.state", package = "RBeast"
  )
  estimates <- parse_beast_state_operators(filename = xml_state_filename)
  expected_names <- c("operator", "p", "accept", "reject", "acceptFC",
    "rejectFC", "rejectIv", "rejectOp")
  expected_operator <- c("treeScaler.t", "treeRootScaler.t",
    "UniformOperator.t", "SubtreeSlide.t", "narrow.t", "wide.t",
    "WilsonBalding.t", "BirthRateScaler.t", "DeathRateScaler.t")
  testit::assert(names(estimates) == expected_names)
  #testit::assert(estimates$operator == expected_operators)

beast-dev/RBeast documentation built on May 12, 2019, 10:02 a.m.