R/calc_ess.R

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

#' Calculates the Effective Sample Size
#' @param trace the values without burn-in
#' @param sample_interval the interval in timesteps between samples
#' @return the effective sample size
#' @examples
#'   filename <- system.file(
#'    "extdata", "beast2_example_output.log", package = "RBeast"
#'  )
#'
#'  # Parse the file as-is and conclude the sampling interval
#'  df <- RBeast::parse_beast_log(
#'    filename = filename
#'  )
#'  sample_interval <- df$Sample[2] - df$Sample[1]
#'
#'  # Only keep the parameter estimates, do not care about the sampling times anymore
#'  estimates <- subset(df, select = -Sample)
#'
#'  esses <- rep(NA, ncol(estimates))
#'  burn_in_fraction <- 0.1
#'  for (i in seq_along(estimates)) {
#'    # Trace with the burn-in still present
#'    trace_raw <- as.numeric(t(estimates[i]))
#'
#'    # Trace with the burn-in removed
#'    trace <- RBeast::remove_burn_in(trace = trace_raw, burn_in_fraction = 0.1)
#'
#'    # Store the effectice sample size
#'    esses[i] <- RBeast::calc_ess(trace, sample_interval = sample_interval)
#'  }
#'
#'  # Use the values that TRACER shows
#'  expected_esses <- c(10, 10, 10, 10, 7, 10, 9, 6)
#'  testit::assert(all(expected_esses - esses < 0.5))
#' @export
#' @author Richel J.C. Bilderbeek
calc_ess <- function(trace, sample_interval) {
  tracerer::calc_ess(trace, sample_interval)
}