R/parse_beast_state.R

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

#' Parses a BEAST2 .xml.state output file to get only the operators
#'   acceptances
#' @param filename name of the BEAST2 .xml.state output file
#' @return data frame with all the operators' success rates
#' @export
#' @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)
#' @author Richel J.C. Bilderbeek
parse_beast_state_operators <- function(
    filename = system.file("extdata", "beast2_example_output.xml.state",
      package = "RBeast")
) {
  tracerer::parse_beast_state_operators(filename)
}