R/sim_alignment_with_std_nsm_from_params.R

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

#' Create an alignment with a standard site model
#' @inheritParams default_params_doc
#' @return an alignment of type \code{DNAbin}
#' @seealso use \link{sim_alignment_with_std_nsm} to simulate an alignment
#' directlt from a mutation rate, root sequence and site model
#' @examples
#' phylogeny <- ape::read.tree(text = "((A:1, B:1):1, C:2);")
#' alignment_params <- create_alignment_params(
#'   root_sequence = "aaaa",
#'   sim_tral_fun = get_sim_tral_with_std_nsm_fun(
#'     mutation_rate = 0.1
#'   )
#' )
#' alignment <- sim_alignment_with_std_nsm_from_params(
#'   phylogeny = phylogeny,
#'   alignment_params = alignment_params
#' )
#' check_alignment(alignment)
#' @author Richèl J.C. Bilderbeek
#' @export
sim_alignment_with_std_nsm_from_params <- function( # nolint indeed a long function name
  phylogeny,
  alignment_params
) {
  mutation_rate <- get(
    "mutation_rate",
    environment(alignment_params$sim_tral_fun)
  )
  site_model <- get(
    "site_model",
    environment(alignment_params$sim_tral_fun)
  )
  pirouette::check_mutation_rate(mutation_rate)
  beautier::check_site_model(site_model)
  pirouette::sim_alignment_with_std_nsm(
    phylogeny = phylogeny,
    root_sequence = alignment_params$root_sequence,
    mutation_rate = mutation_rate,
    site_model = site_model
  )
}