R/get_sim_tral_with_uns_site_model_fun.R

In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny

#' Get a partially evaluated function
#' to simulate a true alignment with an unlinked node substitution site model.
#' @inheritParams default_params_doc
#' @return
#' A partially evaluated function of
#' \link{sim_tral_with_uns_nsm}
#' @seealso
#' Use \link{get_sim_tral_with_lns_nsm_fun}
#' to get a partially evaluated function
#' to simulate a true alignment with a linked node substitution site model.
#' @examples
#' f <- get_sim_tral_with_uns_nsm_fun()
#' check_sim_tral_fun(f)
#' phylogeny <- ape::read.tree(text = "((A:1, B:1):1, C:2);")
#' true_alignment <- f(
#'   true_phylogeny = phylogeny,
#'   root_sequence = "acgt"
#' )
#' @export
get_sim_tral_with_uns_nsm_fun <-
  function(
  branch_subst_matrix = rep(1, 6),
  node_subst_matrix = 1.0,
  branch_mutation_rate = 1.0,
  node_mutation_rate = 1.0,
  base_frequencies = rep(0.25, 4),
  node_time = 0.001
) {
  pryr::partial(
    sim_tral_with_uns_nsm,
    branch_subst_matrix = branch_subst_matrix,
    node_subst_matrix = node_subst_matrix,
    branch_mutation_rate = branch_mutation_rate,
    node_mutation_rate = node_mutation_rate,
    base_frequencies = base_frequencies,
    node_time = node_time
  )
}