R/create_parameter_files_timings.R

In richelbilderbeek/wiritttes: WIRITTE simulation

#' Creates the parameter files in the article, but
#' slimmed down for time measurement
#' @return The filenames of all parameter files created
#' @export
#' @author Richel Bilderbeek
create_parameter_files_timings <- function() {
  filenames <- NULL
  b_index <- 0
  for (b in c(0.3, 0.5)) {
    lambda_index <- 0
    for (lambda in c(0.1, 0.3, 1.0, 1000000)) {
      mu_index <- 0
      for (mu in c(0.0, 0.1, 0.2, 0.4)) {
        if (mu > b) next
        r_index <- 0
        for (r in c(0.1, 0.01, 0.001)) {
          l_index <- 0
          for (l in c(1000, 10000)) {
            filename <- paste0(
              "article_",
              b_index, "_",
              lambda_index, "_",
              mu_index, "_",
              r_index, "_",
              l_index, ".RDa"
            )
            filenames <- c(filenames, filename)
            save_parameters_to_file(
              rng_seed = 1,
              sirg = b,
              siri = b,
              scr = lambda,
              erg = mu,
              eri = mu,
              age = 15,
              mutation_rate = r,
              n_alignments = 2,
              sequence_length = l,
              nspp = 12, # divided by 100
              n_beast_runs = 2,
              filename = filename
            )
            l_index <- l_index + 1
          } # l
          r_index <- r_index + 1
        } # r
        mu_index <- mu_index + 1
      } # mu
      lambda_index <- lambda_index + 1
    } # lambda
    b_index <- b_index + 1
  } # b
  filenames
}