R/create_mbd_params_table.R

In richelbilderbeek/razzo: The Error if Nature is MBD

#' Create a table of which each row holds a unique MBD parameter combination.
#' @inheritParams default_params_doc
#' @seealso use \link{create_mbd_paramses} to create a list
#' of \code{mbd_params}
#' @return a data frame with the following columns:
#' \itemize{
#'   \item lambda the speciation rate
#'   \item mu the extinction rate
#'   \item nu the co-occurring speciation event rate
#'   \item q the proportion of species that speciates at a co-occurring
#'     speciation event
#'   \item crown_age the crown age of the MBD tree
#'   \item cond the conditioning
#'   \item seed the RNG seed for creating an MBD tree
#' }
#' @author Giovanni Laudanno, Richèl J.C. Bilderbeek
#' @examples
#' create_mbd_params_table()
#' @export
create_mbd_params_table <- function(
  lambdas = get_razzo_lambdas(),
  mus = get_razzo_mus(),
  nus = get_razzo_nus(),
  qs = get_razzo_qs(),
  cond = 1,
  crown_age = get_razzo_crown_age(),
  n_replicates = get_razzo_n_replicates()
) {

  x <- expand.grid(lambda = lambdas, mu = mus, nu = nus, q = qs)
  no_mbd_lines <-
    apply(X = x, MARGIN = 1, FUN = function(y) y[3] == 0 | y[4] == 0)
  no_mbd_x <- expand.grid(lambda = lambdas, mu = mus, nu = 0, q = 0)
  x[no_mbd_lines, ] <- no_mbd_x
  x <- dplyr::distinct(x)
  x$crown_age <- crown_age
  x$cond <- cond
  x2 <- x[rep(seq_len(nrow(x)), rep(n_replicates, nrow(x))), ]
  x2$seed <- seq_len(nrow(x2))
  rownames(x2) <- NULL
  x2
}